70
Heartily Welcome You all
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Heartily Welcome
You all
Liverwort
HornwortFern
cones
Meiosis-Driven Genome Variation in
Plants
Contents
bull Introduction
bull Mitosis amp Meiosis
bull How meiosis evolved
bull Insight of Genes for meiotic events in models
bull Meiosis-driven genome variation
bull Conclusion
1
bull Meiotic cell division is a complex and dynamic process with
molecular and cellular events
DNA and chromosome replication
Synapsis and recombination
Chromosome segregation and
Cytokinesis
bull Involved in gametogenesis
Word Meiosis from Greek root meaning ldquo to diminishrdquo 1st described by
Van Beneden in 1883 in the Ascaris
2
Meiosis is a conserved cytological process and serves as a physical foundation for Mendelian genetics
bull Meiosis includes two successive divisions ofthe nucleus with one round of DNAreplication and leads to the formation ofgametes with half of the chromosomes of themother cell during sexual reproduction
3
4
Independent assortmentAnaphase I
5
6
In humans
7
bull Diploid somatic cells of Fungi Animals amp Plants chromosomal crossing over
known as lsquoMitotic crossing overrsquo
Significant contrasts between meiotic and mitotic recombination
1 Mitotic recombination takes at very much lower frequency than in meiosis
2 In mitotic cells Crossing over between sister chromatids is fairly frequent
meiosis is structured to promote crossing over between non-sister chromatids
3 As in yeast cells mitotic recombination is mediated efficiently by either of two
recA homologs rad51 and Dmc1 while meiotic exchange between homologs
requires Dmc1 specifically
Neale and Keeney 2006
8
bull Earliest eukaryotic species were single-cell haploid forms having single set of
chromosomes and propagated by mitosis
bull Simplest contemporary eukaryotes Protists and fungi exhibit the mitotic propagation
of both haploid and diploid states diploidy is almost certainly a derived state
bull Very first diploid cells could have first arisen either by cell fusion or by
endomitosis
bull Hurst and Nurse (1991) First diploids probably arose via rare endomitotic errors
rather than by cell fusion
bull Either route to early diploid states is possible since non-sexual cell and nuclear
fusions can occur independently of sex (lsquolsquoparasexualityrsquorsquo)
9
Liverwort
Hornwort
Club mosses
Cone bearing plants
Green AlgaeAnc
est
or
10
bull All the key molecules employed in eukaryotic mitosis are of
Prokaryotic homologs
Actins required for daughter cell separation in eukaryotes
Tubulins required in eukaryotes for the mitotic spindle and movement
of chromosomes and
bull SMC molecules must for chromosome condensation and
sisterchromatid cohesion members of the so-called Structural
maintenance of chromosomes (SMC) family
Hirano 2005 and Erickson 2007
11
bull Tubulin family FtsZ genes which were first discovered in
Escherichia coli later found in many prokaryotes
bull Product of Ftsz involved in initiation of septum formation
bull minB locus regulate site of septum formation
bull MinCMinDMinE determines location of septum formation
bull The homologs of the SMC proteins are found throughout theEubacterial and Archaebacterial kingdoms
12
For genetic recombination recA family of proteins molecules in
prokaryotes and eukaryotes
Aboussekhra et al 1992
Shinohara et al 1992
Recombinational capacity is found throughout the prokaryotes
and considerably predate eukaryotes so meiosis arisen from pro
Levin 1988
Cavalier-Smith 2002
Marcon and Moens 2005
13
bull Suppression of Kinetochore splitting in MI was key innovation
in meiosis
Cavalier-Smith2002
bull Selection pressure on homologous pairing and high levels of intergenic
recombination are prime force for origin of meiosis
Fisher1930 Muller 1932 Maynard Smith 1978Crow 1988
bull Efficient DNA ds breaks and repair system
Bernstein 19771988
Argueso et al2008
14
bull Genetic cytological and immunochemical characterization done
in
Saccharomyces cerevisiae
Arabidopsis thaliana amp
Drosophila melanogaster etc
15
16
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Liverwort
HornwortFern
cones
Meiosis-Driven Genome Variation in
Plants
Contents
bull Introduction
bull Mitosis amp Meiosis
bull How meiosis evolved
bull Insight of Genes for meiotic events in models
bull Meiosis-driven genome variation
bull Conclusion
1
bull Meiotic cell division is a complex and dynamic process with
molecular and cellular events
DNA and chromosome replication
Synapsis and recombination
Chromosome segregation and
Cytokinesis
bull Involved in gametogenesis
Word Meiosis from Greek root meaning ldquo to diminishrdquo 1st described by
Van Beneden in 1883 in the Ascaris
2
Meiosis is a conserved cytological process and serves as a physical foundation for Mendelian genetics
bull Meiosis includes two successive divisions ofthe nucleus with one round of DNAreplication and leads to the formation ofgametes with half of the chromosomes of themother cell during sexual reproduction
3
4
Independent assortmentAnaphase I
5
6
In humans
7
bull Diploid somatic cells of Fungi Animals amp Plants chromosomal crossing over
known as lsquoMitotic crossing overrsquo
Significant contrasts between meiotic and mitotic recombination
1 Mitotic recombination takes at very much lower frequency than in meiosis
2 In mitotic cells Crossing over between sister chromatids is fairly frequent
meiosis is structured to promote crossing over between non-sister chromatids
3 As in yeast cells mitotic recombination is mediated efficiently by either of two
recA homologs rad51 and Dmc1 while meiotic exchange between homologs
requires Dmc1 specifically
Neale and Keeney 2006
8
bull Earliest eukaryotic species were single-cell haploid forms having single set of
chromosomes and propagated by mitosis
bull Simplest contemporary eukaryotes Protists and fungi exhibit the mitotic propagation
of both haploid and diploid states diploidy is almost certainly a derived state
bull Very first diploid cells could have first arisen either by cell fusion or by
endomitosis
bull Hurst and Nurse (1991) First diploids probably arose via rare endomitotic errors
rather than by cell fusion
bull Either route to early diploid states is possible since non-sexual cell and nuclear
fusions can occur independently of sex (lsquolsquoparasexualityrsquorsquo)
9
Liverwort
Hornwort
Club mosses
Cone bearing plants
Green AlgaeAnc
est
or
10
bull All the key molecules employed in eukaryotic mitosis are of
Prokaryotic homologs
Actins required for daughter cell separation in eukaryotes
Tubulins required in eukaryotes for the mitotic spindle and movement
of chromosomes and
bull SMC molecules must for chromosome condensation and
sisterchromatid cohesion members of the so-called Structural
maintenance of chromosomes (SMC) family
Hirano 2005 and Erickson 2007
11
bull Tubulin family FtsZ genes which were first discovered in
Escherichia coli later found in many prokaryotes
bull Product of Ftsz involved in initiation of septum formation
bull minB locus regulate site of septum formation
bull MinCMinDMinE determines location of septum formation
bull The homologs of the SMC proteins are found throughout theEubacterial and Archaebacterial kingdoms
12
For genetic recombination recA family of proteins molecules in
prokaryotes and eukaryotes
Aboussekhra et al 1992
Shinohara et al 1992
Recombinational capacity is found throughout the prokaryotes
and considerably predate eukaryotes so meiosis arisen from pro
Levin 1988
Cavalier-Smith 2002
Marcon and Moens 2005
13
bull Suppression of Kinetochore splitting in MI was key innovation
in meiosis
Cavalier-Smith2002
bull Selection pressure on homologous pairing and high levels of intergenic
recombination are prime force for origin of meiosis
Fisher1930 Muller 1932 Maynard Smith 1978Crow 1988
bull Efficient DNA ds breaks and repair system
Bernstein 19771988
Argueso et al2008
14
bull Genetic cytological and immunochemical characterization done
in
Saccharomyces cerevisiae
Arabidopsis thaliana amp
Drosophila melanogaster etc
15
16
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Contents
bull Introduction
bull Mitosis amp Meiosis
bull How meiosis evolved
bull Insight of Genes for meiotic events in models
bull Meiosis-driven genome variation
bull Conclusion
1
bull Meiotic cell division is a complex and dynamic process with
molecular and cellular events
DNA and chromosome replication
Synapsis and recombination
Chromosome segregation and
Cytokinesis
bull Involved in gametogenesis
Word Meiosis from Greek root meaning ldquo to diminishrdquo 1st described by
Van Beneden in 1883 in the Ascaris
2
Meiosis is a conserved cytological process and serves as a physical foundation for Mendelian genetics
bull Meiosis includes two successive divisions ofthe nucleus with one round of DNAreplication and leads to the formation ofgametes with half of the chromosomes of themother cell during sexual reproduction
3
4
Independent assortmentAnaphase I
5
6
In humans
7
bull Diploid somatic cells of Fungi Animals amp Plants chromosomal crossing over
known as lsquoMitotic crossing overrsquo
Significant contrasts between meiotic and mitotic recombination
1 Mitotic recombination takes at very much lower frequency than in meiosis
2 In mitotic cells Crossing over between sister chromatids is fairly frequent
meiosis is structured to promote crossing over between non-sister chromatids
3 As in yeast cells mitotic recombination is mediated efficiently by either of two
recA homologs rad51 and Dmc1 while meiotic exchange between homologs
requires Dmc1 specifically
Neale and Keeney 2006
8
bull Earliest eukaryotic species were single-cell haploid forms having single set of
chromosomes and propagated by mitosis
bull Simplest contemporary eukaryotes Protists and fungi exhibit the mitotic propagation
of both haploid and diploid states diploidy is almost certainly a derived state
bull Very first diploid cells could have first arisen either by cell fusion or by
endomitosis
bull Hurst and Nurse (1991) First diploids probably arose via rare endomitotic errors
rather than by cell fusion
bull Either route to early diploid states is possible since non-sexual cell and nuclear
fusions can occur independently of sex (lsquolsquoparasexualityrsquorsquo)
9
Liverwort
Hornwort
Club mosses
Cone bearing plants
Green AlgaeAnc
est
or
10
bull All the key molecules employed in eukaryotic mitosis are of
Prokaryotic homologs
Actins required for daughter cell separation in eukaryotes
Tubulins required in eukaryotes for the mitotic spindle and movement
of chromosomes and
bull SMC molecules must for chromosome condensation and
sisterchromatid cohesion members of the so-called Structural
maintenance of chromosomes (SMC) family
Hirano 2005 and Erickson 2007
11
bull Tubulin family FtsZ genes which were first discovered in
Escherichia coli later found in many prokaryotes
bull Product of Ftsz involved in initiation of septum formation
bull minB locus regulate site of septum formation
bull MinCMinDMinE determines location of septum formation
bull The homologs of the SMC proteins are found throughout theEubacterial and Archaebacterial kingdoms
12
For genetic recombination recA family of proteins molecules in
prokaryotes and eukaryotes
Aboussekhra et al 1992
Shinohara et al 1992
Recombinational capacity is found throughout the prokaryotes
and considerably predate eukaryotes so meiosis arisen from pro
Levin 1988
Cavalier-Smith 2002
Marcon and Moens 2005
13
bull Suppression of Kinetochore splitting in MI was key innovation
in meiosis
Cavalier-Smith2002
bull Selection pressure on homologous pairing and high levels of intergenic
recombination are prime force for origin of meiosis
Fisher1930 Muller 1932 Maynard Smith 1978Crow 1988
bull Efficient DNA ds breaks and repair system
Bernstein 19771988
Argueso et al2008
14
bull Genetic cytological and immunochemical characterization done
in
Saccharomyces cerevisiae
Arabidopsis thaliana amp
Drosophila melanogaster etc
15
16
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull Meiotic cell division is a complex and dynamic process with
molecular and cellular events
DNA and chromosome replication
Synapsis and recombination
Chromosome segregation and
Cytokinesis
bull Involved in gametogenesis
Word Meiosis from Greek root meaning ldquo to diminishrdquo 1st described by
Van Beneden in 1883 in the Ascaris
2
Meiosis is a conserved cytological process and serves as a physical foundation for Mendelian genetics
bull Meiosis includes two successive divisions ofthe nucleus with one round of DNAreplication and leads to the formation ofgametes with half of the chromosomes of themother cell during sexual reproduction
3
4
Independent assortmentAnaphase I
5
6
In humans
7
bull Diploid somatic cells of Fungi Animals amp Plants chromosomal crossing over
known as lsquoMitotic crossing overrsquo
Significant contrasts between meiotic and mitotic recombination
1 Mitotic recombination takes at very much lower frequency than in meiosis
2 In mitotic cells Crossing over between sister chromatids is fairly frequent
meiosis is structured to promote crossing over between non-sister chromatids
3 As in yeast cells mitotic recombination is mediated efficiently by either of two
recA homologs rad51 and Dmc1 while meiotic exchange between homologs
requires Dmc1 specifically
Neale and Keeney 2006
8
bull Earliest eukaryotic species were single-cell haploid forms having single set of
chromosomes and propagated by mitosis
bull Simplest contemporary eukaryotes Protists and fungi exhibit the mitotic propagation
of both haploid and diploid states diploidy is almost certainly a derived state
bull Very first diploid cells could have first arisen either by cell fusion or by
endomitosis
bull Hurst and Nurse (1991) First diploids probably arose via rare endomitotic errors
rather than by cell fusion
bull Either route to early diploid states is possible since non-sexual cell and nuclear
fusions can occur independently of sex (lsquolsquoparasexualityrsquorsquo)
9
Liverwort
Hornwort
Club mosses
Cone bearing plants
Green AlgaeAnc
est
or
10
bull All the key molecules employed in eukaryotic mitosis are of
Prokaryotic homologs
Actins required for daughter cell separation in eukaryotes
Tubulins required in eukaryotes for the mitotic spindle and movement
of chromosomes and
bull SMC molecules must for chromosome condensation and
sisterchromatid cohesion members of the so-called Structural
maintenance of chromosomes (SMC) family
Hirano 2005 and Erickson 2007
11
bull Tubulin family FtsZ genes which were first discovered in
Escherichia coli later found in many prokaryotes
bull Product of Ftsz involved in initiation of septum formation
bull minB locus regulate site of septum formation
bull MinCMinDMinE determines location of septum formation
bull The homologs of the SMC proteins are found throughout theEubacterial and Archaebacterial kingdoms
12
For genetic recombination recA family of proteins molecules in
prokaryotes and eukaryotes
Aboussekhra et al 1992
Shinohara et al 1992
Recombinational capacity is found throughout the prokaryotes
and considerably predate eukaryotes so meiosis arisen from pro
Levin 1988
Cavalier-Smith 2002
Marcon and Moens 2005
13
bull Suppression of Kinetochore splitting in MI was key innovation
in meiosis
Cavalier-Smith2002
bull Selection pressure on homologous pairing and high levels of intergenic
recombination are prime force for origin of meiosis
Fisher1930 Muller 1932 Maynard Smith 1978Crow 1988
bull Efficient DNA ds breaks and repair system
Bernstein 19771988
Argueso et al2008
14
bull Genetic cytological and immunochemical characterization done
in
Saccharomyces cerevisiae
Arabidopsis thaliana amp
Drosophila melanogaster etc
15
16
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull Meiosis includes two successive divisions ofthe nucleus with one round of DNAreplication and leads to the formation ofgametes with half of the chromosomes of themother cell during sexual reproduction
3
4
Independent assortmentAnaphase I
5
6
In humans
7
bull Diploid somatic cells of Fungi Animals amp Plants chromosomal crossing over
known as lsquoMitotic crossing overrsquo
Significant contrasts between meiotic and mitotic recombination
1 Mitotic recombination takes at very much lower frequency than in meiosis
2 In mitotic cells Crossing over between sister chromatids is fairly frequent
meiosis is structured to promote crossing over between non-sister chromatids
3 As in yeast cells mitotic recombination is mediated efficiently by either of two
recA homologs rad51 and Dmc1 while meiotic exchange between homologs
requires Dmc1 specifically
Neale and Keeney 2006
8
bull Earliest eukaryotic species were single-cell haploid forms having single set of
chromosomes and propagated by mitosis
bull Simplest contemporary eukaryotes Protists and fungi exhibit the mitotic propagation
of both haploid and diploid states diploidy is almost certainly a derived state
bull Very first diploid cells could have first arisen either by cell fusion or by
endomitosis
bull Hurst and Nurse (1991) First diploids probably arose via rare endomitotic errors
rather than by cell fusion
bull Either route to early diploid states is possible since non-sexual cell and nuclear
fusions can occur independently of sex (lsquolsquoparasexualityrsquorsquo)
9
Liverwort
Hornwort
Club mosses
Cone bearing plants
Green AlgaeAnc
est
or
10
bull All the key molecules employed in eukaryotic mitosis are of
Prokaryotic homologs
Actins required for daughter cell separation in eukaryotes
Tubulins required in eukaryotes for the mitotic spindle and movement
of chromosomes and
bull SMC molecules must for chromosome condensation and
sisterchromatid cohesion members of the so-called Structural
maintenance of chromosomes (SMC) family
Hirano 2005 and Erickson 2007
11
bull Tubulin family FtsZ genes which were first discovered in
Escherichia coli later found in many prokaryotes
bull Product of Ftsz involved in initiation of septum formation
bull minB locus regulate site of septum formation
bull MinCMinDMinE determines location of septum formation
bull The homologs of the SMC proteins are found throughout theEubacterial and Archaebacterial kingdoms
12
For genetic recombination recA family of proteins molecules in
prokaryotes and eukaryotes
Aboussekhra et al 1992
Shinohara et al 1992
Recombinational capacity is found throughout the prokaryotes
and considerably predate eukaryotes so meiosis arisen from pro
Levin 1988
Cavalier-Smith 2002
Marcon and Moens 2005
13
bull Suppression of Kinetochore splitting in MI was key innovation
in meiosis
Cavalier-Smith2002
bull Selection pressure on homologous pairing and high levels of intergenic
recombination are prime force for origin of meiosis
Fisher1930 Muller 1932 Maynard Smith 1978Crow 1988
bull Efficient DNA ds breaks and repair system
Bernstein 19771988
Argueso et al2008
14
bull Genetic cytological and immunochemical characterization done
in
Saccharomyces cerevisiae
Arabidopsis thaliana amp
Drosophila melanogaster etc
15
16
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
4
Independent assortmentAnaphase I
5
6
In humans
7
bull Diploid somatic cells of Fungi Animals amp Plants chromosomal crossing over
known as lsquoMitotic crossing overrsquo
Significant contrasts between meiotic and mitotic recombination
1 Mitotic recombination takes at very much lower frequency than in meiosis
2 In mitotic cells Crossing over between sister chromatids is fairly frequent
meiosis is structured to promote crossing over between non-sister chromatids
3 As in yeast cells mitotic recombination is mediated efficiently by either of two
recA homologs rad51 and Dmc1 while meiotic exchange between homologs
requires Dmc1 specifically
Neale and Keeney 2006
8
bull Earliest eukaryotic species were single-cell haploid forms having single set of
chromosomes and propagated by mitosis
bull Simplest contemporary eukaryotes Protists and fungi exhibit the mitotic propagation
of both haploid and diploid states diploidy is almost certainly a derived state
bull Very first diploid cells could have first arisen either by cell fusion or by
endomitosis
bull Hurst and Nurse (1991) First diploids probably arose via rare endomitotic errors
rather than by cell fusion
bull Either route to early diploid states is possible since non-sexual cell and nuclear
fusions can occur independently of sex (lsquolsquoparasexualityrsquorsquo)
9
Liverwort
Hornwort
Club mosses
Cone bearing plants
Green AlgaeAnc
est
or
10
bull All the key molecules employed in eukaryotic mitosis are of
Prokaryotic homologs
Actins required for daughter cell separation in eukaryotes
Tubulins required in eukaryotes for the mitotic spindle and movement
of chromosomes and
bull SMC molecules must for chromosome condensation and
sisterchromatid cohesion members of the so-called Structural
maintenance of chromosomes (SMC) family
Hirano 2005 and Erickson 2007
11
bull Tubulin family FtsZ genes which were first discovered in
Escherichia coli later found in many prokaryotes
bull Product of Ftsz involved in initiation of septum formation
bull minB locus regulate site of septum formation
bull MinCMinDMinE determines location of septum formation
bull The homologs of the SMC proteins are found throughout theEubacterial and Archaebacterial kingdoms
12
For genetic recombination recA family of proteins molecules in
prokaryotes and eukaryotes
Aboussekhra et al 1992
Shinohara et al 1992
Recombinational capacity is found throughout the prokaryotes
and considerably predate eukaryotes so meiosis arisen from pro
Levin 1988
Cavalier-Smith 2002
Marcon and Moens 2005
13
bull Suppression of Kinetochore splitting in MI was key innovation
in meiosis
Cavalier-Smith2002
bull Selection pressure on homologous pairing and high levels of intergenic
recombination are prime force for origin of meiosis
Fisher1930 Muller 1932 Maynard Smith 1978Crow 1988
bull Efficient DNA ds breaks and repair system
Bernstein 19771988
Argueso et al2008
14
bull Genetic cytological and immunochemical characterization done
in
Saccharomyces cerevisiae
Arabidopsis thaliana amp
Drosophila melanogaster etc
15
16
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Independent assortmentAnaphase I
5
6
In humans
7
bull Diploid somatic cells of Fungi Animals amp Plants chromosomal crossing over
known as lsquoMitotic crossing overrsquo
Significant contrasts between meiotic and mitotic recombination
1 Mitotic recombination takes at very much lower frequency than in meiosis
2 In mitotic cells Crossing over between sister chromatids is fairly frequent
meiosis is structured to promote crossing over between non-sister chromatids
3 As in yeast cells mitotic recombination is mediated efficiently by either of two
recA homologs rad51 and Dmc1 while meiotic exchange between homologs
requires Dmc1 specifically
Neale and Keeney 2006
8
bull Earliest eukaryotic species were single-cell haploid forms having single set of
chromosomes and propagated by mitosis
bull Simplest contemporary eukaryotes Protists and fungi exhibit the mitotic propagation
of both haploid and diploid states diploidy is almost certainly a derived state
bull Very first diploid cells could have first arisen either by cell fusion or by
endomitosis
bull Hurst and Nurse (1991) First diploids probably arose via rare endomitotic errors
rather than by cell fusion
bull Either route to early diploid states is possible since non-sexual cell and nuclear
fusions can occur independently of sex (lsquolsquoparasexualityrsquorsquo)
9
Liverwort
Hornwort
Club mosses
Cone bearing plants
Green AlgaeAnc
est
or
10
bull All the key molecules employed in eukaryotic mitosis are of
Prokaryotic homologs
Actins required for daughter cell separation in eukaryotes
Tubulins required in eukaryotes for the mitotic spindle and movement
of chromosomes and
bull SMC molecules must for chromosome condensation and
sisterchromatid cohesion members of the so-called Structural
maintenance of chromosomes (SMC) family
Hirano 2005 and Erickson 2007
11
bull Tubulin family FtsZ genes which were first discovered in
Escherichia coli later found in many prokaryotes
bull Product of Ftsz involved in initiation of septum formation
bull minB locus regulate site of septum formation
bull MinCMinDMinE determines location of septum formation
bull The homologs of the SMC proteins are found throughout theEubacterial and Archaebacterial kingdoms
12
For genetic recombination recA family of proteins molecules in
prokaryotes and eukaryotes
Aboussekhra et al 1992
Shinohara et al 1992
Recombinational capacity is found throughout the prokaryotes
and considerably predate eukaryotes so meiosis arisen from pro
Levin 1988
Cavalier-Smith 2002
Marcon and Moens 2005
13
bull Suppression of Kinetochore splitting in MI was key innovation
in meiosis
Cavalier-Smith2002
bull Selection pressure on homologous pairing and high levels of intergenic
recombination are prime force for origin of meiosis
Fisher1930 Muller 1932 Maynard Smith 1978Crow 1988
bull Efficient DNA ds breaks and repair system
Bernstein 19771988
Argueso et al2008
14
bull Genetic cytological and immunochemical characterization done
in
Saccharomyces cerevisiae
Arabidopsis thaliana amp
Drosophila melanogaster etc
15
16
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
6
In humans
7
bull Diploid somatic cells of Fungi Animals amp Plants chromosomal crossing over
known as lsquoMitotic crossing overrsquo
Significant contrasts between meiotic and mitotic recombination
1 Mitotic recombination takes at very much lower frequency than in meiosis
2 In mitotic cells Crossing over between sister chromatids is fairly frequent
meiosis is structured to promote crossing over between non-sister chromatids
3 As in yeast cells mitotic recombination is mediated efficiently by either of two
recA homologs rad51 and Dmc1 while meiotic exchange between homologs
requires Dmc1 specifically
Neale and Keeney 2006
8
bull Earliest eukaryotic species were single-cell haploid forms having single set of
chromosomes and propagated by mitosis
bull Simplest contemporary eukaryotes Protists and fungi exhibit the mitotic propagation
of both haploid and diploid states diploidy is almost certainly a derived state
bull Very first diploid cells could have first arisen either by cell fusion or by
endomitosis
bull Hurst and Nurse (1991) First diploids probably arose via rare endomitotic errors
rather than by cell fusion
bull Either route to early diploid states is possible since non-sexual cell and nuclear
fusions can occur independently of sex (lsquolsquoparasexualityrsquorsquo)
9
Liverwort
Hornwort
Club mosses
Cone bearing plants
Green AlgaeAnc
est
or
10
bull All the key molecules employed in eukaryotic mitosis are of
Prokaryotic homologs
Actins required for daughter cell separation in eukaryotes
Tubulins required in eukaryotes for the mitotic spindle and movement
of chromosomes and
bull SMC molecules must for chromosome condensation and
sisterchromatid cohesion members of the so-called Structural
maintenance of chromosomes (SMC) family
Hirano 2005 and Erickson 2007
11
bull Tubulin family FtsZ genes which were first discovered in
Escherichia coli later found in many prokaryotes
bull Product of Ftsz involved in initiation of septum formation
bull minB locus regulate site of septum formation
bull MinCMinDMinE determines location of septum formation
bull The homologs of the SMC proteins are found throughout theEubacterial and Archaebacterial kingdoms
12
For genetic recombination recA family of proteins molecules in
prokaryotes and eukaryotes
Aboussekhra et al 1992
Shinohara et al 1992
Recombinational capacity is found throughout the prokaryotes
and considerably predate eukaryotes so meiosis arisen from pro
Levin 1988
Cavalier-Smith 2002
Marcon and Moens 2005
13
bull Suppression of Kinetochore splitting in MI was key innovation
in meiosis
Cavalier-Smith2002
bull Selection pressure on homologous pairing and high levels of intergenic
recombination are prime force for origin of meiosis
Fisher1930 Muller 1932 Maynard Smith 1978Crow 1988
bull Efficient DNA ds breaks and repair system
Bernstein 19771988
Argueso et al2008
14
bull Genetic cytological and immunochemical characterization done
in
Saccharomyces cerevisiae
Arabidopsis thaliana amp
Drosophila melanogaster etc
15
16
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
In humans
7
bull Diploid somatic cells of Fungi Animals amp Plants chromosomal crossing over
known as lsquoMitotic crossing overrsquo
Significant contrasts between meiotic and mitotic recombination
1 Mitotic recombination takes at very much lower frequency than in meiosis
2 In mitotic cells Crossing over between sister chromatids is fairly frequent
meiosis is structured to promote crossing over between non-sister chromatids
3 As in yeast cells mitotic recombination is mediated efficiently by either of two
recA homologs rad51 and Dmc1 while meiotic exchange between homologs
requires Dmc1 specifically
Neale and Keeney 2006
8
bull Earliest eukaryotic species were single-cell haploid forms having single set of
chromosomes and propagated by mitosis
bull Simplest contemporary eukaryotes Protists and fungi exhibit the mitotic propagation
of both haploid and diploid states diploidy is almost certainly a derived state
bull Very first diploid cells could have first arisen either by cell fusion or by
endomitosis
bull Hurst and Nurse (1991) First diploids probably arose via rare endomitotic errors
rather than by cell fusion
bull Either route to early diploid states is possible since non-sexual cell and nuclear
fusions can occur independently of sex (lsquolsquoparasexualityrsquorsquo)
9
Liverwort
Hornwort
Club mosses
Cone bearing plants
Green AlgaeAnc
est
or
10
bull All the key molecules employed in eukaryotic mitosis are of
Prokaryotic homologs
Actins required for daughter cell separation in eukaryotes
Tubulins required in eukaryotes for the mitotic spindle and movement
of chromosomes and
bull SMC molecules must for chromosome condensation and
sisterchromatid cohesion members of the so-called Structural
maintenance of chromosomes (SMC) family
Hirano 2005 and Erickson 2007
11
bull Tubulin family FtsZ genes which were first discovered in
Escherichia coli later found in many prokaryotes
bull Product of Ftsz involved in initiation of septum formation
bull minB locus regulate site of septum formation
bull MinCMinDMinE determines location of septum formation
bull The homologs of the SMC proteins are found throughout theEubacterial and Archaebacterial kingdoms
12
For genetic recombination recA family of proteins molecules in
prokaryotes and eukaryotes
Aboussekhra et al 1992
Shinohara et al 1992
Recombinational capacity is found throughout the prokaryotes
and considerably predate eukaryotes so meiosis arisen from pro
Levin 1988
Cavalier-Smith 2002
Marcon and Moens 2005
13
bull Suppression of Kinetochore splitting in MI was key innovation
in meiosis
Cavalier-Smith2002
bull Selection pressure on homologous pairing and high levels of intergenic
recombination are prime force for origin of meiosis
Fisher1930 Muller 1932 Maynard Smith 1978Crow 1988
bull Efficient DNA ds breaks and repair system
Bernstein 19771988
Argueso et al2008
14
bull Genetic cytological and immunochemical characterization done
in
Saccharomyces cerevisiae
Arabidopsis thaliana amp
Drosophila melanogaster etc
15
16
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull Diploid somatic cells of Fungi Animals amp Plants chromosomal crossing over
known as lsquoMitotic crossing overrsquo
Significant contrasts between meiotic and mitotic recombination
1 Mitotic recombination takes at very much lower frequency than in meiosis
2 In mitotic cells Crossing over between sister chromatids is fairly frequent
meiosis is structured to promote crossing over between non-sister chromatids
3 As in yeast cells mitotic recombination is mediated efficiently by either of two
recA homologs rad51 and Dmc1 while meiotic exchange between homologs
requires Dmc1 specifically
Neale and Keeney 2006
8
bull Earliest eukaryotic species were single-cell haploid forms having single set of
chromosomes and propagated by mitosis
bull Simplest contemporary eukaryotes Protists and fungi exhibit the mitotic propagation
of both haploid and diploid states diploidy is almost certainly a derived state
bull Very first diploid cells could have first arisen either by cell fusion or by
endomitosis
bull Hurst and Nurse (1991) First diploids probably arose via rare endomitotic errors
rather than by cell fusion
bull Either route to early diploid states is possible since non-sexual cell and nuclear
fusions can occur independently of sex (lsquolsquoparasexualityrsquorsquo)
9
Liverwort
Hornwort
Club mosses
Cone bearing plants
Green AlgaeAnc
est
or
10
bull All the key molecules employed in eukaryotic mitosis are of
Prokaryotic homologs
Actins required for daughter cell separation in eukaryotes
Tubulins required in eukaryotes for the mitotic spindle and movement
of chromosomes and
bull SMC molecules must for chromosome condensation and
sisterchromatid cohesion members of the so-called Structural
maintenance of chromosomes (SMC) family
Hirano 2005 and Erickson 2007
11
bull Tubulin family FtsZ genes which were first discovered in
Escherichia coli later found in many prokaryotes
bull Product of Ftsz involved in initiation of septum formation
bull minB locus regulate site of septum formation
bull MinCMinDMinE determines location of septum formation
bull The homologs of the SMC proteins are found throughout theEubacterial and Archaebacterial kingdoms
12
For genetic recombination recA family of proteins molecules in
prokaryotes and eukaryotes
Aboussekhra et al 1992
Shinohara et al 1992
Recombinational capacity is found throughout the prokaryotes
and considerably predate eukaryotes so meiosis arisen from pro
Levin 1988
Cavalier-Smith 2002
Marcon and Moens 2005
13
bull Suppression of Kinetochore splitting in MI was key innovation
in meiosis
Cavalier-Smith2002
bull Selection pressure on homologous pairing and high levels of intergenic
recombination are prime force for origin of meiosis
Fisher1930 Muller 1932 Maynard Smith 1978Crow 1988
bull Efficient DNA ds breaks and repair system
Bernstein 19771988
Argueso et al2008
14
bull Genetic cytological and immunochemical characterization done
in
Saccharomyces cerevisiae
Arabidopsis thaliana amp
Drosophila melanogaster etc
15
16
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull Earliest eukaryotic species were single-cell haploid forms having single set of
chromosomes and propagated by mitosis
bull Simplest contemporary eukaryotes Protists and fungi exhibit the mitotic propagation
of both haploid and diploid states diploidy is almost certainly a derived state
bull Very first diploid cells could have first arisen either by cell fusion or by
endomitosis
bull Hurst and Nurse (1991) First diploids probably arose via rare endomitotic errors
rather than by cell fusion
bull Either route to early diploid states is possible since non-sexual cell and nuclear
fusions can occur independently of sex (lsquolsquoparasexualityrsquorsquo)
9
Liverwort
Hornwort
Club mosses
Cone bearing plants
Green AlgaeAnc
est
or
10
bull All the key molecules employed in eukaryotic mitosis are of
Prokaryotic homologs
Actins required for daughter cell separation in eukaryotes
Tubulins required in eukaryotes for the mitotic spindle and movement
of chromosomes and
bull SMC molecules must for chromosome condensation and
sisterchromatid cohesion members of the so-called Structural
maintenance of chromosomes (SMC) family
Hirano 2005 and Erickson 2007
11
bull Tubulin family FtsZ genes which were first discovered in
Escherichia coli later found in many prokaryotes
bull Product of Ftsz involved in initiation of septum formation
bull minB locus regulate site of septum formation
bull MinCMinDMinE determines location of septum formation
bull The homologs of the SMC proteins are found throughout theEubacterial and Archaebacterial kingdoms
12
For genetic recombination recA family of proteins molecules in
prokaryotes and eukaryotes
Aboussekhra et al 1992
Shinohara et al 1992
Recombinational capacity is found throughout the prokaryotes
and considerably predate eukaryotes so meiosis arisen from pro
Levin 1988
Cavalier-Smith 2002
Marcon and Moens 2005
13
bull Suppression of Kinetochore splitting in MI was key innovation
in meiosis
Cavalier-Smith2002
bull Selection pressure on homologous pairing and high levels of intergenic
recombination are prime force for origin of meiosis
Fisher1930 Muller 1932 Maynard Smith 1978Crow 1988
bull Efficient DNA ds breaks and repair system
Bernstein 19771988
Argueso et al2008
14
bull Genetic cytological and immunochemical characterization done
in
Saccharomyces cerevisiae
Arabidopsis thaliana amp
Drosophila melanogaster etc
15
16
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Liverwort
Hornwort
Club mosses
Cone bearing plants
Green AlgaeAnc
est
or
10
bull All the key molecules employed in eukaryotic mitosis are of
Prokaryotic homologs
Actins required for daughter cell separation in eukaryotes
Tubulins required in eukaryotes for the mitotic spindle and movement
of chromosomes and
bull SMC molecules must for chromosome condensation and
sisterchromatid cohesion members of the so-called Structural
maintenance of chromosomes (SMC) family
Hirano 2005 and Erickson 2007
11
bull Tubulin family FtsZ genes which were first discovered in
Escherichia coli later found in many prokaryotes
bull Product of Ftsz involved in initiation of septum formation
bull minB locus regulate site of septum formation
bull MinCMinDMinE determines location of septum formation
bull The homologs of the SMC proteins are found throughout theEubacterial and Archaebacterial kingdoms
12
For genetic recombination recA family of proteins molecules in
prokaryotes and eukaryotes
Aboussekhra et al 1992
Shinohara et al 1992
Recombinational capacity is found throughout the prokaryotes
and considerably predate eukaryotes so meiosis arisen from pro
Levin 1988
Cavalier-Smith 2002
Marcon and Moens 2005
13
bull Suppression of Kinetochore splitting in MI was key innovation
in meiosis
Cavalier-Smith2002
bull Selection pressure on homologous pairing and high levels of intergenic
recombination are prime force for origin of meiosis
Fisher1930 Muller 1932 Maynard Smith 1978Crow 1988
bull Efficient DNA ds breaks and repair system
Bernstein 19771988
Argueso et al2008
14
bull Genetic cytological and immunochemical characterization done
in
Saccharomyces cerevisiae
Arabidopsis thaliana amp
Drosophila melanogaster etc
15
16
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull All the key molecules employed in eukaryotic mitosis are of
Prokaryotic homologs
Actins required for daughter cell separation in eukaryotes
Tubulins required in eukaryotes for the mitotic spindle and movement
of chromosomes and
bull SMC molecules must for chromosome condensation and
sisterchromatid cohesion members of the so-called Structural
maintenance of chromosomes (SMC) family
Hirano 2005 and Erickson 2007
11
bull Tubulin family FtsZ genes which were first discovered in
Escherichia coli later found in many prokaryotes
bull Product of Ftsz involved in initiation of septum formation
bull minB locus regulate site of septum formation
bull MinCMinDMinE determines location of septum formation
bull The homologs of the SMC proteins are found throughout theEubacterial and Archaebacterial kingdoms
12
For genetic recombination recA family of proteins molecules in
prokaryotes and eukaryotes
Aboussekhra et al 1992
Shinohara et al 1992
Recombinational capacity is found throughout the prokaryotes
and considerably predate eukaryotes so meiosis arisen from pro
Levin 1988
Cavalier-Smith 2002
Marcon and Moens 2005
13
bull Suppression of Kinetochore splitting in MI was key innovation
in meiosis
Cavalier-Smith2002
bull Selection pressure on homologous pairing and high levels of intergenic
recombination are prime force for origin of meiosis
Fisher1930 Muller 1932 Maynard Smith 1978Crow 1988
bull Efficient DNA ds breaks and repair system
Bernstein 19771988
Argueso et al2008
14
bull Genetic cytological and immunochemical characterization done
in
Saccharomyces cerevisiae
Arabidopsis thaliana amp
Drosophila melanogaster etc
15
16
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull Tubulin family FtsZ genes which were first discovered in
Escherichia coli later found in many prokaryotes
bull Product of Ftsz involved in initiation of septum formation
bull minB locus regulate site of septum formation
bull MinCMinDMinE determines location of septum formation
bull The homologs of the SMC proteins are found throughout theEubacterial and Archaebacterial kingdoms
12
For genetic recombination recA family of proteins molecules in
prokaryotes and eukaryotes
Aboussekhra et al 1992
Shinohara et al 1992
Recombinational capacity is found throughout the prokaryotes
and considerably predate eukaryotes so meiosis arisen from pro
Levin 1988
Cavalier-Smith 2002
Marcon and Moens 2005
13
bull Suppression of Kinetochore splitting in MI was key innovation
in meiosis
Cavalier-Smith2002
bull Selection pressure on homologous pairing and high levels of intergenic
recombination are prime force for origin of meiosis
Fisher1930 Muller 1932 Maynard Smith 1978Crow 1988
bull Efficient DNA ds breaks and repair system
Bernstein 19771988
Argueso et al2008
14
bull Genetic cytological and immunochemical characterization done
in
Saccharomyces cerevisiae
Arabidopsis thaliana amp
Drosophila melanogaster etc
15
16
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
For genetic recombination recA family of proteins molecules in
prokaryotes and eukaryotes
Aboussekhra et al 1992
Shinohara et al 1992
Recombinational capacity is found throughout the prokaryotes
and considerably predate eukaryotes so meiosis arisen from pro
Levin 1988
Cavalier-Smith 2002
Marcon and Moens 2005
13
bull Suppression of Kinetochore splitting in MI was key innovation
in meiosis
Cavalier-Smith2002
bull Selection pressure on homologous pairing and high levels of intergenic
recombination are prime force for origin of meiosis
Fisher1930 Muller 1932 Maynard Smith 1978Crow 1988
bull Efficient DNA ds breaks and repair system
Bernstein 19771988
Argueso et al2008
14
bull Genetic cytological and immunochemical characterization done
in
Saccharomyces cerevisiae
Arabidopsis thaliana amp
Drosophila melanogaster etc
15
16
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull Suppression of Kinetochore splitting in MI was key innovation
in meiosis
Cavalier-Smith2002
bull Selection pressure on homologous pairing and high levels of intergenic
recombination are prime force for origin of meiosis
Fisher1930 Muller 1932 Maynard Smith 1978Crow 1988
bull Efficient DNA ds breaks and repair system
Bernstein 19771988
Argueso et al2008
14
bull Genetic cytological and immunochemical characterization done
in
Saccharomyces cerevisiae
Arabidopsis thaliana amp
Drosophila melanogaster etc
15
16
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull Genetic cytological and immunochemical characterization done
in
Saccharomyces cerevisiae
Arabidopsis thaliana amp
Drosophila melanogaster etc
15
16
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
16
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
17
bull SPO11 gene required for meiotic recombination by catalyzing DNA ds
Breaks
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Mutation of Spoll-1
(i) Drastic reduction in meiotic recombination and ascospore viability amp no
significant effect on vegetative growth or mitotic exchange
(ii) The low spore survival results from aneuploidy
(iii) It is epistatic to other recombination (Rec) mutants such as rad51 rad52
and rad57 that do not produce viable spores in the presence of spol3-1
alone but do so when spoll-1 is also present
(iv) It does not block either pre-meiotic DNA synthesis or synaptonemal
complex formation
18
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Conthellip
bull Unlike the RAD genes which can affect both meiotic and
mitotic recombination as well as DNA repair the SPO11
function appears to be meiosis specific and unrelated to repair
bull RNA analyses demonstrate that wild-type SPO11 gene acts relatively at
early in the meiotic recombination process or soon after the time of
chromosome pairing
CATHERINE L ATCHESON et al1987
19
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Arabidopsis thaliana 2n=2x=10
bull Scerviceae that initiates meiotic recombination
bull The Model plant Athaliana possesses at least 3 Spo11 homologues
bull Meiotic progression altered by EMS by which AtSpo11-1 gene was disrupted
bull Leading to non-synapsed chromosome in Prophase ndashI and non-functional
gametes due to random chromosome distribution in meiosis ndashI
20
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
6 weeks Wild type6 weeks mutant type
21
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Wild Type (97)
Pollen fertility
Mutant Type spo11-1
(11) Pollen fertility
Differential Interference Contrast (DIC) Microscopy observation
Mature embryo sacs were observedOnly 3 female
gametophyte were differentiated Intermediate stages
were seen Incomplete
differentiation lead to 2-4 nuclei
22
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Irregular Tetrads and
Polyads
23
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
24
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
25
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
26
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
27
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
28
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull Structure Maintenance of Chromosomes (SMC)
bull MRE11
bull RAD51 homologs
bull BRCA2
bull MSH4
bull MER3
bull ZIP1
bull Genes that encode components unique to plants such as POOR
HOMOLOGOUS SYNAPSIS 1 and AMEIOTIC 1 have been cloned
Hamant O Ma H Cande WZ 2006
29
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull Knowledge of meiosis-driven genome variations
Genome evolution and
Genetic variability in plants and evolution in plants
Facilitates plant genome research
30
Meiosis-driven genome variation
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
31
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
32
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull Asynapsis Homologous chromosomes may fail to synapse
bull Desynapsis Homologous chromosomes synapse with each other normally but
the association cannot be held until Anaphase I and they separate
prematurely
bull Both lead to univalents they either get lost or are randomly transmitted to
daughter cells resulting in chromosomally unbalanced gametes and
eventually aneuploids in the offspring
Misdivision such as transverse division lead to Telocentric Acrocentric and
Acentric chromosomes or Isochromosomes in wheat
Sears ER1952
Asynapsis and desynapsis induced aneuploidy in plants
33
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull For accurate segregation Proper Pairing Synapsis and
Recombination of homologous chromosomes at meiosis I are
prerequisites
bull Synapsed Bivalents held together until Anaphase I by the
chiasmata resulting from crossing-over and cohesin
34
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull Cohesin Rec8 is required for reductional chromosome segregation at meiosis
Watanabe Y Nurse P 1999
The rice Os-Rad21-4 an orthologue of yeast Rec8 protein is required for efficient meiosis
Zhang L2006
The Arabidopsis SYN1 cohesion protein is required for sister chromatid arm cohesion and homologous chromosome pairing
Cai X et al2003
AtREC8 and AtSCC are essential to the monopolar orientation of the
Kinetochores during meiosis
Chelysheva L et al2005
35
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Genes Asynapsis and Desynapsis
CROP ASYNAPSIS DESYNAPSIS ASSOCIATED REFERENCES
Soybean st2 st3 st8 st4 ast6 and st7 and st5
Male amp female sterility
Palmer RC Kilen RC1987Palmer RG Horner
HT2000Kato KK2003
Maize phs1 dy and dsy1 Telomere misplacement
Bass HW2003
Arabidopsis thaliana
asy1 dsy1 Male fertility Chaudhury AMet al1994
Single recessive genes amp Duplicated recessive factors
36
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull In many plant spp higher recombination frequency at gene-rich
regions than repetitive DNA sequences
At a number of gene loci in plants
bull In Rice (Oryza sativa) wx locus and
bull In Maize (Zea mays) A1 locus and bronze locus
In Arabidopsis at the csr1 locus intragenic recombination rate was
found almost same as the genome average
37
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull Meiotic recombination can be
Intergenic recombination
Intragenic recombination
Generators of genetic diversity Plays important rolein gene evolution
Fisher 1930 Muller 1932
Maynard Smith 1978 Crow 1988
38
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Intragenic Recombination
bull First described in Drosophila melanogaster in 1940
bull In 1955 fungus Neurospora crassa
bull Results in disruption of a functional gene or generation of new
alleles at the gene locus
bull Reciprocally or via a non-reciprocal process called bdquogene conversion‟
39
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Intragenic recombination Evolution of disease resistance genes
Maize-Rust
Flax-Rust
Arabidopsis-Downy Mildew
Tomato-Leaf Mold
Wheat ndashLeaf Rust
Citrus- Tristeza
Maize rust resistance gene complex Rp1
Recombination within Rp1 gene complex mostly within the coding regions led to new rust resistance specificities
Richter TE 1995 Sun Q2001
40
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Flax (Linum usitatissimum)
gt30 rust resistance genes designated K L M N and P have
been identified
bull Extensive analysis of the L and M loci suggests
The L locus contains a single gene with multiple alleles
Anderson PA 1997
Bent A F 1996
41
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Sequence and genetic analysis of 13 natural and in vitro engineered
recombinant alleles at the L locus by intragenic recombination resulted in
mutant alleles that confer novel resistance specificities
42
Islam MR 1991
Mayo GME 1980
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Arabidopsis downy mildew resistance gene RPP8
McDowell et al 1998
Tomato (Lycopersicon) leaf mold resistance gene Cf-5
Dixon MSet al1988
Wheat (Triticum) leaf rust resistance gene Lr21
Citrus Citrus Tristeza virus resistance gene Ctv
Yang Zet al2003
Revealed occurrence of the recombination within the coding region of disease resistance genes in plants
43
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Intragenic recombination Generates allelic diversity
bull Sorghum (Sorghum vulgare) dwarf mutant dw3 mutant allele was
generated by a direct duplication of an 882 bp interval in Exon 5
bull Instability by loss of the duplication due to unequal crossing-over
between the duplicated regions
bull The intragenic unequal crossing-over event reverted the mutant
allele dw3 to the wild type allele Dw3
Multani D S et al2003
44
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Results in
bull Deletions
bull Duplications
bull Inversions and
bull Translocations
Disrupt the function of a gene
Generate new alleles at a gene
locus and
Cause variations in the genome
structure and size by counter
acting genome expansion
45
Impact
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
unequal crossing-over
bull Unequal alignment of homologous chromosomal regions
and then unequal crossing-over due to sequence
similarity among members of a gene family or other
tandem repeats
bull Unequal crossing-over was first documented at the
Bar locus in Drosophila melanogaster in the 1920s
Sturtevant AH1925
46
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Unequal crossovers Evolution of disease resistance gene families
bull In Tomato Cf-4 and Cf-9 reside within a large gene family on the short arm
of chromosome 1
bull Arabidopsis downy mildew resistance locus RPP5
Parker JE et al1997
bull In Soybean (Glycine max)Intragenic unequal crossing over in nucleotide-
binding-siteleucine-rich-repeat-like sequence lead to deletion of the
phytophthora resistance gene Rps4
Sandhu Det al2004
bull Rsv1 conditioning resistance to soybean mosaic virus
Hayes AJ 2004
47
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Unequal recombination Mechanisms for genome contraction
bull gt50 of nuclear DNA is Repetitive DNA sequences Including
transposable elements and variable number of tandem repeats (VNTRs)
comprise a large portion of the genome in plant species
Flavell RB1974
bull Unequal crossing-over occurred within LTR (long terminal repeat)-
containing retrotransposons due to the LTRs at both ends of the element
removes the internal domain of the retroelement and leads to solo LTRs
Bennetzen JL1997
48
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull In the rice genome ratio of solo LTRs to intact LTR retroelements varies
with the retrotransposon families
Vitte C Panaud O 2003
bull In Rice Oryza sativa L Formation of solo-LTRs through unequal
homologous recombination counterbalances amplifications of LTR
retrotransposons
bull Over 190 Mb of LTR retrotransposon sequences have been removed from
the Rice genome in the last eight million years
Ma J et al2004
49
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull In Maize genome retroelements found to be intact a mechanism
to counterbalance genome expansion
SanMiguel P et al1996
bull Rapid genome divergence at orthologous low molecular weight
Glutenin loci of the A genome of wheat by sequence deletion in
the LTR retrotransposons due to unequal recombination
Wicker T et al 2003
50
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
MEIOTIC CHROMOSOME SEGREGATION
bull Orientation of sister Kinetochores
bull At both meiotic divisions govern chromosome segregation and transmission throughout meiosis
51
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull Monopolar attachment of microtubules to the sister
Kinetochores at metaphase I is prerequisite to ensure accurate
segregation of homologous chromosomes at meiosis I
Watanabe Y2004
bull Bipolar attachment of the microtubules from opposite poles to
the sister Kinetochores ensures equational division of sister
chromatids at meiosis II
52
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
MEIOTIC RESTITUTION amp POLYPLOIDY
bull Meiotic restitution significant driving force behind speciation in plants
bull Normal meiosis includes
The first division is reductional and
The second is equational
bull Failure of the first or second division leads to the formation of restitution
nuclei with unreduced chromosomes
53
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
54
Ramanna MS Jacobsen E 2003
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
55
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull Wheat msg gene affect megasporogenesis leading to unreduced egg
Joppa LR 1987
bull Barley triploid inducer (tri) gene
Finch RA MD Bennett1979
bull Maize elongate (el) gene induces chromosome doubling
Rhoades MM Dempsey E 1966
56
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull In Potato
1 parallel spindles (ps)
2 premature cytokinesis-1 (pc-1) and
3 premature cytokinesis-2 (pc-2)
4 desynaptic (ds-1) and
5 synaptic mutants (sy-1sy-2 sy-3 and sy-4)
Jongedijk E Ramanna MS1988
6 omission of the second division (os)
Werner J E Peloquin SJ1990
57
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull In diploid Alfalfa (Medicago sativa)
Two single recessive genes
1 rp (restitution pollen) and
2 jp (jumbo pollen)
conditioning 2n pollen formation by disorientation ofspindles at metaphase II and failure of cytokinesis at thesecond division
McCoy TJ 1982 amp 1983
58
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
bull In Angiosperms gt30 of species were estimated to be of polyploid
origin
Stebbins GL 1950 amp 1971
bull Polyploidization is considered one of the major processes involved in
plant genome expansion
Bennetzen JL 1997amp 2002
bull Functioning of the unreduced gametes produced through meiotic
restitution lead to polyploidy
Ramanna MS2003
59
POLYPLOIDY
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
60
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
62
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
63
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
64
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
65
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
66
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Lilly (Lillium regale) 2n=2x=24
Welcome for rsquos
Welcome for rsquos
