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WELCOME
PRESENTED BYR. ASHABAM-10-11
GENETIC MARKERS AND PLANT GENETIC
RESOURCE MANAGEMENT
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CONTENTS
1. Introduction
2. Kinds of plant genetic resources
3. Plant genetic resource management
4. Need of plant genetic resource management
5. How genetic markers are useful
6. Different marker techniques
7. Role of markers in plant genetic resource management
8. Conclusions
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• Germplasm of a crop may be defined as the sum total of
hereditary material i.e., all the alleles of various genes, present
in a crop species and its wild and weedy relatives. It is also
termed as Genetic resources.
• Represents entire genetic variability or diversity available in a
crop species.
• Plant genetic resources constitute an invaluable reservoir of
gene pools that are needed by plant breeders for development
of superior varieties.
• Basic material for launching a crop improvement programmes.
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Plant genetic resources are the building blocks and Plant genetic resources are the building blocks and fundamental not only in crop improvement fundamental not only in crop improvement programme, but also for the very survival of the programme, but also for the very survival of the species in time and spacespecies in time and space..
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Plant genetic
Resources are
components of
biodiversity
which sustains
the humankind.
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Kinds of Plant Genetic Resourcesa) Basic Genetic Resources 1. Wild taxa related to a crop species 2. Weedy forms 3. Land races or primitive cultivarsb) Derived Genetic Resources 4. Obsolete varieties 5. Breeding lines with particular genes and performances 6. Prebreeding materials 7. Advanced cultivars 8. Parents of hybrid varieties 9. Cytogenetic stocks/tester 10. Mutants
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Plant Genetic Resource Management
Plant genetic resource management or simply
germplasm management comprises 2 phases
1. Germplasm Conservation
2. Encouraging Utilization
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GERMPLASM
CONSERVATION
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1.Germplasm conservation
Acquisition, or securing germplasm in situ or Ex situ
Maintenance
- Monitoring and protecting germplasm in reserves or
storing it Ex situ under controlled conditions.
2.Encouraging utilization
Evaluation
Genetic enhancement
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NEED OF PLANT GENETIC RESOURCE MANAGEMENT
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• Continued alteration of the environment by man has resulted
unprecedented loss of biodiversity.
• Many species have become extinct or are near extinction due
to destruction and fragmentation of their habitats.
• Consequent erosion of genetic diversity leads to reduced
resilience to environmental changes and altered ecosystem
processes.
• Therefore developing effective conservation strategies is of
fundamental importance (Newton et al., 1999)
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• The realization that the world was rapidly losing much of its
agrobiodiversity led to a global effort to collect and conserve
germplasm.
• An increasing awareness of the narrow genetic base of crops in
advanced agriculture and potential susceptibility to crop failures
further stimulated the efforts to collect & presents new challenges
to genebank managers to determine needs for new collections,
maintain existing collections, determine optimum regeneration
methods, characterize collections for useful agronomic traits,
classify the collections, and reduce the size of the working
collection to a manageable size (The Core collection concept:
Frankel 1984; Hamon et al., 1995).
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HOW GENETIC MARKERS ARE USEFUL IN PLANT GENETIC RESOURCE MANAGEMENT
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• The role of genetic markers in genetic enhancement is
considered in the context of germplasm management as a
whole (Duvick, 1990).
• Genetic markers may assist plant germplasm management,
which when properly conducted provides scientists with high
quality raw genetic materials for analysis and breeding.
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WHAT ARE THE DIFFERENT MARKER TECHNIQUES
GENERALLY USED
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Markers Any identifiable mark on an object
Represent genetic difference between individual organisms
or species
Act as signs or flags
Located in close proximity to genes (tightly linked)
Genetic markers are tags for genes
Markers should be discrete and heritable
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TYPES
PHENOTYPE
PROTEIN
RNA
DNA
Biochemical markers
DNA Markers
Morphological Markers
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Morphological marker
Morphologicallevel
Proteinmarker
Protein level
DNAlevel
DNAmarker
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Morphological Markers
Visually characterized phenotypic characters
Flower colour ,seed shape , growth habit, pigmentation
Germplasm characterization
Indirect selection –
Purple Coleoptiles – BPH resistance in Rice
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Morphological markers
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Advantages:
Inexpensive to score,
Amenable to experiments in natural populations
Disadvantages:
Visible polymorphisms relatively rare.
Most genetic variation not so easily observed (Variants are
ambiguous)
Genetic basis of variation can be complex, and is not necessarily
easy to determine
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Limitations
Environment influence and influenced by many genes
Do not represent the genome adequately
No stable inheritance( Need repeated measures)
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Biochemical markers Isozymes – Allelic variants of enzymes
(Enzymes that differ in amino acid sequences but
catalyze the same chemical changes)
Detected by electrophoresis and specific staining
ELISA (Enzyme Linked Immunosorbant Assay)
Viral disease identification
Example: Wheat Bread making Quality- Gluten by SDS – PAGE Rice Cooking Quality – Amylose
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Protein Allozymes:
Electrophoretic variants of proteins produced
by different alleles at protein-coding genes.
Protein Electrophoresis Gel
Total protein
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Selected samples
Proteins
Western
Blot
Biochemical Markers
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Advantages: • Inexpensive; • Markers are co-dominant.
Disadvantages: • Only reveals small proportion of DNA
variation. • Many DNA variants do not result in
changes in amino acid sequence (e.g., synonymous substitutions).
• Some changes in amino acid sequence do not result in changes in mobility on the gel.
Using Protein Polymorphism
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Limitations
Low level of polymorphism
Expressed at protein/ amino acid
level
Environmental influence
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DNA Markers Identifiable DNA sequences found at specific
locations
Located in the non coding region of DNA
Do not have any biological effect
Follows standard laws of inheritance
Markers
Polymorphic Monomorphic
1. Co dominant
2. Dominant
MK1
MK2
Gene
Chromosome
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BA)
P1 F1 P2
Polymorphic Monomorphic
Codominant Dominant
Markers at DNA level
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Co dominant Dominant
Discriminate b/w homozygous & No discrimination heterozygousNo progeny testing Progeny testing
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MOLECULAR MARKERS
Molecular markers are based on the identification of
polymorphisms in DNA.
They have been termed as Molecular Markers
(Tanksley 1983)
Molecular marker is a DNA sequence readily detected and
whose inheritance can be easily found.
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Molecular Basis of DNA Markers
Base substitution
Insertion
Deletion
Inversion
Duplication
Translocation
Methylation
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MOLECULAR BASIS OF DNA MARKERSMOLECULAR BASIS OF DNA MARKERS
GAATTCGAATTCCTTAAGCTTAAG
GAATTCGAATTCCTTAAGCTTAAG
11) ) Gain or loss of a restriction site, or PCR priming site Gain or loss of a restriction site, or PCR priming site
RFLP, AFLP, CAPSRFLP, AFLP, CAPS
GAATTCGAATTCCTTAAGCTTAAG
GACTTCGACTTCCTGAAGCTGAAG
GAATTCGAATTCCTTAAGCTTAAG
RAPD, AP-PCR, DAFRAPD, AP-PCR, DAF
22) Insertion or deletion between restriction or priming sites) Insertion or deletion between restriction or priming sitesGAATTCGAATTCCTTAAGCTTAAG
GAATTCGAATTCCTTAAGCTTAAG
RFLP, AFLP, CAPSRFLP, AFLP, CAPSRAPD, AP-PCR, DAFRAPD, AP-PCR, DAF
GAATTCGAATTCCTTAAGCTTAAG
GAATTCGAATTCCTTAAGCTTAAG
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• Co-dominant inheritance
• Highly polymorphic.
• Multi-functional.
• High reproducibility
• Frequent occurrence
• No environmental influence
• Ability to be automated.
• Easy access and exchange
PROPERTIES OF A GOOD MARKER Co dominant Dominant
Within population sex-linked visible polymorphism(STAG BEETLE)
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RFLP (1975)
Minisatellites Microsatellites
RAPD (1990)
STS/SCAR (1991)
ISSR (1994)
AFLP (1995)
SNP (1999)
INDEL (1999)
Pre Genome Sequencing
Post Genome Sequencing
Before PCR boom
After PCR boom
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RFLP : The variation(s) in the length of DNA fragments produced by a
specific restriction endonuclease from genomic DNAs of two or
more individuals of a species
39(Devos, K. M. and M. D.Gale,2000.)
Restriction Fragment Length Polymorphism (RFLP)
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Uses of RFLP
Direct identification of genotype in environment
independent manner .
They are co dominant markers & simple as no sequence
specific information is required.
Indirect selection using qualitative traits.
Tagging of monogenic traits with RFLP markers
Indirect selection using quantitative trait loci.
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AFLP : Any difference between corresponding DNA fragments from two organisms A and B, that is detected by the amplified restriction length polymorphism.
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RAPDAny DNA segment that is amplified using short
oligodeoxynucleotide primers of arbitrary nucleotide
sequence (amplifiers) and polymerase chain reaction
procedures. (Kahl,2001).
Laboratory steps are:
Isolating DNA
PCR reaction with a primer
Separating DNA fragments by gel electrophoresis
Visualizing DNA fragments, using ethidium bromide
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RAPD technologyA B C
Genomic DNA
+
Taq polymerase
+
Arbitrary primers
A
+
Nucleotides
+
Buffer
PCR
(under relaxed conditions)
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Advantages of RAPD
small amount of DNA (15-25ng)
Non radioactive assay
Thermocycler- Agarose gel
No probe is required,
Efficient screening for DNA sequence –based polymorphism
at many loci
It does not involve blotting or hybridization steps
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Limitations of RAPD
They are not co- dominant markers
The primers -short,
Sensitive to changes in PCR condition, resulting in changes to
some of amplified fragments
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APPLICATIONS:
Construction of genetic maps
Mapping of traits
Indirect selection of segregating population
Analysis of genetic structure of population
Finger printing.
Identification of somatic hybrids
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OTHER TYPES OF MARKERSSCAR ( Sequenced Charecterised Amplified Region)
Desired RAPD marker can be increased by sequencing its termini and designing a pair of longer primer (24 bp long)
This is for specific amplification of RAPD marker
More reproducible
Used to develop +/- arrays
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CAPS (cleaved amplified polymorphic sequence)
Here specific primers are used to amplify a sequence that
can be genotyped by RFLP assay.
These are codominatant (design of primers needs
sequence information)
Has the advantage of RFLP assay avoiding southern blot
analysis
Also called as PCR – RFLP
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SNP : Any polymorphism between two genomes that is based on
a single nucleotide exchange, small deletion or insertion.
STS : It is a general term given to a marker that defined by its
primer sequences
SSR: Any one of the series of very short (2-10bp) middle,
repetitive, tandemly arranged, highly variable DNA sequences
dispersed through out plant, human and animal genome.
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ROLE IN PLANT GENETIC RESOURCE MANAGEMENT
A. Genetic Markers And Systematic Relationships
B. Acquisition/Distribution Of Collected Material
C. Maintenance Of The Genetic Integrity Of Accessions
D. Utilization Of Genetic Resources
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Genetic Markers and Systematic Relationships
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Genetic Markers and Systematic Relationships
Systematics is defined as the scientific study of types of organisms
and of any and all relationships among the organisms (Simpson, 1961 )
one of the most important roles of genetic markers in plant
germplasm management is elucidating the systematic and
characteristic genetic profiles of germplasm.
Youssef et al. (2011) studied the phylogenetic relationships among
eight sorghum genotypes using RAPD markers and reported that
different levels of genetic similarity between them.
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B. ACQUISITION/DISTRIBUTION OF COLLECTED MATERIAL
1. Assessing Collection Gaps and Redundancies
2. Sampling Strategies
3. Assembly of Core Collections
4. Characterizing Newly Acquired Germplasm
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1. Assessing Collection Gaps and Redundancies
Variety of genetic markers are useful in assessments of how
completely a germplasm collection.
The fingerprints developed by these markers employed to
verify synonymy and thus reduce duplication in collections ,to
note misidentifications and to understand the breadth and
gaps in holdings
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S. No. Name of the Group with Year
Crop Marker (s) Used
1 Treuren et al., (2010) Lettuce AFLP
2 Treuren et al., (2008) Perennial Kale Microsatellites
3 Sretenovic et al., (2008) Wild Lactuca AFLP
4 Treuren et al., (2004) Potato AFLP
5 Treuren et al., (2001) Flax AFLP
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2. Sampling Strategies
Effective approach for optimizing sampling strategies involves
graphing the amount of genetic polymorphism (as determined by
genetic markers) in a sample against the sample size.
Hintum et al., (1995) developed optimal sampling strategies
in Barley by comparing the alternative methods for composing a core
collection using Isozyme markers & stated that clustering on the
basis of location of collection site proved to be best followed by
qualitative descriptive data, where as based on quantitative data did
not improve sampling efficiency.
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3. Assembly of core collections
• Genetic marker data may be instrumental for assembling a
collection with maximum allelic diversity.
• To facilitate utilization, core collections have been developed by
genebanks, following the concept developed by Frankel (1984).
• Treuren et al. (2006) asssemble core collection in Barley using AFLP
• Hintum et al. (1994) in Barley using Isozymes
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4. Characterizing Newly Acquired Germplasm
Genetic markers provide key information for designing and
implementing new in situ or ex situ germplasm management
programs for newly acquired germplasm.
Genetic markers can characterize the genetic profiles and
population genetic structure of newly acquired germplasm as a
prelude to ex situ management per se.
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Marco Pessoa et al. (2007) used a set of multiplex panels of
microsatellite markers for rapid molecular characterisation of rice
accessions.
They studied a collection of 548 accessions ,Pairwise genetic
distances were estimated &classified into two main
clusters,corresponding to materials with a possible indica and japonica
genetic backgrounds .
Allelic frequencies were estimated &taken as a reference for
comparision. The results showed that all 63 samples of the minor
cluster would be more probably described as possessing an indica
background.out of total accessions 485 samples were japonica.
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C. Maintenance of The Genetic Integrity of Accessions1. Maintaining Trueness –To-type
a) Morphological Traits
b) Isozymes, seed Proteins & DNA Markers
c) Secondary Metabolites
d) Comparative Studies
e) Pollination Control Methods
2. Monitoring Shifts in Population Genetic Structure in Heterogenous Germplasm
3. Monitoring Genetic Shifts Caused by Differential Viability in Storage
4. Monitoring Genetic Shifts Caused by In Vitro Culture
5. Monitoring Germplasm Viability and Health
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1.Maintaining Trueness –to-Type
Genetic markers have
_ frequently documented outcrossing rates under
defined conditions of cultivation and
_have measured how effectively various
managerial methods maintain true-to-type populations (i.e.,
Accession integrity)
Various DNA markers are particularly valuable for
identifying specific clones and monitoring their trueness-to-
type during regeneration (Thomas et al., 1993).
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• Iqbal et al.,(2010) carried out SSR analysis in 16 genotypes
of Sunflower for hybrid identification and to determine purity
among them,
of 20 specific SSR primers 18 authenticated the
purity of these hybrids.
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Comparative studies
In some cases more than one type of genetic markers has
documented outcrossing or other genetic changes resulting
from seed regeneration.
Pollination controlling methods
Genetic markers evaluated the efficacy of caging and bagging
for controlling pollen flow in germplasm plantings.
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2.Monitoring shifts in population genetic structure in heterogeneous germplasm
Genetic markers have demonstrated that
genotypic frequencies in a homozygous, heterogeneous
germplasm mixture may shift dramatically after just a few
regeneration cycles through the differential viability of certain
genotypes.
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3.Monitoring in genetic shifts caused by Differential viability in Storage:
• The genetic profiles of germplasm accessions can change
during the course of medium or long term storage.
• Storage effects fall into
The occurrence of mutations
The occurrence of chromosomal aberrations
Shifts in gene frequencies resulting from differential
genotypic viability in heterogeneous populations
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4.Monitoring Genetic Shifts Caused by In Vitro Culture
The genetic stability of germplasm maintained in tissue
culture (in vitro) has generally been monitored with
karyotypic markers .
Other genetic markers ,such as isozymes , cp DNA ,and n DNA
have detected point mutations or chromosomal aberrations
in such cultures.
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5.Monitoring Germplasm Viability and Health
ELISA is a disease detection procedure based on protein antibody
markers diagnostic for plant pathogen genotypes or phenotypes.
The ELISA protocol and other recently developed technologies
involving DNA and RNA hybridisation can help monitor the health
of plant germplasm collections through disease indexing
These techniques are often combined with in vitro culture to
produce disease -free propagules.
This was exploited in Papaya at Hawai for the identification and
conservation of germplasm.
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Utilization Of Plant Genetic Resources
1. Developing Optimal Utilization Strategies From Genetic Marker Data
2. Exploiting Associations Among Traits Of Interest And Genetic Markers
3. Genetic Enhancement
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1.Developing Optimal Utilisation Strategies from
Genetic Marker Data
Genetic Markers help In optimizing germplasm utilisation
strategies by
identifying novel alleles of agronomically valuable
traits with relatively low heritabilities .
Incorporating these valuable traits into breeding
populations .
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• Jaemin cho et al. (2011) tagged SNP markers for gland
morphogenesis in cotton.
• Mariza et al. (2002) used different molecular techniques
(AFLP, SSR, RAPD) for the identification of genetic
characteristics in Maize.
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2.Exploiting Associations among Traits of Interest and Genetic
Markers
Genetic markers exploit valuable traits when the markers and traits
are in tight linkage (i.e., associated genetically)
Some favorable genes may be masked or swamped by more
dominant deleterious genes.
The most valuable contribution of genetic markers to germplasm
utilization may be the efficient detection of these valuable latent
genes.
Jaemin cho et al. (2011) tagged SNP markers for gland
morphogenesis in cotton.
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3.Genetic Enhancement
Genetic Enhancement may involve adapting alien material to
local conditions without eliminating its essential genetic
contributions (i.e., genetic diversity), termed “Base-
broadening" by Simmonds (1993) because it widens the
locally-adapted genetic base for crops.
Genetic markers currently facilitate introgressing specific
high-value traits into adapted, elite germplasm in many
breeding programs.
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• Genetic Markers may facilitate genetic enhancement,
sometimes termed pre-breeding
by identifying novel (relative to the germplasm in
common use) alleles of valuable polygenic traits with
relatively low heritabilities
Sometimes by helping to incorporate these latent traits
into breeding populations
CGIAR Institutes (CIMMYT in Wheat and Maize, IRRI in Rice, CIP
in Potato) have initiated the efforts towards pre-breeding for
important alleles to meet the biotic and abiotic stresses and
also to improve the yield levels in the climate change
scenario.
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Name of centre Group leader
Markers used
Plant system
Area of research
1 Tata Energy Research Institute, NewDelhi
M. S.Lakshmikumaran
RFLP, RAPD, SSR, AFLP, SAMPL
neem, withania, Brassica, poplar
DNA fingerprinting, Germplasm characterization, Diversity study, Gene tagging
2 International Centre for GeneticEngineering & Biotechnology, NewDelhi
Madan Mohan S. Nair
RFLP, RAPD, AFLP
, Rice Gene tagging,Physical mapping,
3 Ch. Charan Singh University, Meerut 12 8 20
P. K. GuptaH. S. Balyan
RFLP, SSR, STS, AFLP, SAMPL,EST
Wheat, barley
DNA fingerprinting,, Diversity study, Gene tagging,Genome and QTL mapping, Association analysis,
A list of institutes in India, involved in molecular marker work in higher plants
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Name of centre Group leader
Markers used
Plant system
Area of research
4 National Chemical Laboratory, Pune
P. K. Ranjekar, Vidya Gupta
RAPD, ISSR, SCAR
Wheat, chickpea
Diversity study, Gene tagging
5 National Research Centre on Plant DNA Fingerprinting, New Delhi
J. L., Karihaloo, K. V. Bhatt
RAPD, SSR, AFLP
All major crops
DNA fingerprinting, Diversity study
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Name of centre Group leader
Markers used
Plant system
Area of research
6 National Research Centre for Plant, Biotechnology, IARI, New Delhi ISSR
T. Mohapatra
RAPD, SSR, AFLP,
Brassica, rice
DNA fingerprinting, Diversity study, Gene tagging, Genome and QTL mapping,
7 M. S. Swaminathan Research, Foundation, Chennai
Ajay Parida RFLP, RAPD,AFLP
Millets, Mangroves,
Diversity study
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Name of centre Group leader
Markers used
Plant system
Area of research
8 Centre for Cellular & Molecular Biology, Hyderabad
Ramesh Agarwal
AFLP Rice Diversity study
9 University of Delhi (South CampusNew Delhi & North Campus, Delhi)
Deepak Pental, S. N. Raina
RFLP,AFLP, RAPD,
Mustard, Vigna
DNA fingerprinting, Diversity study, Gene tagging,
10 Jawaharlal Nehru University, New Delhi
K. C. Upadhyaya
AFLP Chickpea Diversity
study
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Name of centre
Group leader
Markers used
Plant system
Area of research
11 M. S. University of Baroda, Baroda
B. B. Chattoo
RAPD Rice Gene tagging
12 Agriculture Research Institute, Naini .
C. Kole RFLP Brassica Genome and QTL mapping
13 University of Ag. Sciences, Bangalore
H. C. Shashidhar , Shailaja Hittalmani
RAPD Rice Genome and QTL mapping
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Name of centre
Group leader
Markers used
Plant system
Area of research
14 National Botanical Research Institute, Luknow
Ranade Amaranthus
Diversity study
15 International Crops Research Institutefor the Semi-Arid Tropics, Patancheru
S. Sivaramakrishnan, CT Hash, J.Kumar
RFLP, RAPD, isozymes, AFLP, SSR
Pulses, millets
Germplasm characterisation,diversity study,characterisation of cytoplasmic male sterility systems.
Source :Plant Cell, Tissue and Organ Culture 70: 229–234, 2002.
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CONCLUSIONS:
A wide variety of new molecular marker technologies are available to assess genetic variation, and many of them are increasingly being applied to complement traditional approaches in germplasm and genebank management.
Genetic marker data will complement, not replace, managerial experience with germplasm, prudent judgement, and keen knowledge of a plant’s natural history.
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Genetic marker data should be weighed judiciously before
basing germplasm management decisions on them.
When exploited carefully, genetic markers do have
enormous, generally unrealised potential for optimising
germplasm conservation, especially by providing the precise
details of plant germplasm’s genetic architecture which are so
vital for effective and efficient germplasm management.
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