Post on 01-Feb-2018
transcript
Resistance to Phytophthora
cinnamomi in Chestnut (Castanea
sp.)
Bode A. OlukoluC. Dana Nelson
Albert G. Abbott
PhytophthoraPhytophthora
cinnamomicinnamomi
Root rot/ ink disease/diebackRoot rot/ ink disease/dieback
Aggressive primary pathogen with a wide Aggressive primary pathogen with a wide geographical range and nearly 1000 host species.geographical range and nearly 1000 host species.
Huge economic impact in principal food crops like Huge economic impact in principal food crops like avocados and pineapples avocados and pineapples
Also attacks Also attacks CastaneaCastanea, , CinnamomumCinnamomum, , ConiferalesConiferales, , EricaceaeEricaceae (including Rhododendron spp.), Eucalyptus, (including Rhododendron spp.), Eucalyptus, FagusFagus, , JuglansJuglans, , QuercusQuercus and many ornamental trees and many ornamental trees and shrubs.and shrubs.
PhytophthoraPhytophthora
root rot in chestnutroot rot in chestnut
Decline of American Decline of American chestnut: chestnut: PhytophthoraPhytophthoraroot rotroot rot, only second to , only second to chestnut blight chestnut blight ((CryphonectriaCryphonectria parasiticaparasitica))
Widespread death at Widespread death at lower elevations in SE lower elevations in SE states due to states due to P. P. cinnamomicinnamomi
ReRe--introduction of introduction of chestnut into SE states chestnut into SE states requires breeding requires breeding resistance to root rot.resistance to root rot.
http://cals.ncsu.edu/plantpath/activities/societies/ornamental
/2008_talks/Jeffers-Chestnut_Screening.pdf
PhytophthoraPhytophthora
root rot symptomsroot rot symptoms
About 3 phenotypic classes in mapping population indicate few maAbout 3 phenotypic classes in mapping population indicate few major jor QTLsQTLs
underlying resistance to pathogen.underlying resistance to pathogen.
Genetic Mapping and
Marker Analysis
Genetic Mapping Genetic Mapping and and
Marker AnalysisMarker Analysis
DNA Clone LibrariesDNA Clone Librariesandand
Physical MappingPhysical Mapping
cDNASequencing
cDNAcDNASequencingSequencing
Comparative Genomics
Comparative Comparative GenomicsGenomics
GeneDiscoveryGeneGene
DiscoveryDiscovery
Strategy for gene discoveryStrategy for gene discovery
Integrated mapsIntegrated maps
Genetic Mapping and
Marker Analysis
Genetic Mapping Genetic Mapping and and
Marker AnalysisMarker Analysis
DNA Clone LibrariesDNA Clone Librariesandand
Physical MappingPhysical Mapping
cDNASequencing
cDNAcDNASequencingSequencing
Comparative Genomics
Comparative Comparative GenomicsGenomics
GeneDiscoveryGeneGene
DiscoveryDiscovery
Strategy for gene discoveryStrategy for gene discovery
Linkage mapping and QTL analysis Linkage mapping and QTL analysis
••
Parents: Parents: AdairKY1 x GL158AdairKY1 x GL158
••
QTL Analysis:QTL Analysis:
AdairKY1AdairKY1
GL158GL158LGE: LGE: 1212--15 15 cMcM
LGE: LGE: 4646--62 62 cMcM
LOD LOD = 4.42= 4.42
LOD LOD = 5.39= 5.39RR22
= 34.6 = 34.6 ±±
11.111.1
RR22
= 40.4 = 40.4 ±±
10.910.9
Two major Two major QTLsQTLs
CmSNP009470.0
CmSNP001409.5
CmSNP01320CmSNP0113111.2
CmSNP0063113.3
CmSNP0082215.5
CmSNP0124418.1
CmSNP0026820.6
CmSNP0026821.8
CmSNP0012240.4
CmSNP0148642.9
CmSNP0096865.2
Phyto
CmSNP015200.0CmSNP013174.8CmSI09455.3CmSNP008866.1CmSNP008346.5CmSNP000687.0CmSNP011978.0CmSI09449.2CmSNP013789.4CmSI001111.2CmSI038013.4CmSNP0080913.9CmSNP01038CmSNP0067114.3
CmSNP0105614.6CmSNP00006CmSNP0136314.9
CmSNP0002115.5CmSNP0110617.5CmSNP0009818.7CmSNP0095019.0CmSNP0051319.1CmSNP0103119.4CmSNP00214CmSNP0088020.4
CmSNP0024420.6CmSNP0152220.9CmSNP0062521.1CmSNP00921CmSNP0124421.4
CmSNP0119921.7CmSNP0037122.1CmSNP0082222.3CmSNP0077323.2CmSNP0090723.4CmSNP0063923.5CmSNP0041723.8CmSI054124.1CmSI076524.2CmSNP0014824.4CmSNP0026824.6CmSNP0045525.0CmSNP0087525.4CmSNP0153025.6CmSNP0076225.9CmSNP0049526.0CmSI046326.5CmSNP0067827.1CmSNP0026627.6CmSNP0094227.7CmSNP0142528.6CmSNP0021628.9CmSNP00736CmSNP01421CmSNP00631
29.2
CmSI046729.4CmSI060629.7CmSNP00330CmSNP01051CmSNP01367
29.9
CmSI093930.3CmSNP0024931.0CmSNP00166CmSNP00422CmSNP00540CmSI0617
31.5
CmSI076132.3CmSNP0132032.9CmSNP0141533.1CmSNP0015833.4CmSI0321CmSI0076CmSNP00715CmSNP01343
33.5
CmSNP0136433.8CmSNP0151534.3CmSNP0065034.6CmSNP0113134.7CmSNP0014034.9CmSI088335.1CmSI087035.2CmSNP0132435.4CmSNP0098435.5CmSNP0023935.6CmSI082936.1CmSI0908CmSI003536.4
CmSNP0103437.1CmSNP0034937.4CmSNP00957CmSNP01427CmSNP01513
37.7
CmSNP0027338.1CmSNP0022738.2CmSI055838.7CmSNP0027138.8CmSNP0050539.0CmSNP0095539.2CmSNP0145839.5CmSI039640.1CmSNP0133140.4CmSI068140.6CmSNP0149941.3CmSNP00615CmSI088641.8
CmSNP0122244.0CmSNP0114347.5CmSNP0144448.3CmSNP0148651.0CmSNP0105751.3CmSNP0085953.7CmSI080061.5CmSNP0135364.8
CmSNP002680.0
CmSNP012443.4
CmSNP009076.7
CmSNP002689.1
CmSNP0096413.1CmSNP0014013.2CmSNP0149814.0
CmSNP00752CmSNP00045CmSNP00273CmSNP00934
23.9
Phyto
CmSNP0024420.6CmSNP0152220.9CmSNP0062521.1CmSNP00921CmSNP0124421.4
CmSNP0119921.7CmSNP0037122.1CmSNP0082222.3CmSNP0077323.2CmSNP0090723.4CmSNP0063923.5CmSNP0041723.8CmSI054124.1CmSI076524.2CmSNP0014824.4CmSNP0026824.6CmSNP0045525.0CmSNP0087525.4CmSNP0153025.6CmSNP0076225.9CmSNP0049526.0CmSI046326.5CmSNP0067827.1CmSNP0026627.6CmSNP0094227.7CmSNP0142528.6CmSNP0021628.9CmSNP00736CmSNP01421CmSNP00631
29.2
CmSI046729.4CmSI060629.7CmSNP00330CmSNP01051CmSNP01367
29.9
CmSI093930.3CmSNP0024931.0CmSNP00166CmSNP00422CmSNP00540CmSI0617
31.5
CmSI076132.3CmSNP0132032.9CmSNP0141533.1CmSNP0015833.4CmSI0321CmSI0076CmSNP00715CmSNP01343
33.5
CmSNP0136433.8CmSNP0151534.3CmSNP0065034.6CmSNP0113134.7CmSNP0014034.9CmSI088335.1CmSI087035.2CmSNP0132435.4CmSNP0098435.5
CmSNP002689.1
CmSNP0096413.1CmSNP0014013.2CmSNP0149814.0
CmSNP00752CmSNP00045CmSNP00273CmSNP00934
23.9
Phyto
CmSNP0012240.4
CmSNP0148642.9
CmSNP0096865.2
Phyto
CmSNP00540CmSI0617
31.5
CmSI076132.3CmSNP0132032.9CmSNP0141533.1CmSNP0015833.4CmSI0321CmSI0076CmSNP00715CmSNP01343
33.5
CmSNP0136433.8CmSNP0151534.3CmSNP0065034.6CmSNP0113134.7CmSNP0014034.9CmSI088335.1CmSI087035.2CmSNP0132435.4CmSNP0098435.5CmSNP0023935.6CmSI082936.1CmSI0908CmSI003536.4
CmSNP0103437.1CmSNP0034937.4CmSNP00957CmSNP01427CmSNP01513
37.7
CmSNP0027338.1CmSNP0022738.2CmSI055838.7CmSNP0027138.8CmSNP0050539.0CmSNP0095539.2CmSNP0145839.5CmSI039640.1CmSNP0133140.4CmSI068140.6CmSNP0149941.3CmSNP00615CmSI088641.8
CmSNP0122244.0CmSNP0114347.5CmSNP0144448.3CmSNP0148651.0CmSNP0105751.3CmSNP0085953.7CmSI080061.5CmSNP0135364.8
R2
(Contribution to phenotypic variance)
= 40.4 ±
10.9 %
R2
(Contribution to phenotypic variance)
= 34.6 ±
11.1 %
GL158LGE
AdairKY1LGE
ReferenceLGE
GL158LGE
AdairKY1LGE
Genetic Mapping and
Marker Analysis
Genetic Mapping Genetic Mapping and and
Marker AnalysisMarker Analysis
DNA Clone LibrariesDNA Clone Librariesandand
Physical MappingPhysical Mapping
cDNASequencing
cDNAcDNASequencingSequencing
Comparative Genomics
Comparative Comparative GenomicsGenomics
GeneDiscoveryGeneGene
DiscoveryDiscovery
Strategy for gene discoveryStrategy for gene discovery
Chestnut physical map vs. peach genomeChestnut physical map vs. peach genome
Peach genomic regions matching chestnut QTL1 (AdairKY1)Peach genomic regions matching chestnut QTL1 (AdairKY1)ChestnutChestnut cMcM PeachPeachCmSNP00268CmSNP00268 24.624.6 LG_3:2932267LG_3:2932267CmSNP00455CmSNP00455 2525 LG_3:2845467LG_3:2845467CmSNP00875CmSNP00875 25.425.4 LG_3:3140292LG_3:3140292CmSNP01530CmSNP01530 25.625.6 LG_3:3277460LG_3:3277460CmSNP00762CmSNP00762 25.925.9 LG_3:3721967LG_3:3721967CmSNP00495CmSNP00495 2626 LG_3:3688184LG_3:3688184CmSNP00678CmSNP00678 27.127.1 LG_3:4409620LG_3:4409620CmSNP00942CmSNP00942 27.727.7 LG_3:4572171LG_3:4572171CmSNP01425CmSNP01425 28.628.6 LG_3:5421927LG_3:5421927CmSNP00216CmSNP00216 28.928.9 LG_3:5440098LG_3:5440098CmSNP00736CmSNP00736 29.229.2 LG_3:5723426LG_3:5723426CmSNP01421CmSNP01421 29.229.2 LG_8 LG_8 CmSNP00631CmSNP00631 29.229.2 LG_3:17002563LG_3:17002563CmSI0606CmSI0606 29.729.7 LG_4:2287344LG_4:2287344CmSNP00330CmSNP00330 29.929.9 LG_3:6227869LG_3:6227869CmSNP01051CmSNP01051 29.929.9 LG_3:6619565LG_3:6619565 CCR1 (CINNAMOYL COA REDUCTASE 1) CCR1 (CINNAMOYL COA REDUCTASE 1) CmSNP01367CmSNP01367 29.929.9 LG_3:37733971LG_3:37733971CmSNP00249CmSNP00249 3131 LG_3:8870658LG_3:8870658CmSNP01331CmSNP01331 -- LG_3:16700504LG_3:16700504CmSNP00166CmSNP00166 31.531.5 LG_4:3319300LG_4:3319300CmSNP00422CmSNP00422 31.531.5 LG_4:3125280LG_4:3125280CmSNP00540CmSNP00540 31.531.5 LG_4:2631682LG_4:2631682CmSNP01320CmSNP01320 32.932.9 LG_4:3753512LG_4:3753512CmSNP01415CmSNP01415 33.133.1 LG_4:3681607LG_4:3681607CmSNP00158CmSNP00158 33.433.4 LG_4:3861914LG_4:3861914CmSI0321CmSI0321 33.533.5 LG_4:3662029LG_4:3662029CmSNP00715CmSNP00715 33.533.5 LG_4:3854177LG_4:3854177CmSNP01343CmSNP01343 33.533.5 LG_4:3888841LG_4:3888841CmSNP00506CmSNP00506 -- LG_4:3889444LG_4:3889444CmSNP01515CmSNP01515 34.334.3 LG_4:2966642LG_4:2966642CmSNP00650CmSNP00650 34.634.6 LG_4:4168374LG_4:4168374CmSNP01131CmSNP01131 34.734.7 LG_4:4175873LG_4:4175873CmSNP00140CmSNP00140 34.934.9 LG_4:4290718LG_4:4290718 BAG1 (BCLBAG1 (BCL--22--ASSOCIATED ATHANOGENE 1)ASSOCIATED ATHANOGENE 1)
CmSNP01324CmSNP01324 3535 LG_4:4365241LG_4:4365241
CmSNP00984CmSNP00984 3636 LG_4:4540309LG_4:4540309
CmSNP00239CmSNP00239 3636 LG_4:4495081LG_4:4495081
Sufficient marker Sufficient marker
saturation to identify saturation to identify
BACs for genome BACs for genome
comparison in SYMAPcomparison in SYMAP
Peach genomic regions matching chestnut QTL2 (GL158)Peach genomic regions matching chestnut QTL2 (GL158)
ChestnutChestnut cMcM PeachPeachCmSNP01222CmSNP01222 4444 scaffold_4:851071scaffold_4:851071CmSNP00283CmSNP00283 scaffold_4:30241182scaffold_4:30241182CmSNP01444CmSNP01444 4848 scaffold_4:1226101scaffold_4:1226101CmSNP01143CmSNP01143 47.547.5 scaffold_4:1702667scaffold_4:1702667CmSNP00934CmSNP00934 scaffold_4:653794scaffold_4:653794CmSNP01486CmSNP01486 51.051.0 scaffold_3:7697721scaffold_3:7697721CmSNP01057CmSNP01057 51.351.3 scaffold_3:593023scaffold_3:593023CmSNP00859CmSNP00859 53.753.7 scaffold_4:1820922scaffold_4:1820922
Insufficient marker saturation on end of linkage group required Insufficient marker saturation on end of linkage group required
additional hybridization on BAC Filters and isolation of positivadditional hybridization on BAC Filters and isolation of positive BACs e BACs
for genome comparison.for genome comparison.
ReRe--constructing genomic region spanning chestnut QTLconstructing genomic region spanning chestnut QTL
Chestnut
PeachLG4:
2.6 – 4.5 MBLG3:
2.8 ‐8.9 MBLG4:
0.6 ‐1.7 MBLG3:
0.5 ‐7.7 MBLG4:
1.7‐
? MB
QTL 1 : LGE QTL 2 : LGE
24.6 cM 35.5 cM 51.0 cM 61.8 cM
BAG1BCL‐2‐
Associated
Athanogene
1
CCR1 Cinnamoyl CoA
Reductase 1
NPR3/NPR4Non‐Expresser of
PR Genes
RPH1Resistance to
Phytophtora
BAG4BCL‐2‐
Associated
Athanogene
4
Peach physical map length: ~ 8 MBPeach physical map length: ~ 8 MB Peach physical map length: > 8.3 MBPeach physical map length: > 8.3 MB
Candidate Genes underlying Resistance to PhytophthoraCandidate Genes underlying Resistance to Phytophthora
Candidate GeneCandidate Gene FunctionFunction
Resistance to Phytophtora (RPH1)Resistance to Phytophtora (RPH1) Involved in Involved in immune responseimmune response
to to PhytophthoraPhytophthora
NonNon--Expresser of PR Genes Expresser of PR Genes (NPR3(NPR3))
Negative regulation of defense responses against Negative regulation of defense responses against bacterial and oomycete pathogens. npr3 mutants bacterial and oomycete pathogens. npr3 mutants has elevated has elevated level of PR1 expressionlevel of PR1 expression
Cinnamoyl CoA Reductase 1 Cinnamoyl CoA Reductase 1 (CCR1(CCR1))
Involved in Involved in lignin biosynthesislignin biosynthesis
BCLBCL--22--Associated Athanogene 1 Associated Athanogene 1 /4 (BAG1 and BAG4/4 (BAG1 and BAG4))
Plant homolog of mammalian regulators of Plant homolog of mammalian regulators of apoptosis. Plant BAG proteins are multiapoptosis. Plant BAG proteins are multi--functional functional and remarkably similar to their animal and remarkably similar to their animal counterparts, as they counterparts, as they regulate apoptoticregulate apoptotic--like like processes processes ranging from pathogen attack, to abiotic ranging from pathogen attack, to abiotic stress, to plant development.stress, to plant development.
AcknowledgementAcknowledgement
A. Abbott M. StatonE. Fang B.BlackmonC. Saski
D. HenryS. Ficklin
T. ZhebentyayevaC.H. Cheng
M. AtkinsL. Georgi
R. SederoffN. Wheeler
T. KubisiakC.D.Nelson
Fred HebardPaul SiscoJoseph James