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

Slide Number 1Slide Number 2Slide Number 3Slide Number 4Slide Number 5Integrated mapsSlide Number 7Linkage mapping and QTL analysis Slide Number 9Slide Number 10Chestnut physical map vs. peach genomePeach genomic regions matching chestnut QTL1 (AdairKY1)Peach genomic regions matching chestnut QTL2 (GL158)Re-constructing genomic region spanning chestnut QTLCandidate Genes underlying Resistance to PhytophthoraSlide Number 16