Antagonistic Interactions Among Stripe and Stem Rust Resistance QTLs in Wheat

Antagonistic Interactions Among Stripe and Stem Rust Resistance QTLs in Wheat

Abdulqader Jighly

The International Center for Agricultural Research in the Dry Areas (ICARDA)

Borlaug Global Rust Initiative Technical Workshop

Obregon - Mexico, 22-28 March, 2014

Acknowledgments

Funding Agencies Colleagues and collaborators

ICARDA K. Nazari, W. Tadesse

O. Abdalla

GRDC F.C. Ogbonnaya

Bonn University B.C. Oyiga

University of Aleppo

F. Makdis

Yokohama City University M. Alagu

EIAR

A. Badebo

GCSAR O. Youssef

Organizers of the BGRI workshop

Stem and Stripe Rusts on Wheat

10 – 80% yield loss in CWANA 2010

Puccinia graminis f. sp. tri0ci

Up to 100% loss

Puccinia striiformis f.sp. tri0ci

Wheat Mega-Cultivars Affected by the Recent Stripe Rust Epidemic in CWANA

Inquilab

Gereck; Gun91; Bezostaya, Katya

Cham6; 8 Sardari; Chamran; Shiroudi

Polovchanka, Kroshka

Nazhtsu; Pamyat 47; Yuzhnaya

PBW343

Azametli 95

Achtar; Aguilal; Arrihane

Giza167

Kubsa

Imam

Hidhab

Gul-96, Pamir-94, Ghori-96

Tamuz 2; Maxipak; Azadi

Rust Epidemics

Seeking and use new resources of effec2ve gene2c resistance is the solu2on

Association Mapping

Todays’ Haplotypes

Resistant

Suscep?ble

Ancestral Haplotypes

Resistance gene

Gene-Gene Interaction in Plant Breeding

Epistasis

Antagonis2c (nega2ve) Synergis2c (posi2ve)

Searching for neutral alleles (don’t interact)

Avoiding them in the following crosses

The investment in these requires con?nuous tracking for both genes

Gene-Gene Interaction Based on Multiple Disease Resistance Data

•  The aim is to avoid the pyramiding of nega?vely interac?ng resistance loci that are associated with different diseases.

•  For example, the materials that have Sr2 gene on 3BS with a Leaf rust QTL on 3AL in a synthe?c hexaploid wheat germplasm exhibited a suscep?ble stem rust response (Jighly et al. submi:ed).

•  The strategy: 1.  Phenotyping for different diseases 2.  Genome wide associa?on mapping analysis 3.  Gene-‐Gene interac?on analysis among all detected QTLs

for the described phenotype and the detected QTLs that are associated with the other phenotypes.

Objectives of this Research

•  To characterize stripe and stem rust resistances in a collec?on of ICARDA elite germplasm

•  To detect stripe and stem rust QTLs through genome wide associa?on mapping

•  To define gene-‐gene interac?ons among the detected QTLs

Materials and Methods

• Plant material: 200 elite germplasm mostly of ICARDA origin, synthe?c deriva?ves and some Australian cul?vars

• Phenotyping: Data from stripe rust screening in 2010 and 2011 in two loca?ons; and data from stem rust screening in 2010 in one loca?on

• Genotyping: 1.  A set of 4235 polymorphic SNP markers 2.  A set of 2504 polymorphic DArT markers

Materials and Methods

•  Sta?s?cal analyses: 1.  STRUCTURE (Pritchard et al. 2000) for

popula?on structure 2.  Tassel 3 (Bradbury et al. 2007) for marker/trait

associa?on: Mixed Linear Model (MLM) 3.  Gene-‐gene Interac?on: Linear regression

model was used to calculate P values for pair-‐wise marker interac?ons. The significance threshold for the interac?ons analysis was P ≤ 10-‐5

4.  The interac?on graph was drawn using the soeware Circos 0.63-‐4 (Krzywinski et al. 2009)

Results 1- Response to the disease

29 22

12

24 20

53

37

0

10

20

30

40

50

60

2 3 4 5 6 7 8

Num

ber o

f Plants

Field Score

Stripe Rust Response

10

36

73 81

0

10

20

30

40

50

60

70

80

90

R MR MS S

Num

ber o

f Plants

Infec2on Type

Stem Rust Response

2- Population Structure

0%

20%

40%

60%

80%

100%

0%

20%

40%

60%

80%

100%

Using DArT markers

Using SNP markers

3- Linkage Disequilibrium Decay

Using DArT markers

Using SNP markers

4- Linkage Disequilibrium – 1B/1R

5- Association Mapping

5- Association Mapping – Stripe Rust Marker Chr Posi2on P MAF Allele R2 Effect Reference QTL in the region

DArT Markers wPt-‐741323 1DS 49.9 0.0010 93.3 0 5.77 1.7 Novel

tPt-‐1663 2BS 6.2 0.0023 80.2 1 5.04 1.1 QRYr2B.1 (Dedryver et al. 2009; Vazquez et al. 2012)

wPt-‐6271 2BS 0.2 0.0007 75.8 1 6.28 1.1 wPt-‐8918 2BS 6.2 0.0025 79.1 1 4.78 1.1 wPt-‐800213 3BS 26.7 0.0013 76.1 0 6.24 1.0

Yr30/Sr2 (Hao et al. 2011) tPt-‐6487 3BS 33.8 0.0029 78.5 1 4.67 1.0 wPt-‐664393 3BS 51.5 0.0032 84.1 1 5.16 1.0

wPt-‐4868 3AS 52.2 0.0029 65.4 0 5.12 -‐1.0 Novel

wPt-‐731936 6AL -‐ 0.0009 84.3 0 5.9 1.6 QRYr6A.2 (Lillemo et al. 2008)

wPt-‐741831 6DL 121.4 0.0020 52.5 0 5.41 -‐0.7 QRYr6D.2 (Boukhatem et al. 2002)

wPt-‐668026 7DS 1.1 0.0031 91.3 1 6.13 1.7 Yr18/Lr34/Sr57 (Rosewarne et al. 2012)

SNP markers wsnp_BG274584B_Ta_2_3 2AL 158.9 0.0021 92.5 A 5.24 2.2 QRYr2A.2 (Dedryver et al. 2009)

wsnp_Ex_c14711_22788263 2BS 44.0 0.0019 55.1 A 5.66 1.3 QYr.caas-‐2BS (Guo et al. 2008)

wsnp_JD_c14691_14352459 3AS 100.8 0.0013 53.8 A 5.75 -‐1.6 Novel

wsnp_Ex_c1558_2976128 3BS 33.2 0.0011 82.0 B 5.92 1.4 QRYr3B.1 (Hao et al. 2011) wsnp_Ex_c210_411604 5BL 86.1 0.0008 88.0 B 6.36 1.8

QRYr5B.2 (Bariana et al. 2010) wsnp_Ex_c33431_41918732 5BL 86.1 0.0020 85.2 B 5.33 1.4

wsnp_Ex_c34641_42914170 6AL 138.6 0.0006 60.5 B 6.79 1.5

QRYr6A.3 (Vazquez et al. 2012) wsnp_Ex_c965_1845447 6AL 138.6 0.0006 81.5 A 6.08 1.8

wsnp_Ex_rep_c105594_89968727 6AL 131.8 0.0016 71.8 B 5.67 1.4

5- Association Mapping – Stem Rust Marker Chr Posi2on P MAF Allele R2 Effect Reference QTL in the region

DArT Markers wPt-‐732812 2BS -‐ 0.00083 84.5 1 6.1 7.2

Sr40 (Wu et al., 2009) wPt-‐1064 2BS 66.4 0.00284 83.4 1 4.74 5.4 wPt-‐6011 3DL 160.2 0.00003 94.4 0 9.61 15.6

Sr24 (Mago et al. 2005; Yu et al., 2012; McIntosh et al. 2012)

wPt-‐667430 3DL -‐ 0.00080 84.5 1 6 7.0 wPt-‐0485 3DL 160.2 0.00043 90.1 1 6.75 9.5 wPt-‐0524 3DL 160.2 0.00001 94.9 0 11.19 17.8 wPt-‐2374 3DL 160.2 0.00003 94.4 0 9.61 15.7 wPt-‐2795 3DL 160.2 0.00003 94.4 0 9.58 15.7 wPt-‐4276 3DL 160.2 0.00003 94.4 0 9.58 15.7 wPt-‐7265 3DL -‐ 0.00187 89.6 1 5.23 7.5 wPt-‐9470 3DL 160.2 0.00003 94.7 0 9.68 16.1 wPt-‐9989 3DL 151.8 0.00293 89.2 1 4.69 6.8 wPt-‐5231 5AL 111.5 0.00204 53.6 0 5.79 -‐5.4 QTL (Leka et al., 2013) wPt-‐5462 7BL 214.8 0.00189 61.7 1 5.13 5.8 Sr17/Lr14a/Pm5 (Yu et al. 2011, 2012)

SNP Markers wsnp_Ra_rep_c109853_92677055 2BS 188.8 0.00076 89.1 B 6.44 10.6 QTL (Kolmer et al. 2011) wsnp_Ex_c8695_14561512 3BS 64.6 0.00168 81.6 B 5.32 -‐8.3 Sr2 (Spielmeyer et al. 2003) wsnp_CAP11_c575_392117 4BS 68.3 0.00054 70.3 A 7 -‐6.7

QSr.spa-‐4B.1 (Singh et al., 2013) wsnp_Ex_c13849_21698240 4BS 67.5 0.00020 68.0 A 8.27 -‐7.8 wsnp_Ex_c2219_4159221 7AL 69.8 0.00055 64.8 B 6.87 -‐7.3 Sr15 (Crossa et al., 2007); Sr22 (Yu et al.,

2012) wsnp_Ku_c340_706774 7AL 69.8 0.00055 64.8 B 6.87 -‐7.3 wsnp_BF483648B_Ta_2_1 7BL 65.6 0.00038 57.9 A 9.47 10.8 Sr17/Lr14a/Pm5 (Yu et al. 2011, 2012)

6- Gene-Gene Interaction

6- Gene-Gene Interaction Marker1 Chr1 Marker2 Chr2 Best R2 Best P

Yr wsnp_JD_c14691_14352459 3AS 4 Markers 2AL 11.43 8E-‐06 wPt-‐731936; wsnp_Ex_c34641_42914170 6AL 4 Markers 3AS 13.63 1.6E-‐06 wPt-‐731936 6AL 11 Markers 5B 14.34 7.5E-‐07 wsnp_Ex_c34641_42914170; wsnp_Ex_rep_c105594_89968727; wPt-‐731936

6AL 10 markers 6AL 15.55 4.3E-‐07

Sr wPt-‐732812 2BS 4 Markers 1B 16.04 2.3E-‐07 wPt-‐732812; wsnp_Ra_rep_c109853_92677055 2BS 12 Markers 2B 15.21 4.2E-‐07 wPt-‐732812 2BS 6 Markers 2D 15.71 2.4E-‐07 wPt-‐0485; wPt-‐667430; wPt-‐7265 3DL 85 Markers 1A 15.1 3.9E-‐07 wPt-‐0485; wPt-‐667430; wPt-‐7265 3DL 42 Markers 2B 16.05 1E-‐07 wPt-‐0485; wPt-‐7265 3DL 49 Markers 4A 16.01 1.4E-‐07 wPt-‐0485; wPt-‐7265 3DL 46 Markers 5B 16.92 6.2E-‐08 wPt-‐0485; wPt-‐667430; wPt-‐7265 3DL 67 Markers 6A 15.54 1.4E-‐07 wPt-‐0485; wPt-‐7265 3DL 29 Markers 7B 17 1.3E-‐07 wsnp_Ex_c13849_21698240 4B 3 Markers 2B 13.98 1.6E-‐06 wsnp_Ex_c2219_4159221 7A 10 Markers 4B 16.68 1.4E-‐07 wsnp_BF483648B_Ta_2_1 7BL 20 Markers 1A 14.9 1.3E-‐06

6- Gene-Gene Interaction Yr Phenotype

Yr/Sr

Yr/Yr QTL First (R) Allele Mean Pheno

Second (R) Allele Mean Pheno

Both Yr (R) Alleles Mean Pheno

6AL/6AL 3.2 3.9 4.7

No sig LD

6- Gene-Gene Interaction Sr Phenotype

Sr/Yr QTLs R Allele Mean Pheno

S Allele Mean Pheno

Sr (R) Allele & Yr (S) Allele Mean Pheno

Sr (R) Allele & Yr (R) Allele Mean Pheno

2BS/2BS 23.3 28.2 16.4 29.1

3DL/2BS 23.5 27.8 10.3 30.6

3DL/6AL 22.5 27.8 7.3 30.1

Sr/Sr

No sig LD

6- Gene-Gene Interaction 3DL/2BS Novel Allele

Genotype Pedigree Yr Score

Sr Score

HAMAM-‐4 T.AEST/SPRW'S'//CA8055/3/BACANORA86 2 36 NS 5510/BOW'S'//KOEL'S'/VEE'S' NS 5510/BOW'S'//KOEL'S'/VEE'S' 3 40 BABAGA-‐3 TRACHA'S'//CMH76-‐252/PVN'S' 3 32

BAASHA-‐29 ISD-‐75-‐3-‐1/MO88//PRL/VEE#6 /4/GHURAB'S'/3/AHGAF//MXC/TOB 4 24

N-‐ABYAD-‐15 CHAM-‐6//KAUZ'S'/3/AO41/EMU'S'//TEVEE'S' 2 24 ZAFIR-‐6 CHAM-‐4//SHUHA'S'/3/SD 8036 4 27 ZAFIR-‐7 CHAM-‐4//SHUHA'S'/3/SD 8036 4 32 ZAFIR-‐10 CHAM-‐4//SHUHA'S'/3/SD 8036 4 32 ZAFIR-‐5 CHAM-‐4//SHUHA'S'/3/SD 8036 4 36 N-‐AZRAQ-‐1 CHAM-‐6/GHURAB'S'//REGRAG-‐1 5 27 N-‐AZRAQ-‐6 CHAM-‐6/GHURAB'S'//REGRAG-‐1 5 32

KOUKAB-‐2 DVERD-‐2/AE.SQUARROSA(214) //2*ESDA/3/NS732/HER 2 18

AUS34514 CETA/AE.SQUARROSA (1031) //JANZ/3/PELSART 4 18

Novel 3DL allele that are neutral for this interac?on derived from

synthe?c Background

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Antagonistic Interactions Among Stripe and Stem Rust Resistance QTLs in Wheat

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