Diversity of Yellow Rust Resistance: Inferences from GWAS in some elite wheat germplasm

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Francis Ogbonnaya, ICARDA

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Diversity of Yellow Rust Resistance: Inferences from GWAS in some elite wheat germplasm

  1. 1. Diversity of Yellow Rust Resistance: Inferences from GWAS in some elite wheat germplasm Francis C. Ogbonnaya BGRI Meeting, St. Paul, Minnesota, June 13-18, 2010
  2. 2. AcknowledgmentsFunding Agencies Colleagues and collaborators  ICARDA  K. Nazari (ICARDA)  A. Jighly (ICARDA)  O. Abdalla & Izzat Tahir (ICARDA)  A. Yahyaoui (ICARDA-CIMMYT)  Wuletaw Tadesse (ICARDA)  Aleppo University  F. Makdis (Aleppo University) • GCSAR  O. Youssef (GCSAR)  E. Essa (GCSAR) Organizers of BGRI 2011 workshop
  3. 3. Wheat yellow (stripe) rust P uccinia striiform is fsp tritici Most common and widespread rust disease of wheatYield losses (10-80%) in CWANAEst. value of crop loss could reach > 1 billion USD. BGRI workshopCourtesy: S. Rajaram and A. Yahyaou, 2011 St. Paul, MN June, 2011
  4. 4. Stripe Rust Summary - 2010 Uzbekistan: worse Bulgaria: “First than 2009 – all outbreaks in 20 varieties years” susceptible. extensive chemicaTurkey: Severe in control (x3 sprayssouth-east. USDAestimating1M ton lossesSyria: Estimates of 300,00 haaffected.USDA: Possible 1.25M ton losses Iraq: Estimated 10-15% yield Ethiopia: Over 400,000 losses in north ha affected. Losses?? BGRI workshopCourtesy: Dave Hudson, April 2011 St. Paul, MN June, 2011
  5. 5. Yellow rust epidemics 2010:farmers paddock Hassakieh yellow rust April 2010• With no timely fungicide losses estimated at more than 80% BGRI workshop• Harvest from 6-7 tons/hectares to less than 1 ton/hectare St. Paul, MN June, 2011
  6. 6. Resistance Sources – How diverse and what genes? TH_2011 47 % 17.5% 21% 14.5% S MS MR R Mal_2010 45.5% 22% 17.5% 15% S MS MR RThe frequency of elite lines under different yellow rust severity classes at Tel-Hadya and Malkiyeh in 2011 and 2010
  7. 7. Resistance Sources – How diverse and what genes? 31% The frequency of elite lines under different yellow rustseverity classes at seedling and adult plant growth stages BGRI workshop St. Paul, MN June, 2011
  8. 8. Summary of Yr genesChromosome Genes Chromo. Count1A YrDa1 12A Yr1, Yr8, Yr17, Yr32 43A YrTr2 14A YrHVII, YrMin, YrND 35A Yr34, Yr48 26A Yr42, YrD,YrDru2,YrH46 47A - 0 Yr9, Yr10, Yr15, Yr21, Yr24, Yr26, Yr29, YrC143, YrAlp, YrH52, YrExp1,1B 13 YrR212, YrCN17 Yr5, Yr7, Yr27, Yr31, Yr41, Yr43, Yr44, YrCn19, YrZak, YrV23, YrSte,2B 14 YrP81, YrS2199, YrSP3B Yr4, Yr30, YrS, YrSte2, Yrns-B1 54B YrCle, YrMor, YrYam 35B Yr3, Yr19, Yr47, YrDru, YrExp2 56B Yr35, Yr36 27B Yr2,Yr6, Yr39, YrC591, YrZH84 51D Yr25 12D Yr16, Yr37, YrCK 33D Yr45 14D Yr22,Yr28,Yr46,YrAS2388 45D Yr40,YrDa2 26D Yr20, Yr23, YrTye, YrTr1 47D Yr18,Yr33 2Total 79
  9. 9. Recently reported sources and linked markersGene Chromo. Sources Linked markers Ref. Avalon, Bolac, Emu S, Rubric Bansal et al. Yr4 3BS Xcfb3530 AUS33333 (Bread wheat) 2010 PI 591045, Lolo, many IDO377s Cheng and Chen Yr43 2BL Xwgp110, Xwgp113 derivatives (Spring Wheat) 2009 Yr44 2BL PI 607839 (Spring Wheat) Xwgp100 Sui et al. 2009 Yr45 3DL PI 181434 (Spring Wheat) Xwp115, Xwp118 Li et al. 2010 Herrera-Foessel Yr46 4D PI 250413 (common wheat) Xcfd71, Xbarc98 et al. 2009 5 2 cM proximal to Bansal U et al. Yr47 5BS AUS28183 (common wheat) Lr52 2011 Dubcovsky 2010; Yr48 5AL PI 610750 (Bread wheat) Xwms291 Lowe et al. 2011 BGRI workshop St. Paul, MN June, 2011
  10. 10. Association mappingObjective is to detect correlations between genotypes andphenotypes in a set of unrelated individuals from naturalpopulations on the basis of linkage disequilibriumAdvantages over biparental mapping No news crosses variation for many phenotypic traits, thus several traitscan be studied in the same population using same genotype much higher mapping resolution - recombinationreduces association between a QTL and distant markers A higher proportion of molecular markers likely to bepolymorphic because of better genome coverage A. Rafaselski, 2002
  11. 11. Association Mapping (AM) Plant material: 200 elite germplasm mostly of ICARDA origin, synthetic derivatives and some Australian cultivars Phenotyping: Data from yellow rust screening in 2010 and 2011 Genotyping: Triticarte Pty Ltd (http://www.triticarte.com.au)2688 polymorphic DArT markers plus 42 SSR and STS markers linked to various Yr gene Statistics: STRUCTURE (Pritchard et al. 2000) - population structureTassel 2.0.1 (Bradbury et al. 2007) - marker/trait association: General Linear Model (GLM) and Mixed Linear Model (MLM)
  12. 12. Of the 2688 polymorphic DArT markers: 42 SSR markersDArT loci with known map position 372 Simple Sequence RepeatsMarkers for A genome = 141 covered 576.91 CMMarkers for B genome = 181 covered 854.60 CMMarkers for D genome = 50 covered 289.05 CM Total 1720.55 CMChromosome 4A 43 MarkersDArT marker density varied amongst chromosomes from lessthan 5cM to more than 25cM between markers. However, LDis within the range reported in literature at about 20cM
  13. 13. Population structure K =11Ln P(D) 1 2 3 4 5 6 7 8 9 10 11The population structure was calculated using 50 unlinked markers
  14. 14. Model ResultsModel No of markers associated with Yr at p<0.05 R2GLM 913 2 to 24%GLM + Q 397 1 to 10%MLM + Q + K 167 3 to 14 %125 DArT markers were assigned to several chromosome regionswhile 42 were unmapped BGRI workshop St. Paul, MN June, 2011
  15. 15. DArT Markers with Chromosome Effects A B D 1 2 3 4 5 6 7Loci on 1B, 1D, 2B, 2D, 3B, 4A, 6B, 6D and 7D were identified at P ≤ 0.00001 with R2 from 5 to 14%
  16. 16. MLM-QMarker Chr. P-value R2 Chromosome arm ReferenceswPt-3870 1A 0.0052 5.27 1AS Crossa et al 2007; Francki et al 2009wPt-5678 1B 0.0477 3.05 1BS Crossa et al 2007 - Yr9, -10, -24, -26wPt-3465 1B 0.0235 3.79 1BS Crossa et al 2007 - Yr9, -10, -24, -26wPt-4916 2B 0.0042 5.49 2BS Crossa et al 2007 - Yr27, -31wPt-1489 2B 0.0462 3.05 2BS Crossa et al 2007 - Yr27, -31; Lowe et al 2011wPt-7757 2B 0.0153 4.22 2BS Crossa et al 2007 - Yr27, -31wPt-9402 2B 0.0401 3.19 2BS Crossa et al 2007 - Yr27, -31wPt-9423 2B 0.0482 3.04 2BS Lowe et al 2011;wPt-9350 2B 0.0098 3.12 2BL* Crossa et al 2007 - Yr5, -7; Lowe et al 2011wPt-7350 2B 0.0041 3.70 2BL* Crossa et al 2007 - Yr5, -7; Lowe et al 2011wPt-4413 2D 0.0025 4.02 2DL Crossa et al 2007 - Yr37wPt-6704 2D 0.0116 4.46 2DL Lowe et al 2011wPt-1596 3A 0.0005 7.71 3AL Lowe et al 2011wPt-9268 3A 0.0099 4.65 3AL Francki et al 2009wPt-2045 3B 0.0000 12.50 3BS Lowe et al 2011wPt-8238 3B 0.0033 5.79 3BS Crossa et al 2007 - Yr30; Lowe et al 2011wPt-6132 3B 0.0034 5.77 3BS Lowe et al 2011wPt-5105 3B 0.0492 3.01 3BS Crossa et al 2007-Yr30wPt-9401 3D 0.0403 3.26 3DS Crossa et al 2007; Francki et al 2009wPt-1336 3D 0.0342 3.42 3DS Crossa et al 2007; Francki et al 2009wPt-6440 4A 0.0028 5.98 4AL Lowe et al 2011wPt-2084 4A 0.0059 5.19 4AL Crossa et al 2007; Lowe et al 2011wPt-1903 5A 0.0003 8.50 5AL Lowe et al 2011wPt-7061 5A 0.0053 3.91 5AL Lowe et al 2011-Yr48wPt-7251 7B 0.0489 3.02 7BS Crossa et al 2007 - Yr39wPt-666850 7D 0.0000 10.52wPt-5049 7D 0.0293 3.54 7DS Crossa et al 2007-Yr18wPt-733631 NA 0.0003 8.27 7DS Crossa et al 2007-Yr33 (?); Lowe et al 2011
  17. 17. Allelic effects of some of the linked DArT markers
  18. 18. Some DArT haplotypes associated with Yr resistance 4D 2D 2B 2B 2B 0.01 0.4 wPt-0431 0.01 0.5 wPt-6003 0.03 0.3 wPt-743630 0.04 0.3 wPt-7985 0.05 0.3 wPt-9423 Name Cross PhenotypeGenotype GCP_90 N-ABYAD-15 CHAM-6//KAUZS/3/AO41/EMUS//TEVEES 2 1 1 1 1 1 GCP_147 NAYZAK-6 TEVEES//KAUZS/3/FOWS//NS732/HER 2.3 1 1 1 1 1 GCP_86 NAYZAK-2 TEVEES//KAUZS/3/FOWS//NS732/HER 2.3 1 1 1 1 1 GCP_93 ZAKIA-12 CHAM-6//KAUZS/3/FOWS//NS732/HER 2.3 1 1 1 1 1 GCP_89 N-ABYAD-13 CHAM-6//KAUZS/3/AO41/EMUS//TEVEES 7.3 0 0 0 0 0 GCP_61 WATAN-2 KAUZ/FLORKWA-1 7.7 0 0 0 0 0 GCP_92 ZAKIA-11 CHAM-6//KAUZS/3/FOWS//NS732/HER 7.7 0 0 0 0 0 GCP_3 CHAM-8 KAUZ = JUP/BJY//URES 8 0 0 0 0 0 GCP_62 WATAN-9 KAUZ/FLORKWA-1 8 0 0 0 0 0 GCP_91 ZAKIA-10 CHAM-6//KAUZS/3/FOWS//NS732/HER 8 0 0 0 0 0 2BS – Yr27, Yr31, Yr41, YrSP , YrP 81
  19. 19. Some DArT haplotypes associated with Yr resistance 3B 3B 3B 3B 4D 2D 0.02 0.04 tPt-9267 0.00 0.06 wPt-6132 0.00 0.06 wPt-0264 0.01 0.04 wPt-0431 0.01 0.05 wPt-6003 Name/Pedigee Cross PhenotypeGenotype GCP_90 N-ABYAD-15 CHAM-6//KAUZS/3/AO41/EMUS//TEVEES 2 1 1 1 1 1GCP_147 NAYZAK-6 TEVEES//KAUZS/3/FOWS//NS732/HER 2 1 1 1 1 1GCP_146 NAYZAK-3 TEVEES//KAUZS/3/FOWS//NS732/HER 3 1 1 1 1 1GCP_145 AFFRAH-3 AO41/EMUS//TEVEES/3/SD 8036 7 0 0 0 0 0 GCP_87 N-ABYAD-10 CHAM-6//KAUZS/3/AO41/EMUS//TEVEES 7 0 0 0 0 0 Loci that confers multiple root GCP_88 N-ABYAD-12 diseased resistance 0 CHAM-6//KAUZS/3/AO41/EMUS//TEVEES 7 0 0 0 0 GCP_89 N-ABYAD-13 CHAM-6//KAUZS/3/AO41/EMUS//TEVEES 7 0 0 0 0 0 3BS - Yr4, Yr30, YrS, YrSte2, Yrns-B1
  20. 20. Conclusions/what next• Identified list of DArT markers closely linked to existing and potentially uncharacterized Yr resistance• Better understanding of the Yr genes in the existing pool of elite germplasm• Better position to utilize genetic profiling – modified genomic selection approach in germplasm enhancement for Yr resistance• Validation using bi-parental and multi-parent mapping populations• Conversion of 100 DArT markers to diagnostic markers to facilitate MAS in known genes
  21. 21. ICARDAThanks
  22. 22. CAIGE meetingAdelaide March 11, 2011

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