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A genome-wide SNP scan for QTL     associated with adult plant rust resistance            in East African bread wheat     ...
Outline• Section 1: General overview, definitions• Section 2: Materials, Methods, Pre-analyses• Section 3: Association map...
Section 1 BGRI Workshop_2012
Cereal Production targets                                                                    yield gap                    ...
Wheat: projecting ahead• Wheat needs to contribute 25% by 2025                          Global wheat yield growth         ...
Confronting the yield gap         BGRI Workshop_2012
Source: CIMMYT, 2011BGRI Workshop_2012
Breeding for Durable resistance• Key to circumvent rust-associated losses• An opportunity to tap cutting edge techniques  ...
Association Mapping• Identification of significant statistical  association between a phenotypic trait  and molecular mark...
Linkage Disequilibrium• Non-random co-inheritance of alleles at  different Loci                   …higher marker density  ...
Population Structure• Subpopulations at differing allele frequencies                       Mapping panel                  ...
Section 2Materials, Methods & pre-analyses             BGRI Workshop_2012
Bread wheat mapping panel• 160 Kenyan lines• 70 Ethiopian        Historicals to recent releases• 37 Founders• Additionally...
Phenotyping    Trait        Location            YearStem rust APR  St Paul, MN           2010               St Paul, MN   ...
Disease scoring• 2 to 3 scores taken for each line• Last score converted to Coefficient of infection          Modified Cob...
Stem rust BGRI Workshop_2012
Leaf rustBGRI Workshop_2012
Genotyping• 9000 SNP Illumina’s infinium assay• GenomeStudio® for ‘Allele calling’         Polymorphic                    ...
Genotyping• Low quality SNPs, MAF < 0.05 eliminated• 5987 polymorphic SNPs used                 BGRI Workshop_2012
Population Structure (Q)• Estimated using 235 SNPs >4 cM apart• Software: ‘STRUCTURE v.2.3.4’       (Pritchard et al., 200...
Subdivisions inferred     • Four, plus a ‘Mixed group’‘CIMMYT_1’ ‘North_ Am.’   ‘CIMMYT_2’            ‘Landraces’   ‘Mixed...
Principal Component Analysis• 3 sets (each 500 random SNPs) used                 BGRI Workshop_2012
Kinship (K)Based on 5965 SNPs    BGRI Workshop_2012
Linkage Disequilibrium (LD)• Software: TASSEL v3.0             (maizegenetics.net)• 2547 unlinked SNPs• r2 used to estimat...
LD decayA- 13cM         B- 18cM            D- 11cM          Estimated LD extent              BGRI Workshop_2012
Section 3Association mapping results          BGRI Workshop_2012
Mixed-effects Linear Model    y=Qv + Mα + Kµ + e       y: vector of phenotype       Q: structure matrix       v: random ef...
Njoro stem rust_2011FDR=0.01  1A       1B 1D 2A   2B   2D 3A 3B 3D 4A4B4D5A 5B 5D 6A 6B 6D 7A 7B 7D Unknown               ...
Njoro stem rust_2012FDR=0.01    1A 1B 1D 2A   2B   2D 3A 3B 3D 4A4B4D5A 5B 5D 6A 6B 6D 7A 7B 7D Unknown                   ...
St Paul stem rust_2010FDR=0.01   1A 1B 1D 2A 2B   2D 3A   3B 3D 4A4B4D 5A 5B 5D 6A 6B 6D 7A 7B 7D Unknown                 ...
St Paul stem rust_2011FDR=0.01   1A 1B 1D 2A   2B   2D 3A 3B 3D 4A4B4D 5A 5B 5D 6A 6B 6D 7A 7B 7D Unknown                 ...
St Paul stem rust_2012FDR=0.01   1A 1B 1D 2A   2B   2D 3A 3B 3D 4A4B4D5A 5B 5D 6A 6B 6D 7A 7B 7D Unknown                  ...
St Paul leaf rust_2010FDR=0.01 1A 1B 1D 2A    2B   2D 3A 3B 3D 4A4B4D5A 5B 5D 6A 6B 6D7A 7B 7D Unknown                    ...
St Paul leaf rust_2011FDR=0.011A    1B 1D 2A   2B   2D 3A 3B 3D 4A4B4D5A 5B 5D 6A 6B 6D7A 7B 7D Unknown                   ...
St Paul leaf rust_2012FDR=0.01 1A 1B 1D 2A   2B 2D 3A    3B 3D 4A4B4D5A 5B 5D 6A 6B 6D7A 7B 7D Unknown                    ...
El Batan leaf rust_2011FDR=0.01 1A 1B 1D 2A   2B 2D 3A 3B 3D 4A4B4D5A 5B 5D 6A 6B 6D7A 7B 7D Unknown                      ...
Crookston leaf rust_2012FDR=0.011A 1B 1D 2A    2B   2D 3A 3B 3D 4A4B4D5A 5B 5D 6A 6B 6D7A 7B 7D Unknown                   ...
Summary:Map positions of Significant markers              BGRI Workshop_2012
Stem rust (FDR=0.01)                                                         5.72                                         ...
Leaf rust (FDR=0.01)                  13.1                                                                                ...
Section 4Research highlights     BGRI Workshop_2012
• Utility of AM for APR QTLs demonstrated• The 9K chip assay invaluable (90K better!)• > 20 significant associations (need...
AcknowledgementsGermplasm                                         Field Experiments• Peter Njau (K.A.R.I.)            • Ra...
Thank you  BGRI Workshop_2012
BGRI Workshop_2012
Summary: Detected Stem Rust ‘APR’ QTLsFalse Discovery Rate =0.001                Total= 18                  R2 = 6% to 15%...
Summary: Detected Leaf Rust ‘APR’ QTLsFalse Discovery Rate =0.001                 Total= 19                  R2 = 6% to 13...
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A genome-wide SNP scan for QTL associated with adult plant rust resistance in East African bread wheat

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Godwin Macharia, University of Minnesota

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A genome-wide SNP scan for QTL associated with adult plant rust resistance in East African bread wheat

  1. 1. A genome-wide SNP scan for QTL associated with adult plant rust resistance in East African bread wheat G. Macharia1 , S. Chao2 and J. Anderson11University of Minnesota, Department of Agronomy and Plant Genetics, ST PAUL MN 2USDA-ARS Biosciences Research Laboratory, FARGO ND BGRI Workshop_2012
  2. 2. Outline• Section 1: General overview, definitions• Section 2: Materials, Methods, Pre-analyses• Section 3: Association mapping results• Section 4: Research highlights BGRI Workshop_2012
  3. 3. Section 1 BGRI Workshop_2012
  4. 4. Cereal Production targets yield gap Source: Tester and Langridge, 2007• 37% increase required to meet 2050 demand BGRI Workshop_2012
  5. 5. Wheat: projecting ahead• Wheat needs to contribute 25% by 2025 Global wheat yield growth 4 3.6 3 2.8 Rate (%) 2 1 1.1 0 1966-79 1984-94 1995-05 Period Data source: CIMMYT• At 1.1% growth, wheat can only contribute 17% BGRI Workshop_2012
  6. 6. Confronting the yield gap BGRI Workshop_2012
  7. 7. Source: CIMMYT, 2011BGRI Workshop_2012
  8. 8. Breeding for Durable resistance• Key to circumvent rust-associated losses• An opportunity to tap cutting edge techniques Marker assisted recurrent selection Genomic selection Association mapping• Gene/QTL discovery a pre-requisite BGRI Workshop_2012
  9. 9. Association Mapping• Identification of significant statistical association between a phenotypic trait and molecular marker based on LD BGRI Workshop_2012
  10. 10. Linkage Disequilibrium• Non-random co-inheritance of alleles at different Loci …higher marker density Source: Hamblin et al, 2011 …greater resolution BGRI Workshop_2012
  11. 11. Population Structure• Subpopulations at differing allele frequencies Mapping panel P1 P2 P3• Could arise from adaptation, domestication• Creates LD between unlinked loci (false positives) BGRI Workshop_2012
  12. 12. Section 2Materials, Methods & pre-analyses BGRI Workshop_2012
  13. 13. Bread wheat mapping panel• 160 Kenyan lines• 70 Ethiopian Historicals to recent releases• 37 Founders• Additionally, 35 Minnesota lines BGRI Workshop_2012
  14. 14. Phenotyping Trait Location YearStem rust APR St Paul, MN 2010 St Paul, MN 2011 St Paul, MN 2012 Njoro, Ken 2011 Njoro, Ken 2012Leaf rust APR St Paul,MN 2010 St Paul, MN 2011 St Paul, MN 2012 El Batan, MX 2011 Crookston, MN 2012 BGRI Workshop_2012
  15. 15. Disease scoring• 2 to 3 scores taken for each line• Last score converted to Coefficient of infection Modified Cobb Scale Severity (%) × Infection type = Coefficient of infection 0 - 100 R (0.0) MR (0.4) e.g. 60MS MS (0.8) (60 x 0.8) = 48 S (1.0) BGRI Workshop_2012
  16. 16. Stem rust BGRI Workshop_2012
  17. 17. Leaf rustBGRI Workshop_2012
  18. 18. Genotyping• 9000 SNP Illumina’s infinium assay• GenomeStudio® for ‘Allele calling’ Polymorphic Ambiguous BGRI Workshop_2012
  19. 19. Genotyping• Low quality SNPs, MAF < 0.05 eliminated• 5987 polymorphic SNPs used BGRI Workshop_2012
  20. 20. Population Structure (Q)• Estimated using 235 SNPs >4 cM apart• Software: ‘STRUCTURE v.2.3.4’ (Pritchard et al., 2000)• K=1…10 subpopulations assumed Each K= 4 replications BGRI Workshop_2012
  21. 21. Subdivisions inferred • Four, plus a ‘Mixed group’‘CIMMYT_1’ ‘North_ Am.’ ‘CIMMYT_2’ ‘Landraces’ ‘Mixed’ Mean Fst = 0.1329 BGRI Workshop_2012
  22. 22. Principal Component Analysis• 3 sets (each 500 random SNPs) used BGRI Workshop_2012
  23. 23. Kinship (K)Based on 5965 SNPs BGRI Workshop_2012
  24. 24. Linkage Disequilibrium (LD)• Software: TASSEL v3.0 (maizegenetics.net)• 2547 unlinked SNPs• r2 used to estimate LD• r2 plotted against genetic distance BGRI Workshop_2012
  25. 25. LD decayA- 13cM B- 18cM D- 11cM Estimated LD extent BGRI Workshop_2012
  26. 26. Section 3Association mapping results BGRI Workshop_2012
  27. 27. Mixed-effects Linear Model y=Qv + Mα + Kµ + e y: vector of phenotype Q: structure matrix v: random effects due to structure M: vector of marker genotype α: marker fixed effect K: Kinship matrix µ: fixed effects due to ancestry e: residual effects Implemented in TASSEL v.3 (maizegenetics.net) BGRI Workshop_2012
  28. 28. Njoro stem rust_2011FDR=0.01 1A 1B 1D 2A 2B 2D 3A 3B 3D 4A4B4D5A 5B 5D 6A 6B 6D 7A 7B 7D Unknown Chromosome BGRI Workshop_2012
  29. 29. Njoro stem rust_2012FDR=0.01 1A 1B 1D 2A 2B 2D 3A 3B 3D 4A4B4D5A 5B 5D 6A 6B 6D 7A 7B 7D Unknown Chromosome BGRI Workshop_2012
  30. 30. St Paul stem rust_2010FDR=0.01 1A 1B 1D 2A 2B 2D 3A 3B 3D 4A4B4D 5A 5B 5D 6A 6B 6D 7A 7B 7D Unknown Chromosome BGRI Workshop_2012
  31. 31. St Paul stem rust_2011FDR=0.01 1A 1B 1D 2A 2B 2D 3A 3B 3D 4A4B4D 5A 5B 5D 6A 6B 6D 7A 7B 7D Unknown Chromosome BGRI Workshop_2012
  32. 32. St Paul stem rust_2012FDR=0.01 1A 1B 1D 2A 2B 2D 3A 3B 3D 4A4B4D5A 5B 5D 6A 6B 6D 7A 7B 7D Unknown Chromosome BGRI Workshop_2012
  33. 33. St Paul leaf rust_2010FDR=0.01 1A 1B 1D 2A 2B 2D 3A 3B 3D 4A4B4D5A 5B 5D 6A 6B 6D7A 7B 7D Unknown Chromosome BGRI Workshop_2012
  34. 34. St Paul leaf rust_2011FDR=0.011A 1B 1D 2A 2B 2D 3A 3B 3D 4A4B4D5A 5B 5D 6A 6B 6D7A 7B 7D Unknown Chromosome BGRI Workshop_2012
  35. 35. St Paul leaf rust_2012FDR=0.01 1A 1B 1D 2A 2B 2D 3A 3B 3D 4A4B4D5A 5B 5D 6A 6B 6D7A 7B 7D Unknown Chromosome BGRI Workshop_2012
  36. 36. El Batan leaf rust_2011FDR=0.01 1A 1B 1D 2A 2B 2D 3A 3B 3D 4A4B4D5A 5B 5D 6A 6B 6D7A 7B 7D Unknown Chromosome BGRI Workshop_2012
  37. 37. Crookston leaf rust_2012FDR=0.011A 1B 1D 2A 2B 2D 3A 3B 3D 4A4B4D5A 5B 5D 6A 6B 6D7A 7B 7D Unknown Chromosome BGRI Workshop_2012
  38. 38. Summary:Map positions of Significant markers BGRI Workshop_2012
  39. 39. Stem rust (FDR=0.01) 5.72 16.7 75.9 124.4 143.4 163.7 211.72B 3B 3D 4A 4B 17.1 45.9 Unknown Unknown 66.7 Unknown Njoro_2011 St Paul_2010 St Paul_2011 156.9 St Paul_2012 193.3 BGRI Workshop_2012 5A 6B R2 = 6% to 15%
  40. 40. Leaf rust (FDR=0.01) 13.1 28.1 57.7 94.1 123.8 136.3 184.3 387.21A 1B 1D 2B 3A 3B 5A 5B Lr9,Lr14 28.5 115.6 32.2 68.1 Lr61 Unknown 137.0 El Bata_2011 St Paul_2010 St Paul_2011 Crksto._2012 BGRI Workshop_20126A 7D R2 = 6% to 13% 6B 7B
  41. 41. Section 4Research highlights BGRI Workshop_2012
  42. 42. • Utility of AM for APR QTLs demonstrated• The 9K chip assay invaluable (90K better!)• > 20 significant associations (needs validation) BGRI Workshop_2012
  43. 43. AcknowledgementsGermplasm Field Experiments• Peter Njau (K.A.R.I.) • Ravi Singh (CIMMYT)• Solomon Gelalcha (E.A.R.I.) • Yue Jin (USDA ARS CDL)• Harold Bockelman (USDA ARS NSGC) • Jim Kolmer (USDA ARS CDL) • Matt Rouse (USDA ARS CDL)Integrated SNP Map Adviser• Eduard Akhunov et al (Kansas St Univ.) • Jim Anderson (Univ. of Min.) Study Leave Funding BGRI Workshop_2012
  44. 44. Thank you BGRI Workshop_2012
  45. 45. BGRI Workshop_2012
  46. 46. Summary: Detected Stem Rust ‘APR’ QTLsFalse Discovery Rate =0.001 Total= 18 R2 = 6% to 15%SNP marker Chrom. Pos Environment logpvalue markerR2wsnp_Ex_c23509_32746909 5A 66.7 Njoro_2011 3.7746503 0.1002736wsnp_Ku_rep_c102220_89250165 5A 17.11 Njoro_2011 3.7220425 0.0979537wsnp_Ex_c23509_32746806 5A 67.23 Njoro_2011 3.5750289 0.0915756wsnp_Ex_c22018_31193171 2B 163.67 Njoro_2011 3.1322173 0.084855wsnp_Ex_c2718_5038502 5A 45.9 Njoro_2011 3.0466039 0.0772597wsnp_Ex_c1383_2652398 6B 193.34 Njoro_2011 3.0078695 0.0741373wsnp_Ex_c3044_5620102 2B 163.67 Njoro_2011 3.0067282 0.0827768wsnp_Ex_c2718_5038582 5A 65.62 Njoro_2011 2.9157554 0.0766549wsnp_BE490763A_Ta_1_3 unknown unknown St Paul_2010 3.2363714 0.1497071wsnp_Ex_rep_c70265_69211592 4B 75.95 St Paul_2010 3.2237278 0.1489716wsnp_BE405849A_Ta_1_1 5A 156.98 St Paul_2010 3.1839175 0.1466602wsnp_Ex_c7489_12809914 4A 5.72 St Paul_2011 3.2203025 0.06896wsnp_Ex_c5457_9632050 3B 143.44 St Paul_2011 3.0865325 0.0656068wsnp_Ra_rep_c70864_68811286 unknown unknown St Paul_2012 4.3207025 0.0967225wsnp_Ex_c9758_16120551 unknown unknown St Paul_2012 4.0542393 0.0916218wsnp_Ex_c13505_21253168 3B 211.65 St Paul_2012 3.6055684 0.0793914wsnp_JD_rep_c53979_36270209 3B 124.4 St Paul_2012 3.1090116 0.0650714wsnp_BE444579D_Ta_2_3 3D 16.66 St Paul_2012 3.0200302 0.0643022 BGRI Workshop_2012
  47. 47. Summary: Detected Leaf Rust ‘APR’ QTLsFalse Discovery Rate =0.001 Total= 19 R2 = 6% to 13%SNP marker Chrom. Pos Environment LogPvalue markerR2wsnp_Ex_c8588_14419007 1A 123.8 St Paul_2010 3.9900017 0.1163485wsnp_Ku_c13229_21142792 1B 13.07 ElBatan_2011 3.287268 0.0807828wsnp_Ex_c1130_2166731 1D 57.66 ElBatan_2011 3.6755068 0.0935952wsnp_Ex_c16720_25268525 1D 57.66 ElBatan_2011 3.6755068 0.0935952wsnp_Ex_rep_c108057_91436561 1D 57.66 ElBatan_2011 3.6755068 0.0935952wsnp_Ra_c58860_60407020 2B 387.23 St Paul_2011 3.2171866 0.0889992wsnp_Ex_rep_c104884_89459472 3A 136.29 ElBatan_2011 3.6811409 0.094023wsnp_Ex_rep_c67033_65490126 3B 31.01 Crookst._2012 3.4344695 0.0766409wsnp_Ex_rep_c67625_66279491 3B 28.39 Crookst._2012 2.9931129 0.0588606wsnp_Ex_c31799_40545376 5A 184.34 St Paul_2011 3.1406512 0.0656255wsnp_Ku_c6464_11320381 5B 94.06 St Paul_2011 3.5574842 0.0770563wsnp_BF202329A_Ta_2_2 6A 115.65 ElBatan_2011 3.0862858 0.0746064wsnp_BM134512A_Ta_2_2 6A 115.65 ElBatan_2011 3.0862858 0.0746064wsnp_Ex_c9502_15748469 6A 137.04 ElBatan_2011 3.1096994 0.0765279wsnp_Ex_rep_c115803_95396724 6B 28.49 ElBatan_2011 4.8781808 0.1316431wsnp_Ex_c11106_18002976 7B 32.15 Crookst._2012 3.0027851 0.0588665wsnp_Ku_c27221_37168065 7D 68.1 Crookst._2012 3.0509121 0.059267wsnp_Ex_c23850_33089300 unknown unknown ElBatan_2011 4.5646064 0.121684wsnp_be490219A_Ta_1_1 unknown unknown ElBatan_2011 3.5737042 0.0904964 BGRI Workshop_2012

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