Antagonistic Interactions Among Stripe and Stem Rust Resistance QTLs in Wheat

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Abdulqader Jighly, ICARDA

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Antagonistic Interactions Among Stripe and Stem Rust Resistance QTLs in Wheat

  1. 1. 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
  2. 2. 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
  3. 3. 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  
  4. 4. 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
  5. 5. Rust Epidemics Seeking  and  use  new   resources  of  effec2ve  gene2c   resistance  is  the  solu2on  
  6. 6. Association Mapping Todays’  Haplotypes   Resistant   Suscep?ble   Ancestral  Haplotypes   Resistance  gene  
  7. 7. 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  
  8. 8. 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.  
  9. 9. 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  
  10. 10. 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    
  11. 11. 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)  
  12. 12. 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   Number  of  Plants   Field  Score   Stripe  Rust  Response   10   36   73   81   0   10   20   30   40   50   60   70   80   90   R   MR   MS   S   Number  of  Plants   Infec2on  Type   Stem  Rust  Response  
  13. 13. 2- Population Structure 0%   20%   40%   60%   80%   100%   0%   20%   40%   60%   80%   100%   Using  DArT  markers   Using  SNP  markers  
  14. 14. 3- Linkage Disequilibrium Decay Using  DArT  markers   Using  SNP  markers  
  15. 15. 4- Linkage Disequilibrium – 1B/1R
  16. 16. 5- Association Mapping
  17. 17. 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  
  18. 18. 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  
  19. 19. 6- Gene-Gene Interaction
  20. 20. 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  
  21. 21. 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  
  22. 22. 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  
  23. 23. 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  
  24. 24. Thank you

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