Wild Triticum and Aegilops Species: A Mine of Rust Resistance Genes for Future Harvest


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Parveen Chhuneja

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Wild Triticum and Aegilops Species: A Mine of Rust Resistance Genes for Future Harvest

  1. 1. Wild  Tri$cum  and  Aegilops  species:   A  mine  of  rust  resistance  genes  for   future  harvest   Parveen  Chhuneja   School  of  Agricultural  Biotechnology   Punjab  Agricultural  University   Ludhiana  
  2. 2. Phylogeny of Triticum and Aegilops species BS  Gill,  WGGRC  
  3. 3. s   Primary  gene  pool   Secondary  gene  pool   TerDary  gene  pool   v  all  diploid  and  tetraploid  Tri$cum  &  Aegilops    species   with  A,  B,  &  D  genomes   v  landraces,  early  domesDcates   v  wild  species  that  hybridize  directly  with  the   culDvated   " tetraploid  species   with  one  genome     common  with   wheat   "   diploid  S-­‐genome   species  from   Aegilops  secDon   Sitopsis     all  non-­‐progenitor  diploid  &   tetraploid  species   Wheat  Gene  Pools  
  4. 4. T.  monococcum  (AA)   Ae.  speltoides  (SS)   Progenitor  Species   Ae.  tauschii  (DD)   Leaf  rust   Stripe  rust   Stem  rust   Foliar  blights   Stay  Green   Anther  Extrusion   Leaf  rust   Stripe  rust   Stem  rust   Powdery  mildew   Karnal  bunt   Grain  size   Spike  size   Leaf  rust   Stripe  rust   Stem  rust   Powdery  mildew   Karnal  bunt   Grain  size   Grain  micronutrient     Thermotolerance   Aphid  Resistance  ??  
  5. 5. T.  arara$cum  (AAGG)   T.  dicoccoides  (AABB)   Leaf  rust   Stripe  rust   Powdery  mildew   Leaf  rust   Stripe  rust   Stem  rust   Powdery  mildew   Grain  protein   Grain  size   Grain  micronutrient  
  6. 6. Ae.  triuncialis  (UUCC)   Non-­‐progenitor  species   Ae.  geniculata  (UM)   Ae.  kotschyi  (US)   Leaf  rust   Stripe  rust   Powdery  mildew   Karnal  bunt   Thermotolerance   Leaf  rust   Stripe  rust   Grain  micronutrient   Leaf  rust   Stripe  rust   Stem  rust   Thermotolerance   Ae.  variabilis  (US)   Leaf  rust   Stripe  rust   Grain  micronutrient   Thermotolerance  
  7. 7. Wild  wheat  germplasm  at  PAU,  Ludhiana   Species Genome Total Aegilops  tauschii DD 270 Tri$cum  boeo$cum AbAb 70 Tri$cum  monococcum AmAm 60 Aegilops  speltoides SS 140 other  S  genome  species   SS 20 Tri$cum  dicoccoides   AABB 120 Tri$cum  arara$cum     AAGG 20 Aegilops  cylindrica DDCC 20 Aegilops  ventricosa   DDNN 10 Aegilops  umbellulata   UU 4 Aegilops  triuncialis UUCC 10 Aegilops  geniculata UUMM 10 Aegilops  markgrafii   UUMM 4 Aegilops  neglecta UUMM 6 Aegilops  kotschyi   UUSS 22 Aegilops  peregrina   UUSS 44 Misc.   20 850
  8. 8. Variability  for  rust  resistance  in  wild  wheats  
  9. 9. Species     Acc.     Seedling  ReacDon    Leaf  Rust     Stripe  Rust    77     77-­‐1     77-­‐2     104-­‐1     K     M    Ae.   geniculata     3514     R     R     R     R     S     S    3547     R     R     R     R     R     S    3565     R     R     R     R     S     S    5507     R     R     -­‐     -­‐     R     R    Ae.   triuncialis     3549     R     R     R     R     R     S    3621     -­‐     R     R     R     R     R    3669     S     R     S     R     S     R    Ae.   longissima     3770     S     R     R     R     R     R    3819     S     -­‐     R     -­‐     S     R    3821     R     R     -­‐     -­‐     R     S    Ae.  tauschii     3737     S     R     S     X     R     R    3748     -­‐     R     R     R     R     R    3749     -­‐     R     R     R     R     R    T.  urartu     5319     S     R     S     -­‐     R     R    5343     R     R     R     R     S     S    5357     S     -­‐     S     -­‐     R     R    5360   R   S   S   S   S   R   Variability for rust resistance in different wild species
  10. 10. Stripe  rust  reacDon  of  Ae.  tauschii   accessions  at  adult  plant  stage   0 0.2 P B W 343 WH 542 894-­‐S 3472-­‐T 3738-­‐T 3743-­‐S 3750-­‐S 3751-­‐S 3753-­‐T 3757-­‐S 3758-­‐S 3759-­‐T 3760-­‐S 3761-­‐S 3769-­‐S 3786-­‐S 3805-­‐S3822-­‐S 3823-­‐S 3826-­‐T 5514-­‐S 9385-­‐T 9785-­‐T 9787-­‐S 9790-­‐S 9791-­‐S 9793-­‐S 9794-­‐S 9795-­‐T 9796-­‐S 9799-­‐S 9804-­‐S 9807-­‐S 9809-­‐S 9810-­‐S 9821-­‐S 9824-­‐T 9826-­‐S 9827-­‐T9830-­‐S 13757-­‐T 13764-­‐T 14091-­‐S 14102-­‐S 14106-­‐T 14109-­‐S 14122-­‐T 14159-­‐S 14163-­‐T 14164-­‐T 14165-­‐S 14171-­‐S 14173-­‐S 14175-­‐S 14180-­‐S 14183-­‐T 14189-­‐T14192-­‐T 14195-­‐T 14197-­‐T 14198-­‐T 14199-­‐T 14219-­‐T 14233-­‐T14236-­‐T14240-­‐S 14245-­‐T14251-­‐T 14318-­‐T 14323-­‐S 14330-­‐S 14331-­‐S 14333-­‐S 14334-­‐S 14335-­‐S 14336-­‐S 14337-­‐S 14339-­‐S 14342-­‐S 14344-­‐S 14350-­‐T14351-­‐T 14354-­‐T 14361-­‐S 14576-­‐S 14577-­‐S 14578-­‐T 100 73 59 42 62 100 83 84 56 33 35 30 61 99 100 63 25 42 61 94 100 47 26 99 71 96 42 100 8336 67 28 51 42 34 7182 99 93 31 29 26 60 55 21 Cluster I-ssp strangulata Cluster II-ssp. tauschii & strangulata Level  of  geneDc  diversity  in  Ae.  tauschii    
  11. 11. Ae. speltoides (SS) 0 0.2 P DW233P DW291P DW274Ac onc hi89 P BW343 P BW550 3566 3595 3601 3603 3635 3808 38093809 TA1784 3571 3574 3575 3578 3579 3580 3581 3582 3583 3584 3585 3590 3591 3592 3593 3596 3598 3599 3602 3604 3605 3607 3608 3637 3638 3804 402471 TA1770 TA1772 TA1776 TA1778 TA1781 TA1786 TA1787 TA1788 TA1791 TA1792 TA1793 TA1845 TA2357 Level  of  geneDc  diversity  in  Ae.  speltoides     Stripe  rust  reacDon  of  Ae.  speltoides   accessions  at  adult  plant  stage  
  12. 12. 0   20   40   60   Accessions   ReacDon  type   NON  PROGENITOR  SPECIES   T.  boeo$cum  T.  monococcum   0   10   20   30   40   50   60   70   0   TR   20MR   20S   Accession   ReacDon  Type   0   5   10   15   20   25   30   35   40   45   0   TR   5MR   10MR   20MR   40S-­‐60S   Accessions   ReacDon  type     T.  dicoccoides    
  13. 13. UDlizaDon  of  wild  species  in  wheat  for  disease  resistance   Disease   Total  genes   catalogued   From  alien  sources   Leaf  rust   71   32   Stripe  rust   53   25   Stem  rust   57   24   Powdery  mildew   47   26   CCN   10   8   McIntosh  et  al.  2012  
  14. 14. Alien  introgressions:  Some  Case   Studies   "  5M  of  Ae.  geniculata:  resistance  genes  for  all   the  three  rusts   " Homoeologous  gp.  5:  Distal  region   " Ae.  triuncialis:  A  single  accession  carry   resistance  for  mulDple  diseases   "  A  genome  species:  source  of  mulDple   resistance  
  15. 15. 5M  chromosome  of  Ae.  geniculata  acc.  pau3547  have  genes  for  leaf   rust,  stripe  rust  and  stem  rust  resistance   Lr57 Yr40 Lr57 Yr40 Lr57 Yr40 Sr53
  16. 16. BS  Gill,  WGGRC   Sr53  in  spontaneous  translocaDon  stocks  with  reduced  alien   chromaDn  -­‐  Liu  et  al.  2011  
  17. 17. 5US  chromosome  of  Ae.  umbellulata  carries  closely  linked  leaf   rust  and  stripe  rust  resistance  genes     *YrU0.0 *LrU0.7 *Lr57-Yr40CAPS4.6 *Xgwm1909.1 *Xwmc805c32.8 5DS Disease    RILs   Stripe  rust   Total   HR   H   HS   Leaf   rust   HR   113   7   3   123   H   0   11   1   12   HS   0   1   106   107   Total   113   19   110   242   Leaf  rust  reacDon  in  the  mapping  populaDon   IL373   IL403   Resistant  RILs   PBW343   WL711   SuscepDble  RILs  
  18. 18. 5CS  chromosome  of  Ae.  caudata  carries  closely  linked  leaf  rust   and  stripe  rust  resistance  genes     Stage   Resistant   Susceptible   T o t a l plants   χ2(3:1)   Seedling   208   78   286   0.79   Adult plant   206   78   284   0.92   5DS  
  19. 19. Leaf  rust  and  Stripe  rust  resistance  genes  on  5DS  from  three   different  alien  genomes-­‐M,  U  &  C   *YrU0.0 *LrU0.7 *Lr57-Yr40CAPS4.6 *Xgwm1909.1 *Xwmc805c32.8 5DS Ae.  geniculata                  Ae.  umbellulata                    Ae.  caudata   Lr57/Yr40   Lr57-­‐Yr40                          LrU,  YrU                    LrC,  YrC  
  20. 20. Wheat-Ae. triuncialis substitution line-DS5U(5A)  5U  chromosome  carries  genes  for     "   A  leaf  rust  resistance-­‐slow  rusDng   "   A  powdery  mildew  resistance  gene   "   A  CCN  resistance  gene   Single  Accession  of  Ae.  triuncialis  acc.  pau  3549  carries  two  leaf   rust,  powdery  mildew,  CCN  and  KB  resistance  genes  
  21. 21. Ae. triuncialis addition line for chromosome 2U/2C: KB, leaf rust and powdery mildew resistance Derivative ID Mean KB % KB Range Leaf rust Powdery mildew WL711 60.2 - 80S 9 PBW343 10.7 - 40S 9 2205 2.6 0-12.6 60S 1 2238 15.1 0-27.2 0 1 2288 2.3 0-13.2 0 0-3 2291 2.2 0-9.9 0 1 WL711 AT 2205 2238 2288 2291                AT      PBW343  2288    BC1F3  
  22. 22. A Wheat-Ae. triuncialis spontaneous translocation carries Lr58 Lr58
  23. 23. A-­‐genome  Tri(cum  species:  MulDple  disease   resistance  
  24. 24. Triticum boeoticum/ T. monococcum RIL population " Leaf  rust  resistance   " Stripe  rust  resistance   " Karnal  bunt  resistance   " Cereal  cyst  nematode  resistance   " Powdery  mildew  resistance   " Single  vs  two  seeds  per  spikelet   " Many  Agronomic  traits   " Stem  rust  resistance    
  25. 25. Disease  resistance  gene  segregaDon  in    T.  boeo(cum/T.  monococcum  RILs   Disease   ReacDon  in   parental  accession   SegregaDon  in  RILs   CulDvated   Germplasm     Leaf  rust     Resistance   Both  parents   resistant   No  segregaDon;   Both  parents  have   same  gene  (s)   WL711,  PBW343   Stripe  rust   Resistance   Both  parents   resistant   Two  gene;     One  gene  from   each  parent   WL711,  PBW343   Stem  rust   Resistance   Both  parents   resistant   No  segregaDon;   Both  parents  have   Sr22   WL711     Powdery  mildew   resistance   T.  boeoDcum   resistant   Two  genes;   Both  genes  from  Tb   PBW343   Cereal  cyst   nematode   resistance   T.  monococcum   resistant   Two  genes;   Both  genes  from   Tm   4x  &  6x  background  
  26. 26. Linkage  map  of  A  genome  of  T.  monococcum    T. boeoticum/T. monococcum likage map based on 200 markers BE4893230.0 GluAlmw13.3 bcd13035.3 gdm3350.2 gwm3355.4 cfd5856.7 gwm13661.1 cfa215363.2 BE44489066.8 Mwg710b Psr549b67.3 mwg2021a67.8 gwm110474.1 BE442682 barc20476.7 BE49983581.7 cfa2158 cfd2186.0 BE44340188.3 BE44310391.2 BE59168294.1 gwm39196.4 BE495292100.0 barc9109.8 gdm36124.6 wmc475146.1 cfd65 cfd59 cfd83 155.1 cfa2135 wmc470a159.4 gwm135164.5 GluAy173.1 BE443103213.0 1 Mwg8510.0 KsuD1818.5 BE49835819.6 wmc38223.6 barc124a25.1 gwm63633.9 Psr66652.3 Psr108 wmc17757.8 fba198 fba17858.7 wmc26460.6 fba27268.5 BE49749481.2 BE49947884.9 gwm27587.5 BE406808 wmc47490.1 BE406584 gwm51591.3 gwm1011 gwm1045 BE406923 gwm71 cfd26 94.7 wmc42095.9 BE425962 Psr630117.6 barc5119.5 Psr681129.1 Psr933129.5 wmc407129.7 wmc170 Psr331133.3 fba374134.4 gwm30140.9 Psr540152.3 cfd267165.8 cfd223199.1 2 wmc1470.0 gwm75721.4 barc5725.1 barc1233.6 wmc1134.3 cfd7950.5 gwm36954.7 barc21867.6 gwm77968.9 wmc150a78.0 wmc7998.0 barc1998.6 barc6798.9 wmc26999.2 cfa2134105.5 Psr570106.6 gwm1121108.6 Psr74117.0 wmc492119.5 barc152135.2 wmc96c137.5 cfa2193140.7 bcd131173.6 wmc153186.1 cfa2170189.8 cfd62192.7 wmc326201.6 wmc322209.7 wmc169210.9 gwm391237.6 3 Br0.0 Gnu_A30.2 Ba259.7 gwm19272.6 gwm16576.5 cfa225677.9 cfd7180.8 barc10681.4 wmc89 wmc4882.9 gwm61486.9 cfa2173104.9 gwm494118.4 mwg2021b125.3 cdo484125.9 wmc468134.4 Mwg676175.3 4 BE4969030.0 barc18618.1 barc1 wmc150b18.7 cfd4019.3 barc11721.9 gwm44349.0 BE49983559.5 gwm20560.6 gwm15464.3 barc14183.0 gwm18688.0 wmc37194.5 cfd2b96.3 gwm639103.3 barc151120.6 cfd12129.5 gwm271133.6 Psr426139.4 cfd2a144.3 Psr549a147.9 barc124b150.0 cfa2163 barc142153.6 cfa2141154.5 wmc470b158.4 bcd98160.7 KsuG14182.2 cfd39205.3 wmc399206.5 gwm126210.8 gwm6214.4 cfd47225.6 wmc74227.6 5 cfd1900.0 wmc96b1.2 barc371.8 barc11313.0 gwm57026.7 wmc17932.5 gwm101744.0 wmc41746.2 gwm61757.1 gwm42760.1 gwm108963.4 Psr96667.8 Psr687 barc10489.0 6 gwm4710.0 barc7036.2 gwm635 gwm63547.9 cfd3172.5 cfa204993.4 wm6100.8 wmc283 gwm130101.9 barc154103.6 cfa2028106.6 wmc405122.1 wmc58123.8 cfa2174134.9 RC_A138.2 gwm573 wmc17142.5 cfd68145.3 wmc96a149.7 gwm473153.7 barc29163.6 Mwg710c192.0 7
  27. 27. Disease   Genes  Mapped   Leaf  rust  Resistance     Lr_Tm   Stripe  rust  Resistance   QYrtm.pau-­‐2A,  QYrtb.pau-­‐5A     Stem  rust  Resistance   Sr22   Powdery  mildew   resistance   PmTb7A.1  &  PmTb7A.2     Cereal  cyst  nematode   resistance   Qcretm.pau-­‐1A,  Qcretm.pau-­‐2A     R  genes  mapped  on  Tm/Tb  RIL  populaDon  
  28. 28. 14  QTL/genes  mapped  in  T.  boeo$cum/T.  monococcum   RIL  populaDon     Br   7AL  
  29. 29. Summary of Gene transfers from Progenitor and non- progenitor species at PAU Ludhiana Donor Trait Chromosome Gene(s) Ae.  geniculata   (UUMM) Leaf  rust   Stripe  rust 5DS Lr57   Yr40 Ae.  triuncialis     (UUCC) Leaf  rust   Powdery  mildew   Karnal  bunt,  CCN 2BL   5U Lr58 Ae.  umbellulata   (UU) Leaf  rust   Stripe  rust 5DS   5DS   LrU   YrU Ae.  caudata    (CC) Leaf  rust   Stripe  rust 5DS LrC Ae.  variabilis     (UUSS) Leaf  rust   Stripe  rust 2AL   -­‐ LrV   YrV T.  monococcum  &     T.  boeo(cum    (AA) Leaf  rust   Stripe  rust   CCN     Powdery  mildew 6A   2A,  5A   1A,  2A   7A Lr_Tm   QYrtm.pau-­‐2A,  QYrtb.pau-­‐5A   Qcretm.pau-­‐1A,   Qcretm.pau-­‐2A   PmTb7A.1  &  PmTb7A.2 Ae.  tauschii    (DD) Leaf  rust,  stripe  rust   Karnal  bunt 1D,  2D,  6D -­‐ T.  arara(cum     (AAGG) Powdery  mildew   Leaf  rust   Stripe  rust -­‐ -­‐
  30. 30. Challenges..   "   SystemaDc  large  scale  evaluaDon  and  uDlizaDon   of  wild  species   "   Restricted  RecombinaDon   "   Linkage  Drag   "   UDlizing  genomic  advances  for  precision   introgression   "   Acceptance  of  alien  genes  by  breeders  
  31. 31. OpportuniDes   "  Huge  variaDon:  major  proporDon  unuDlized   "  SNP  based  marker  pla`orms  and  sequencing   technologies:  lead  to  beber  germplasm   characterizaDon  and  uDlizaDon   "  Chromosome  engineering:  understanding  Ph1   locus   "  ComparaDve  Genomics   "  Combined  efforts  of  cytogeneDcists,  molecular   biologists  and  breeders  required  for  idenDficaDon,   transfer  and  uDlizaDon  of  alien  genes  
  32. 32. InternaDonal  Collaborators   Bikram  S  Gill,  KSU     Beat  Keller,  IPMB,  Zurich   Harbans  Bariana,  Australia   Cristobal  Uauy,  JIC,  UK   Brande  Wulff,  TSL,  UK                Funding  agencies:     Department  of  Biotechnology,  GOI,   India   USIF,  USA   SDC,  Switzerland   ICAR,  India    BMGF,  USA     Dr  HS  Dhaliwal