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  

Phylogeny of Triticum and Aegilops species

BS  Gill,  WGGRC  

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  

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  ??  

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  

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  

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

Variability  for  rust  resistance  in  wild  wheats  

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

Stripe  rust  reacDon  of  Ae.  tauschii  accessions  at  adult  plant  stage  

0 0.2

PB W343WH 542

894-­‐S

3472-­‐T

3738-­‐T

3743-­‐S

3750-­‐S3751-­‐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-­‐T9787-­‐S

9790-­‐S

9791-­‐S

9793-­‐S9794-­‐S

9795-­‐T

9796-­‐S9799-­‐S

9804-­‐S9807-­‐S

9809-­‐S

9810-­‐S

9821-­‐S

9824-­‐T

9826-­‐S

9827-­‐T9830-­‐S13757-­‐T

13764-­‐T14091-­‐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-­‐S14336-­‐S

14337-­‐S

14339-­‐S

14342-­‐S

14344-­‐S

14350-­‐T14351-­‐T14354-­‐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

4261

94

100

47

26

99

71

96

42

100

8336

67

28

5142

347182

99

93

31

29

26

60

55

21

Cluster I-ssp strangulata

Cluster II-ssp. tauschii & strangulata

Level  of  geneDc  diversity  in  Ae.  tauschii    

Ae. speltoides (SS)

0 0.2PDW233PDW291PDW274Ac onc hi89

P BW343

PBW550

3566

3595

3601

36033635

3808

38093809

TA1784

3571

3574

3575

3578

357935803581

3582

3583

3584

3585

3590

3591

3592

3593

3596

3598

3599

3602

3604

3605

3607

36083637

3638

3804

402471TA1770

TA1772

TA1776

TA1778

TA1781

TA1786

TA1787

TA1788

TA1791

TA1792TA1793TA1845

TA2357

Level  of  geneDc  diversity  in  Ae.  speltoides    

Stripe  rust  reacDon  of  Ae.  speltoides  accessions  at  adult  plant  stage  

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  

 

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  

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  

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

BS  Gill,  WGGRC  

Sr53  in  spontaneous  translocaDon  stocks  with  reduced  alien  chromaDn  -­‐  Liu  et  al.  2011  

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  PBW

343  

WL711   SuscepDble  RILs  

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  

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  

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  

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  

A Wheat-Ae. triuncialis spontaneous translocation

carries Lr58

Lr58

A-­‐genome  Tri(cum  species:  MulDple  disease  resistance  

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    

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  

Linkage  map  of  A  genome  of  T.  monococcum    T. boeoticum/T. monococcum likage map based on 200 markers

BE4893230.0GluAlmw13.3bcd13035.3gdm3350.2gwm3355.4cfd5856.7gwm13661.1cfa215363.2BE44489066.8Mwg710bPsr549b67.3

mwg2021a67.8gwm110474.1BE442682barc20476.7

BE49983581.7cfa2158cfd2186.0

BE44340188.3BE44310391.2BE59168294.1gwm39196.4BE495292100.0barc9109.8gdm36124.6wmc475146.1cfd65cfd59cfd83

155.1

cfa2135wmc470a159.4

gwm135164.5GluAy173.1

BE443103213.0

1

Mwg8510.0KsuD1818.5BE49835819.6wmc38223.6barc124a25.1gwm63633.9Psr66652.3Psr108wmc17757.8

fba198fba17858.7

wmc26460.6fba27268.5BE49749481.2BE49947884.9gwm27587.5BE406808wmc47490.1

BE406584gwm51591.3

gwm1011gwm1045BE406923gwm71cfd26

94.7

wmc42095.9BE425962Psr630117.6

barc5119.5Psr681129.1Psr933129.5wmc407129.7wmc170Psr331133.3

fba374134.4gwm30140.9Psr540152.3cfd267165.8cfd223199.1

2

wmc1470.0

gwm75721.4barc5725.1barc1233.6wmc1134.3

cfd7950.5gwm36954.7

barc21867.6gwm77968.9wmc150a78.0

wmc7998.0barc1998.6barc6798.9wmc26999.2cfa2134105.5Psr570106.6gwm1121108.6Psr74117.0wmc492119.5barc152135.2wmc96c137.5cfa2193140.7

bcd131173.6

wmc153186.1cfa2170189.8cfd62192.7wmc326201.6wmc322209.7wmc169210.9

gwm391237.6

3

Br0.0

Gnu_A30.2

Ba259.7

gwm19272.6gwm16576.5cfa225677.9cfd7180.8barc10681.4wmc89wmc4882.9

gwm61486.9cfa2173104.9gwm494118.4mwg2021b125.3cdo484125.9wmc468134.4

Mwg676175.3

4

BE4969030.0barc18618.1barc1wmc150b18.7

cfd4019.3barc11721.9

gwm44349.0BE49983559.5gwm20560.6gwm15464.3barc14183.0gwm18688.0wmc37194.5cfd2b96.3gwm639103.3barc151120.6cfd12129.5gwm271133.6Psr426139.4cfd2a144.3Psr549a147.9barc124b150.0cfa2163barc142153.6

cfa2141154.5wmc470b158.4bcd98160.7

KsuG14182.2

cfd39205.3wmc399206.5gwm126210.8gwm6214.4cfd47225.6wmc74227.6

5

cfd1900.0wmc96b1.2barc371.8barc11313.0

gwm57026.7wmc17932.5

gwm101744.0wmc41746.2gwm61757.1gwm42760.1gwm108963.4Psr96667.8

Psr687barc10489.0

6

gwm4710.0

barc7036.2

gwm635gwm63547.9

cfd3172.5

cfa204993.4wm6100.8wmc283gwm130101.9

barc154103.6cfa2028106.6wmc405122.1wmc58123.8cfa2174134.9RC_A138.2gwm573wmc17142.5

cfd68145.3wmc96a149.7gwm473153.7barc29163.6

Mwg710c192.0

7

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  

14  QTL/genes  mapped  in  T.  boeo$cum/T.  monococcum  RIL  populaDon    

Br  

7AL  

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

-­‐ -­‐

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  

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  

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