Wild Tricum and 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 Gene Pools

Terary gene pool all non-progenitor diploid & tetraploid species Secondary gene pool

tetraploid species with one genome s common with Primary gene pool wheat diploid S-genome species from Aegilops secon Sitopsis

v all diploid and tetraploid Tricum & Aegilops species with A, B, & D genomes v landraces, early domescates v wild species that hybridize directly with the culvated Progenitor Species

Leaf rust Stripe rust Leaf rust Stem rust Stripe rust Leaf rust Foliar blights Stem rust Stripe rust Stay Green Powdery mildew Stem rust Anther Extrusion Powdery mildew Grain size Karnal bunt Spike size Grain size Grain micronutrient Thermotolerance Ae. speltoides (SS) Aphid Resistance ?? T. monococcum (AA) Ae. tauschii (DD) Leaf rust Stripe rust Stem rust Leaf rust Powdery mildew Stripe rust Grain protein Powdery mildew Grain size Grain micronutrient

T. dicoccoides (AABB)

T. araracum (AAGG) Non-progenitor species

Leaf rust Leaf rust Stripe rust Stripe rust Powdery mildew Leaf rust Stem rust Karnal bunt Stripe rust Thermotolerance Thermotolerance Grain micronutrient Thermotolerance

Ae. triuncialis (UUCC)

Leaf rust Stripe rust Ae. geniculata (UM) Ae. variabilis (US) Grain micronutrient

Ae. kotschyi (US) Wild wheat germplasm at PAU, Ludhiana

Species Genome Total Aegilops tauschii DD 270 Tricum boeocum AbAb 70 Tricum monococcum AmAm 60 Aegilops speltoides SS 140 other S genome species SS 20 Tricum dicoccoides AABB 120 Tricum araracum 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 Variability for rust resistance in different wild species

Species Acc. Seedling Reacon Leaf Rust Stripe Rust 77 77-1 77-2 104-1 K M Ae. 3514 R R R R S S geniculata 3547 R R R R R S 3565 R R R R S S 5507 R R - - R R Ae. 3549 R R R R R S triuncialis 3621 - R R R R R 3669 S R S R S R Ae. 3770 S R R R R R longissima 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

Level of genec diversity in Ae. tauschii

Cluster I-ssp strangulata 3750-S894-S 3823-S14323-S3751-S9794-S 9821-S 9793-S 14577-S 9807-S 9804-S 14318-T 9385-T 3769-S 14337-S9826-S 3760-S9809-S 5514-S 14175-S 3786-S 14165-S14163-T 3761-S9824-T 56 61 3758-S 14122-T 14361-S9791-S14330-S 100 99 14576-S14336-S14344-S 100 73 9795-T 3757-S 14333-S14335-S 14339-S 3426 100 8225 47 71 31 60 35 26 42 14180-S 61 9790-S 21 14109-S 63 42 14183-T 94 42 55 29 9796-S 9799-S 84 3738-T 100 14173-S 96

PBW343 67 WH542 3759-T 30

36 2871 83 14195-T 14171-S 14102-S 62 42 5933 14164-T 83 99 14192-T 99 51 14189-T 100 9830-S 14199-T 9827-T 3826-T 13757-T 14342-S 93 14240-S 14236-T14233-T

14219-T 14198-T 14106-T 3743-S 9787-S 14350-T14351-T 9785-T14245-T14251-T 14334-S 14197-T 14354-T 3753-T 14091-S 3472-T 13764-T 9810-S14578-T14159-S3805-S3822-S 14331-S 0 0.2 Cluster II-ssp. tauschii & strangulata Stripe rust reacon of Ae. tauschii accessions at adult stage Level of genec diversity in Ae. speltoides

TA1787 TA1788 TA1845 TA1778 TA1793 3583 3596 TA1792TA1786 TA1772 TA2357 402471 TA1781 3638 TA1791TA1770 3605 3599 3607 3604 3804 3591 3602 3585 3637 3590 3608 3598 3574 Ae. speltoides (SS) 3635 3592 3603 3601 3809 3809 TA1776 3579 3808 3580 3575 3593 3581 3571 3578 3566 TA1784 3595 3584 PBW343

PBW550 3582

PDW233PDW274Aconchi89PDW291 0 0.2

Stripe rust reacon of Ae. speltoides accessions at adult plant stage T. monococcum T. boeocum 70 45 40 60 35 50 30 40 25 30

20 Accession Accessions 15 20 10 10 5 0 0 0 TR 20MR 20S 0 TR 5MR 10MR 20MR 40S-60S Reacon Type Reacon type

T. dicoccoides NON PROGENITOR SPECIES 60 40

Accessions 20 0

Reacon type Ulizaon of wild species in wheat for disease resistance

Disease Total genes From alien sources catalogued

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 mulple diseases A genome species: source of mulple resistance 5M chromosome of Ae. geniculata acc. pau3547 have genes for leaf rust, stripe rust and stem rust resistance

Lr57 Yr40 Lr57 Lr57 Sr53 Yr40 Yr40 Sr53 in spontaneous translocaon stocks with reduced alien chroman - Liu et al. 2011

BS Gill, WGGRC 5US chromosome of Ae. umbellulata carries closely linked leaf rust and stripe rust resistance genes

Disease RILs Stripe rust Total HR H HS Leaf HR 113 7 3 123 rust H 0 11 1 12 HS 0 1 106 107 Total 113 19 110 242

5DS PBW343 WL711 IL373 IL403 Resistant RILs 0.0 *YrU Suscepble RILs 0.7 *LrU

4.6 *Lr57-Yr40CAPS Leaf rust reacon in the mapping populaon

9.1 *Xgwm190

32.8 *Xwmc805c 5CS chromosome of Ae. caudata carries closely linked leaf rust and stripe rust resistance genes

Stage Resistant Susceptible Total 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

Lr57-Yr40 LrU5DS, YrU LrC, YrC

0.0 *YrU Lr57/Yr40 0.7 *LrU 4.6 *Lr57-Yr40CAPS

9.1 *Xgwm190

32.8 *Xwmc805c

Ae. geniculata Ae. umbellulata Ae. caudata Single Accession of Ae. triuncialis acc. pau 3549 carries two leaf rust, powdery mildew, CCN and KB resistance genes

Wheat-Ae. triuncialis substitution line-DS5U(5A) 5U chromosome carries genes for A leaf rust resistance-slow rusng A powdery mildew resistance gene A CCN resistance gene Ae. triuncialis addition line for chromosome 2U/2C: KB, leaf rust and powdery mildew resistance

WL711 AT 2205 2238 2288 2291

Derivative Mean KB KB Range Leaf rust Powdery ID % 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

AT PBW343 2288 BC1F3 A Wheat-Ae. triuncialis spontaneous translocation carries Lr58

Lr58 A-genome Tricum species: Mulple disease resistance Triticum boeoticum/ T. monococcum RIL population

Leaf rust resistance

Stripe rust resistance Stem rust resistance

Karnal bunt resistance

cyst nematode resistance

Powdery mildew resistance

Single vs two seeds per

Many Agronomic traits Disease resistance gene segregaon in T. boeocum/T. monococcum RILs

Disease Reacon in Segregaon in RILs Culvated parental accession Germplasm Leaf rust Both parents No segregaon; WL711, PBW343 Resistance resistant Both parents have same gene (s) Stripe rust Both parents Two gene; WL711, PBW343 Resistance resistant One gene from each parent Stem rust Both parents No segregaon; WL711 Resistance resistant Both parents have Sr22 Powdery mildew T. boeocum Two genes; PBW343 resistance resistant Both genes from Tb Cereal cyst T. monococcum Two genes; 4x & 6x background nematode resistant Both genes from resistance Tm Linkage map of A genome of T. monococcum T. boeoticum/T. monococcum likage map based on 200 markers

1 2 3 4 5 6 7

0.0 BE489323 0.0 Mwg851 0.0 wmc147 0.0 Br 0.0 BE496903 0.0 cfd190 0.0 gwm471 GluAlmw KsuD18 wmc96b 13.3 18.5 18.1 barc186 1.2 35.3 bcd130 19.6 BE498358 barc1 1.8 barc37 50.2 gdm33 23.6 wmc382 21.4 gwm757 18.7 wmc150b 13.0 barc113 55.4 gwm33 25.1 barc124a 25.1 barc57 19.3 cfd40 26.7 gwm570 56.7 cfd58 33.9 gwm636 Gnu_A 33.6 barc12 30.2 21.9 barc117 32.5 wmc179 61.1 gwm136 52.3 Psr666 34.3 wmc11 36.2 barc70 63.2 cfa2153 Psr108 44.0 gwm1017 57.8 gwm635 66.8 BE444890 wmc177 46.2 wmc417 50.5 cfd79 49.0 gwm443 47.9 gwm635 Mwg710b fba198 57.1 gwm617 67.3 58.7 54.7 gwm369 59.5 BE499835 Psr549b fba178 Ba2 60.1 gwm427 59.7 60.6 gwm205 67.8 mwg2021a 60.6 wmc264 barc218 63.4 gwm1089 67.6 64.3 gwm154 74.1 gwm1104 68.5 fba272 72.6 gwm192 Psr966 68.9 gwm779 67.8 72.5 cfd31 BE442682 81.2 BE497494 76.5 gwm165 83.0 barc141 76.7 78.0 wmc150a barc204 84.9 BE499478 77.9 cfa2256 88.0 gwm186 93.4 cfa2049 81.7 BE499835 87.5 gwm275 98.0 wmc79 80.8 cfd71 94.5 wmc371 Psr687 89.0 100.8 wm6 cfa2158 BE406808 98.6 barc19 81.4 barc106 96.3 cfd2b barc104 86.0 90.1 wmc283 cfd21 wmc474 98.9 barc67 wmc89 103.3 gwm639 82.9 101.9 gwm130 88.3 BE443401 BE406584 99.2 wmc269 wmc48 120.6 barc151 91.3 103.6 barc154 91.2 BE443103 gwm515 105.5 cfa2134 86.9 gwm614 129.5 cfd12 106.6 cfa2028 94.1 BE591682 gwm1011 106.6 Psr570 104.9 cfa2173 133.6 gwm271 122.1 wmc405 96.4 gwm391 gwm1045 108.6 gwm1121 118.4 gwm494 139.4 Psr426 123.8 wmc58 100.0 BE495292 94.7 BE406923 117.0 Psr74 125.3 mwg2021b 144.3 cfd2a 134.9 cfa2174 109.8 barc9 gwm71 119.5 wmc492 125.9 cdo484 147.9 Psr549a 138.2 RC_A 124.6 gdm36 cfd26 135.2 barc152 134.4 wmc468 150.0 barc124b gwm573 146.1 wmc475 95.9 wmc420 137.5 wmc96c cfa2163 153.6 142.5 wmc17 cfd65 BE425962 140.7 cfa2193 barc142 117.6 145.3 cfd68 155.1 cfd59 Psr630 154.5 cfa2141 149.7 wmc96a cfd83 119.5 barc5 158.4 wmc470b 153.7 gwm473 cfa2135 129.1 Psr681 160.7 bcd98 159.4 163.6 barc29 wmc470a 129.5 Psr933 173.6 bcd131 175.3 Mwg676 164.5 gwm135 129.7 wmc407 wmc153 182.2 KsuG14 173.1 GluAy wmc170 186.1 133.3 cfa2170 Psr331 189.8 192.0 Mwg710c cfd62 134.4 fba374 192.7 wmc326 140.9 gwm30 201.6 205.3 cfd39 wmc322 152.3 Psr540 209.7 206.5 wmc399 BE443103 wmc169 213.0 165.8 cfd267 210.9 210.8 gwm126 199.1 cfd223 214.4 gwm6 225.6 cfd47 227.6 wmc74 237.6 gwm391 R genes mapped on Tm/Tb RIL populaon

Disease Genes Mapped

Leaf rust Resistance Lr_Tm

Stripe rust Resistance QYrtm.pau-2A, QYrtb.pau-5A

Stem rust Resistance Sr22

Powdery mildew PmTb7A.1 & PmTb7A.2 resistance

Cereal cyst nematode Qcretm.pau-1A, Qcretm.pau-2A resistance 14 QTL/genes mapped in T. boeocum/T. monococcum RIL populaon

7AL

Br Summary of Gene transfers from Progenitor and non- progenitor species at PAU Ludhiana Donor Trait Chromosome Gene(s) Ae. geniculata Leaf rust 5DS Lr57 (UUMM) Stripe rust Yr40

Ae. triuncialis Leaf rust 2BL Lr58 (UUCC) Powdery mildew 5U Karnal bunt, CCN Ae. umbellulata Leaf rust 5DS LrU (UU) Stripe rust 5DS YrU Ae. caudata (CC) Leaf rust 5DS LrC Stripe rust Ae. variabilis Leaf rust 2AL LrV (UUSS) Stripe rust - YrV T. monococcum & Leaf rust 6A Lr_Tm T. boeocum Stripe rust 2A, 5A QYrtm.pau-2A, QYrtb.pau-5A (AA) CCN 1A, 2A Qcretm.pau-1A, Powdery mildew 7A Qcretm.pau-2A PmTb7A.1 & PmTb7A.2 Ae. tauschii (DD) Leaf rust, stripe rust 1D, 2D, 6D - Karnal bunt T. araracum Powdery mildew - - (AAGG) Leaf rust Stripe rust Challenges..

Systemac large scale evaluaon and ulizaon of wild species Restricted Recombinaon Linkage Drag Ulizing genomic advances for precision introgression Acceptance of alien genes by breeders Opportunies

Huge variaon: major proporon unulized SNP based marker plaorms and sequencing technologies: lead to beer germplasm characterizaon and ulizaon Chromosome engineering: understanding Ph1 locus Comparave Genomics Combined efforts of cytogenecists, molecular biologists and breeders required for idenficaon, transfer and ulizaon of alien genes Internaonal Collaborators Bikram S Gill, KSU Beat Keller, IPMB, Zurich Harbans Bariana, Australia Cristobal Uauy, JIC, UK Brande Wulff, TSL, UK Dr HS Dhaliwal

Funding agencies: Department of Biotechnology, GOI, India USIF, USA SDC, Switzerland ICAR, India BMGF, USA