Characterization of pleiotropic adult plant resistance loci to wheat diseases Caixia Lan, Ravi P Singh, Sybil Herrera-Foessel, Julio Huerta-Espino, Bhoja R Basnet, Evans S Lagudah* * CSIRO Plant Industry, Australia
Contents ► Introduction ► PAPR research in CIMMYT ► Breeding for PAPR in wheat ► Future plan
Wheat major diseases Black (stem) rust Yellow (stripe) rust Puccinia graminis Puccinia striiformis Brown (leaf) rust Powdery mildew Puccinia triticina Blumeria graminis
Resistance loci for wheat diseases Seedling resistance gene (race-specific) and adult plant resistance gene (non-race specific) Resistance genes: 72 leaf rust, 63 stripe rust, 58 stem rust and 47 powdery mildew Resistance QTL: 80 for leaf rust, 140 stripe rust, 114 powdery mildew, stem rust?
“Boom-and-Bust”: Race-specific genes Year Variety Resistance genes Released Breakdown Race Country Bread Wheat: Yecora 70 Lr1, 13 1970 1973 ? Mexico Tanori 71 Lr13, 17 1971 1975 ? Mexico Jupateco 73 Lr17, 27+31 1973 1977 TBD/TM Mexico Genaro 81 Lr13, 26 1981 1984 TCB/TB Mexico Seri 82 Lr23, 26 1982 1985 TCB/TD Mexico Baviacora 92 Lr14b, 27+31 1992 1994 MCJ/SP Mexico Lovrin derived lines Yr9 1971-1972 1985 CYR29 China Moro Yr10 ? 2011 ? Canada Milan Yr17 ? 2006 134 E16 A+ Australia Chuanmai 42 Yr24/26 2004 2010 V26 China Opata 85 Yr27 1985 1996 Mex96.11 Mexico Pastor Yr31 ? 2008 Mex08.13 Mexico Lovrin 10 Pm8 1970s 1990-1991 ? China Kavkaz Sr31 1980s 1998 Ug99 Uganda Durum Wheat: Altar 84 Lr72 1984 2001 BBG/BN Mexico Jupare 2001 Lr72, 27+31 2001 2007 BBG/BP Mexico Khapstein/ Sr13, Sr13+Sr9e ? 2009 TRTTF and Ethiopia 9*LMPG and JRCQC Vernal
Pleiotropic adult plant resistance (PAPR) genes Lr34 [Syn.= Yr18 = Sr57 = Pm38 = Ltn1=Sb1=Bdv1 ] chromosome 7DS (leaf rust, yellow rust, stem rust, powdery mildew, leaf tip necrosis, spot blotch, barley yellow dwarf virus ) Lr46 [Syn.= Yr29 = Sr58 = Pm39 = Ltn2=Ts? ] chromosome 1BL Lr67 [Syn.= Yr46 = Sr55 = Pm46 = Ltn3 ] chromosome 4DL Lr68 [yellow rust, powdery mildew and stem rust?] chromosome 7BL Yr54 [leaf rust, powdery mildew and stem rust?] chromosome 2DL Apav (susceptible) Formation of cell wall appositions (instead of Lr67 hypersensitivity with Lr68 NBS-LRR type race- Lr46 specific genes) Lr34 Avocet (susceptible)
Potential PAPR QTLs for rusts 1BS, 2AL, 2BS, 2DL, 5AL, 5BL, 6AL and 7BL
CIMMYT PAPR research ► Norman Borlaug, 1950s ► Goes back to mid. 1970s and initiated by Sanjay Rajaram (breeder) and Jesse Dubin (pathologist) ► Late 1980s: Breeding strategy to develop high yielding varieties with near-immune resistance ► Early 2000s: Genetics and mapping of resistance genes
PAPR QTL analysis in Avocet/Sujata PVEs: QYL.cim-1AS explained 10.5-13.8% and 7.9-8.2% of stripe rust and leaf rust, respectively; QYL.cim-7BL explained 16.6-20.4% and 5.7-13.0% of for stripe rust and leaf rust, respectively Lr46 / Yr29 and Lr67/Yr46 were also mapped in the population
PAPR QTL analysis in Avocet/Francolin#1 PVE: 17.8–27.9% PVE: 10.3–21.1% ► Additional QTL have been detected on 1BL ( Lr46/ Yr29 ), 3BS ( LR/Yr30 ) and 7DS (PVE:3.3-4.2 for LR) ► Flanking makers to Lr16 and YrF can be used in MAS based on testing in 350 lines from 45 th IBWSN Lan et al. 2014 Molecular Breeding, DOI: 10.1007/s11032-014-0075-6
PAPR QTL analysis in Avocet/Quaiu #3 ► QYr.tam-2D, explained 49-64% of total phenotypic variation and was designated as Yr54 ► QYLr.tam-3D explained up to 6 and 7% of the phenotypic variance, respectively ► Known resistance genes Lr46/Yr29, Sr2/Yr30 and Lr42 Basnet et al. 2014 Molecular Breeding 33 (2):385-399
PAPR QTL analysis in Avocet/Kenya Kongoni PVE: LR (12-57%) and YR (25-35%) PVE: LR (5-13% ) and YR (10%) LR: QLr.cim-1DS ( Lr42 , 6-21%), QLr.cim-2BL (20% in BV2011) and QLr.cim-3BS (5-10%) YR: QYr.cim-2BS (7-12%) and QYr.cim-5BL (6-8%)
Fine mapping Single QTL/gene mapping populations Minor QTL with fixed genetic background populations Deletion produced by γ -ray
Identification of deletion mutants for Lr67/ Yr46/Sr55/Pm46 ► Mutagenesis by gamma-irradiation using a 60 Co source at ININ, Mexico. ► 4000 seed radiated ► Grow M1, individually harvest plants ► Grow M2 (2000 lines, 20 space planted plants/M2), identify susceptible, harvest… ► M3, M4 plots ► 1 mutant was 15 bp deletion (M55), 1 mutant was 3bp deletion (M157) and 3 mutants were complete deletion of Lr67 (M87, M147, M168)
MAS in rust Genes Markers Type Cultivar Reference PAPR genes Lr34/Yr18/Pm38/Sr57 Lr34SNP STS, SNP Parula Lagudah et al., 2009 Lr46/Yr29/Pm39/Sr58 csLv46 CAPS Pavon 76 Lagudah ES, pers comm Lr46/Yr29/Pm39/Sr58 csLV46G22 CAPS not in Parula Lagudah ES, pers comm Lr67/Yr46/Pm46/Sr55 Lr67SNP SNP RL6077 Lagudah ES, pers comm Lr68 CSGS, cs7BLNLRR CAPS Parula Herrera-Foessel et al. 2012 Sr2/Yr30 csSr2 CAPS Pavon76 Mago et al. 2011 Sr2/Yr30/Lr? gwm533 SSR Quaiu#3 Basnet et al. 2014 Yr54 Xgwm301 SSR Quaiu#3 Basnet et al. 2014 HTAP genes Yr36 Gpc-B1 Glupro, ND?? Uauy et al. 2006 Yr39 Xwgp36, Xwgp45, Xgwm18, Xgwm11 RGA, SSR Alpowa Lin and Chen, 2007 Yr52 Xbarc182, Xwgp5258 RGA, SSR PI 183527 Ren et al. 2012 Yr59 Xwgp5175, Xbac32, Xbac182 RGA, SSR PI 178759, PI 660061 Chen XM, pers comm Seedling genes Lr16 Xgwm210, Xwmc661 SSR Francolin#1 Lan et al. 2014 Lr19/Sr25 Psy1Da-g_SNP, PSY-E SNP, SSR Misr#1 Lr21 D14 Talbert et al. 1994 Lr42 cfd15, wmc432 SSR Quaiu#3 Basnet et al. 2014 Lr47 PS10R/ PS10L, PS10R/PS10L2 Helguera et al. 2000 Lr51 S30-13L/AGA7-759R Helguera et al. 2005 Yr17 VENTRIU/LN2, URIC/LN2 Milan Helguera et al. 2003 Yr24/26 CYD15, Xgwm11 Chuanmai 42 Zakari et al. 2003 Xgwm410, Xgwm374 SSR Yr41 Chuannong 19 Luo et al. 2008 Xwgp110, Xwgp103, Xbarc139 RGA, SSR Yr43 ID0377S Cheng and Chen 2010 XpWB5/N1R1, Xwgp100, Xgwm501 RGA, SSR Yr44 Zak Cheng and Chen 2010 Xgwm540, Xbarc1096, Xwmc47, Xwmc310 SSR Yr50 CH223 Liu et al. 2013 Yr60 Xwmc776,Xwmc313,Xwmc219 SSR Lal Bahadur Herrera-Foessel, pers comm
Breeding strategy of wheat rusts (Obregon) Adapted cultivar Sujata X F1 Adapted cultivar (Batan/Toluca) X BC1 (400-500 plants per cross, MR) (Obregon) MAS Bulk selected (Batan/Toluca) F2 (1000-1600 plants per cross, low to MR) Phenotype and Bulk selected MAS (Obregon,Bat F3-F4 (400 plants per cross, grain characteristics ) an/Toluca) Pedigree Breeder for YT and EYT F5-F6 (60-80 lines per coss, small plot, grain characteristics (Batan/Toluca) Self-crossing F7 (30-40 lines, yield and quality tests) (Obregon)
Why do we use PAPR in breeding? ► Leads to resistance durability- good for farmers and donors’ investment ► Genes have pleiotropic genetic control on rusts, powdery mildew and some other diseases ► Field based selection simultaneously with other traits increases high genetic gains for multiple traits
Utilization of PAPR genes in breeding: challenges ► Small to intermediate effects of individual genes ► Dispersed presence of genes in different cultivars and germplasm ► Field selection environment lacking uniform and high disease pressure ► Need for growing larger population sizes for selection ► Difficulty in distinguishing small effect race-specific genes from slow rusting genes (especially for resistance to yellow rust) ► Higher G x E interaction on the expression and effectiveness of genes Despite numerous challenges, significant progress was made at CIMMYT for resistance to all three rusts
Breeding for PAPR in CIMMYT Mexico (Cd. Obregon-Toluca/El Batan)- Kenya International Shuttle Breeding A five-year recurrent breeding cycle Njoro, Oct. 2008 Cd. Obregón 39 masl High yield (irrigated), Water-use efficiency, Heat tolerance, Leaf rust, Stem rust (not Ug99) Njoro, Kenya 2185 masl El Batán 2249 masl Stem rust (Ug99 group) Leaf rust, Fusarium Yellow rust Toluca 2640 masl Yellow rust Septoria tritici ► Targeted crosses for shuttle breeding made in 2006 and 1 st group of populations planted in Kenya in 2008 ► 2000 F3/F4 populations undergo Mexico-Kenya shuttle ► High yielding, resistant lines derived from 1 st group of Mexico-Kenya shuttle distributed worldwide in 2011 and 2012 ► Distribution of new materials to continue each year
Future plan ► New PAPR gene discovery in bi-parental and association mapping panels ► Fine mapping and cloning genes Lr68 , Yr54 , YrF , YrSuj , SrND643 and SrSHA7/SrHaril, and QTL on 1AS and 3DC ► Understanding the PAPR gene mechanism ► PAPR gene pyramiding and marker assistant selection in wheat breeding
Acknowledgements Donors: Collaborators: Norway: China: Morten Lillemo Zhonghu He Xianchun Xia Thank you South Africa Zaifeng Li Zakkie Pretorius Fangping Yang Kenya: Garry Rosewarne Sridhar Bhavani Ennian Yang Jin Feng India: Yelun Zhang DRRW Arun Kumar Joshi Global Wheat Program (GWP)
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