Caixia Lan, CIMMYT

1. 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

2. ► Introduction
► PAPR research in CIMMYT
► Breeding for PAPR in wheat
► Future plan
Contents

3. Wheat major diseases
Black (stem) rust
Puccinia graminis
Yellow (stripe) rust
Puccinia striiformis
Brown (leaf) rust
Puccinia triticina
Powdery mildew
Blumeria graminis

4. 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?

5. “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 linesYr9 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/
9*LMPG and
Vernal
Sr13, Sr13+Sr9e ? 2009 TRTTF and
JRCQC
Ethiopia

6. 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)
Lr67
Lr68
Lr46
Lr34
Avocet (susceptible)
Formation of cell wall
appositions (instead of
hypersensitivity with
NBS-LRR type race-
specific genes)

7. Potential PAPR QTLs for rusts
1BS, 2AL, 2BS, 2DL,
5AL, 5BL, 6AL and 7BL

8. 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

9. 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

10. PAPR QTL analysis in Avocet/Francolin#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 45th IBWSN
PVE: 17.8–27.9% PVE: 10.3–21.1%
Lan et al. 2014 Molecular Breeding, DOI: 10.1007/s11032-014-0075-6

11. 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

12. PAPR QTL analysis in Avocet/Kenya Kongoni
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%)
PVE: LR (12-57%) and YR (25-35%) PVE: LR (5-13% ) and YR (10%)

13. Fine mapping
„ Single QTL/gene mapping populations
„ Minor QTL with fixed genetic background
populations
„ Deletion produced by γ-ray

14. 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)

15. MAS in rustGenes 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
Yr41 Xgwm410, Xgwm374 SSR Chuannong 19 Luo et al. 2008
Yr43 Xwgp110, Xwgp103, Xbarc139 RGA, SSR ID0377S Cheng and Chen 2010
Yr44
XpWB5/N1R1, Xwgp100, Xgwm501 RGA, SSR
Zak Cheng and Chen 2010
Yr50
Xgwm540, Xbarc1096, Xwmc47, Xwmc310 SSR
CH223 Liu et al. 2013
Yr60 Xwmc776,Xwmc313,Xwmc219 SSR Lal Bahadur Herrera-Foessel, pers comm

16. Breeding strategy of wheat rusts
Adapted cultivar X Sujata
Adapted cultivarF1 X
(Obregon)
(Batan/Toluca)
BC1 (400-500 plants per cross, MR)(Obregon)
F2 (1000-1600 plants per cross, low to MR)(Batan/Toluca)
Bulk selected
F7 (30-40 lines, yield and quality tests)
F3-F4 (400 plants per cross, grain characteristics )
F5-F6 (60-80 lines per coss, small plot, grain characteristics
(Obregon,Bat
an/Toluca)
Bulk selected
(Batan/Toluca)
(Obregon)
Pedigree
Self-crossing
MAS
Phenotype and
MAS
Breeder for YT
and EYT

17. 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

18. 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

19. Cd. Obregón 39 masl
High yield (irrigated), Water-use
efficiency, Heat tolerance, Leaf rust,
Stem rust (not Ug99)
Toluca 2640 masl
Yellow rust
Septoria tritici
El Batán 2249 masl
Leaf rust, Fusarium
Njoro, Kenya 2185 masl
Stem rust (Ug99 group)
Yellow rust
► Targeted crosses for shuttle breeding made in 2006 and 1st group of populations
planted in Kenya in 2008
► 2000 F3/F4 populations undergo Mexico-Kenya shuttle
► High yielding, resistant lines derived from 1st group of Mexico-Kenya shuttle
distributed worldwide in 2011 and 2012
► Distribution of new materials to continue each year
Njoro, Oct. 2008
Breeding for PAPR in CIMMYT
Mexico (Cd. Obregon-Toluca/El Batan)- Kenya International Shuttle Breeding
A five-year recurrent breeding cycle

20. 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

21. China:
Zhonghu He
Xianchun Xia
Zaifeng Li
Fangping Yang
Garry Rosewarne
Ennian Yang
Jin Feng
Yelun Zhang
Acknowledgements
Collaborators:
Norway:
Morten Lillemo
South Africa
Zakkie Pretorius
Kenya:
Sridhar Bhavani
India:
Arun Kumar Joshi
Donors:
DRRW
Thank you
Global Wheat Program (GWP)