Francis Ogbonnaya, ICARDA

1. Diversity of Yellow Rust Resistance: Inferences
from GWAS in some elite wheat germplasm
Francis C. Ogbonnaya
BGRI Meeting, St. Paul,
Minnesota, June 13-18, 2010

2. Acknowledgments
Funding Agencies Colleagues and collaborators
 ICARDA
 K. Nazari (ICARDA)
 A. Jighly (ICARDA)
 O. Abdalla & Izzat Tahir (ICARDA)
 A. Yahyaoui (ICARDA-CIMMYT)
 Wuletaw Tadesse (ICARDA)
 Aleppo University
 F. Makdis (Aleppo University)
• GCSAR
 O. Youssef (GCSAR)
 E. Essa (GCSAR)
Organizers of BGRI 2011 workshop

3. Wheat yellow (stripe) rust
P uccinia striiform is fsp tritici
Most common and
widespread rust disease of
wheat
Yield losses (10-80%) in CWANA
Est. value of crop loss could reach > 1 billion USD.
BGRI workshop
Courtesy: S. Rajaram and A. Yahyaou, 2011 St. Paul, MN June, 2011

4. Stripe Rust Summary - 2010
Uzbekistan: worse
Bulgaria: “First than 2009 – all
outbreaks in 20 varieties
years” susceptible.
extensive chemica
Turkey: Severe in
control (x3 sprays
south-east. USDA
estimating
1M ton losses
Syria: Estimates of 300,00 ha
affected.
USDA: Possible 1.25M ton losses
Iraq: Estimated 10-15% yield Ethiopia: Over 400,000
losses in north ha affected. Losses??
BGRI workshop
Courtesy: Dave Hudson, April 2011 St. Paul, MN June, 2011

5. Yellow rust epidemics 2010:farmers paddock
Hassakieh yellow rust April 2010
• With no timely fungicide losses estimated at more than 80%
BGRI workshop
• Harvest from 6-7 tons/hectares to less than 1 ton/hectare
St. Paul, MN June, 2011

6. Resistance Sources – How diverse and what genes?
TH_2011
47 %
17.5% 21%
14.5%
S MS MR R
Mal_2010
45.5%
22% 17.5% 15%
S MS MR R
The frequency of elite lines under different yellow rust severity
classes at Tel-Hadya and Malkiyeh in 2011 and 2010

7. Resistance Sources – How diverse and what genes?
31%
The frequency of elite lines under different yellow rust
severity classes at seedling and adult plant growth stages
BGRI workshop
St. Paul, MN June, 2011

8. Summary of Yr genes
Chromosome Genes Chromo. Count
1A YrDa1 1
2A Yr1, Yr8, Yr17, Yr32 4
3A YrTr2 1
4A YrHVII, YrMin, YrND 3
5A Yr34, Yr48 2
6A Yr42, YrD,YrDru2,YrH46 4
7A - 0
Yr9, Yr10, Yr15, Yr21, Yr24, Yr26, Yr29, YrC143, YrAlp, YrH52, YrExp1,
1B 13
YrR212, YrCN17
Yr5, Yr7, Yr27, Yr31, Yr41, Yr43, Yr44, YrCn19, YrZak, YrV23, YrSte,
2B 14
YrP81, YrS2199, YrSP
3B Yr4, Yr30, YrS, YrSte2, Yrns-B1 5
4B YrCle, YrMor, YrYam 3
5B Yr3, Yr19, Yr47, YrDru, YrExp2 5
6B Yr35, Yr36 2
7B Yr2,Yr6, Yr39, YrC591, YrZH84 5
1D Yr25 1
2D Yr16, Yr37, YrCK 3
3D Yr45 1
4D Yr22,Yr28,Yr46,YrAS2388 4
5D Yr40,YrDa2 2
6D Yr20, Yr23, YrTye, YrTr1 4
7D Yr18,Yr33 2
Total 79

9. Recently reported sources and linked markers
Gene Chromo. Sources Linked markers Ref.
Avalon, Bolac, Emu S, Rubric Bansal et al.
Yr4 3BS Xcfb3530
AUS33333 (Bread wheat) 2010
PI 591045, Lolo, many IDO377s Cheng and Chen
Yr43 2BL Xwgp110, Xwgp113
derivatives (Spring Wheat) 2009
Yr44 2BL PI 607839 (Spring Wheat) Xwgp100 Sui et al. 2009
Yr45 3DL PI 181434 (Spring Wheat) Xwp115, Xwp118 Li et al. 2010
Herrera-Foessel
Yr46 4D PI 250413 (common wheat) Xcfd71, Xbarc98
et al. 2009
5 2 cM proximal to Bansal U et al.
Yr47 5BS AUS28183 (common wheat)
Lr52 2011
Dubcovsky 2010;
Yr48 5AL PI 610750 (Bread wheat) Xwms291
Lowe et al. 2011
BGRI workshop
St. Paul, MN June, 2011

10. Association mapping
Objective is to detect correlations between genotypes and
phenotypes in a set of unrelated individuals from natural
populations on the basis of linkage disequilibrium
Advantages over biparental mapping
No news crosses
variation for many phenotypic traits, thus several traits
can be studied in the same population using same genotype
much higher mapping resolution - recombination
reduces association between a QTL and distant markers
A higher proportion of molecular markers likely to be
polymorphic because of better genome coverage
A. Rafaselski, 2002

11. Association Mapping (AM)
Plant material:
200 elite germplasm mostly of ICARDA origin, synthetic
derivatives and some Australian cultivars
Phenotyping:
Data from yellow rust screening in 2010 and 2011
Genotyping:
Triticarte Pty Ltd (http://www.triticarte.com.au)
2688 polymorphic DArT markers plus 42 SSR and STS markers
linked to various Yr gene
Statistics:
STRUCTURE (Pritchard et al. 2000) - population structure
Tassel 2.0.1 (Bradbury et al. 2007) - marker/trait association:
General Linear Model (GLM) and Mixed Linear Model (MLM)

12. Of the 2688 polymorphic DArT markers:
42 SSR markers
DArT loci with known
map position 372 Simple Sequence
Repeats
Markers for A genome = 141 covered 576.91 CM
Markers for B genome = 181 covered 854.60 CM
Markers for D genome = 50 covered 289.05 CM
Total 1720.55 CM
Chromosome 4A 43 Markers
DArT marker density varied amongst chromosomes from less
than 5cM to more than 25cM between markers. However, LD
is within the range reported in literature at about 20cM

13. Population structure
K =11
Ln P(D)
1 2 3 4 5 6 7 8 9 10 11
The population structure was calculated using 50 unlinked markers

14. Model Results
Model No of markers associated with Yr at p<0.05 R2
GLM 913 2 to 24%
GLM + Q 397 1 to 10%
MLM + Q + K 167 3 to 14 %
125 DArT markers were assigned to several chromosome regions
while 42 were unmapped
BGRI workshop
St. Paul, MN June, 2011

15. DArT Markers with Chromosome Effects
A B D
1
2
3
4
5
6
7
Loci on 1B, 1D, 2B, 2D, 3B, 4A, 6B, 6D and 7D were identified at P ≤ 0.00001 with R2 from 5 to 14%

16. MLM-Q
Marker Chr. P-value R2 Chromosome arm References
wPt-3870 1A 0.0052 5.27 1AS Crossa et al 2007; Francki et al 2009
wPt-5678 1B 0.0477 3.05 1BS Crossa et al 2007 - Yr9, -10, -24, -26
wPt-3465 1B 0.0235 3.79 1BS Crossa et al 2007 - Yr9, -10, -24, -26
wPt-4916 2B 0.0042 5.49 2BS Crossa et al 2007 - Yr27, -31
wPt-1489 2B 0.0462 3.05 2BS Crossa et al 2007 - Yr27, -31; Lowe et al 2011
wPt-7757 2B 0.0153 4.22 2BS Crossa et al 2007 - Yr27, -31
wPt-9402 2B 0.0401 3.19 2BS Crossa et al 2007 - Yr27, -31
wPt-9423 2B 0.0482 3.04 2BS Lowe et al 2011;
wPt-9350 2B 0.0098 3.12 2BL* Crossa et al 2007 - Yr5, -7; Lowe et al 2011
wPt-7350 2B 0.0041 3.70 2BL* Crossa et al 2007 - Yr5, -7; Lowe et al 2011
wPt-4413 2D 0.0025 4.02 2DL Crossa et al 2007 - Yr37
wPt-6704 2D 0.0116 4.46 2DL Lowe et al 2011
wPt-1596 3A 0.0005 7.71 3AL Lowe et al 2011
wPt-9268 3A 0.0099 4.65 3AL Francki et al 2009
wPt-2045 3B 0.0000 12.50 3BS Lowe et al 2011
wPt-8238 3B 0.0033 5.79 3BS Crossa et al 2007 - Yr30; Lowe et al 2011
wPt-6132 3B 0.0034 5.77 3BS Lowe et al 2011
wPt-5105 3B 0.0492 3.01 3BS Crossa et al 2007-Yr30
wPt-9401 3D 0.0403 3.26 3DS Crossa et al 2007; Francki et al 2009
wPt-1336 3D 0.0342 3.42 3DS Crossa et al 2007; Francki et al 2009
wPt-6440 4A 0.0028 5.98 4AL Lowe et al 2011
wPt-2084 4A 0.0059 5.19 4AL Crossa et al 2007; Lowe et al 2011
wPt-1903 5A 0.0003 8.50 5AL Lowe et al 2011
wPt-7061 5A 0.0053 3.91 5AL Lowe et al 2011-Yr48
wPt-7251 7B 0.0489 3.02 7BS Crossa et al 2007 - Yr39
wPt-666850 7D 0.0000 10.52
wPt-5049 7D 0.0293 3.54 7DS Crossa et al 2007-Yr18
wPt-733631 NA 0.0003 8.27 7DS Crossa et al 2007-Yr33 (?); Lowe et al 2011

17. Allelic effects of some of the linked DArT markers

18. Some DArT haplotypes associated with Yr resistance
4D
2D
2B
2B
2B
0.01 0.4 wPt-0431
0.01 0.5 wPt-6003
0.03 0.3 wPt-743630
0.04 0.3 wPt-7985
0.05 0.3 wPt-9423
Name
Cross
Phenotype
Genotype
GCP_90 N-ABYAD-15 CHAM-6//KAUZ'S'/3/AO41/EMU'S'//TEVEE'S' 2 1 1 1 1 1
GCP_147 NAYZAK-6 TEVEE'S'//KAUZ'S'/3/FOW'S'//NS732/HER 2.3 1 1 1 1 1
GCP_86 NAYZAK-2 TEVEE'S'//KAUZ'S'/3/FOW'S'//NS732/HER 2.3 1 1 1 1 1
GCP_93 ZAKIA-12 CHAM-6//KAUZ'S'/3/FOW'S'//NS732/HER 2.3 1 1 1 1 1
GCP_89 N-ABYAD-13 CHAM-6//KAUZ'S'/3/AO41/EMU'S'//TEVEE'S' 7.3 0 0 0 0 0
GCP_61 WATAN-2 KAUZ/FLORKWA-1 7.7 0 0 0 0 0
GCP_92 ZAKIA-11 CHAM-6//KAUZ'S'/3/FOW'S'//NS732/HER 7.7 0 0 0 0 0
GCP_3 CHAM-8 KAUZ = JUP/BJY//URES 8 0 0 0 0 0
GCP_62 WATAN-9 KAUZ/FLORKWA-1 8 0 0 0 0 0
GCP_91 ZAKIA-10 CHAM-6//KAUZ'S'/3/FOW'S'//NS732/HER 8 0 0 0 0 0
2BS – Yr27, Yr31, Yr41, YrSP , YrP 81

19. Some DArT haplotypes associated with Yr resistance
3B
3B
3B
3B
4D
2D
0.02 0.04 tPt-9267
0.00 0.06 wPt-6132
0.00 0.06 wPt-0264
0.01 0.04 wPt-0431
0.01 0.05 wPt-6003
Name/Pedigee
Cross
Phenotype
Genotype
GCP_90 N-ABYAD-15 CHAM-6//KAUZ'S'/3/AO41/EMU'S'//TEVEE'S' 2 1 1 1 1 1
GCP_147 NAYZAK-6 TEVEE'S'//KAUZ'S'/3/FOW'S'//NS732/HER 2 1 1 1 1 1
GCP_146 NAYZAK-3 TEVEE'S'//KAUZ'S'/3/FOW'S'//NS732/HER 3 1 1 1 1 1
GCP_145 AFFRAH-3 AO41/EMU'S'//TEVEE'S'/3/SD 8036 7 0 0 0 0 0
GCP_87 N-ABYAD-10 CHAM-6//KAUZ'S'/3/AO41/EMU'S'//TEVEE'S' 7 0 0 0 0 0
Loci that confers multiple root
GCP_88 N-ABYAD-12
diseased resistance 0
CHAM-6//KAUZ'S'/3/AO41/EMU'S'//TEVEE'S' 7 0 0 0 0
GCP_89 N-ABYAD-13 CHAM-6//KAUZ'S'/3/AO41/EMU'S'//TEVEE'S' 7 0 0 0 0 0
3BS - Yr4, Yr30, YrS, YrSte2, Yrns-B1

20. Conclusions/what next
• Identified list of DArT markers closely linked to existing and
potentially uncharacterized Yr resistance
• Better understanding of the Yr genes in the existing pool of
elite germplasm
• Better position to utilize genetic profiling – modified genomic
selection approach in germplasm enhancement for Yr resistance
• Validation using bi-parental and multi-parent mapping
populations
• Conversion of 100 DArT markers to diagnostic markers to
facilitate MAS in known genes

21. ICARDA
Thanks

22. CAIGE meeting
Adelaide March 11, 2011