A North-South partnership identifies
genetic biodiversity for durable rust
resistance in African wheat genotypes
SARID pro...
Project focus: Durable rust resistance
Objectives:
QTL mapping approach
1) Fine map YrAPR QTL on 2B & 4AL (Kariega)
2) Gen...
Kariega Yr16DH70 (Cappelle-Desprez)
Fine map QTL Identify QTL
Susceptible parent Avocet S Palmiet
Mapping population 254 D...
Kariega: EST marker approach
5	
  
BLAT
	
  
Kariega: Chromosome 2BS QTL
Kariega: Chromosome 4AL QTL
Slow rusting
CD-derived resistance (Yr16DH70)
Theor Appl Genet 125: 109-120 (2012)
R2 =23-53% (LAI & RT)
wPt-743339
wPt-731381
wPt-7333...
Association analysis: plant materials and phenotypes
Seedling test : Greenhouse 2010, RSA
PTKST
SDL~ seedling resistance
F...
0	
  
10	
  
20	
  
30	
  
40	
  
50	
  
60	
  
70	
  
80	
  
90	
  
100	
  
1	
   5	
   10	
   20	
   30	
   40	
   50	
 ...
Association analyses
y = Xα + Qβ + Kv + ε
Statistical analyses:
Q1: GLM with Q1
Q2: GLM with Q2 (PCA eigenvectors)
K2: GLM...
Population structure
DArT Gene-specific markers
MTAs: SDL~ seedling resistance
- Multiple testing correction: False discovery rate (FDR)
- R2 between 0.09 and 0.28
- Sr36...
Next step: Validation of MTAs
Two ‘novel’ Sr sources were identified for DH population development
Linkage maps completed
...
Project outputs
3)Association analysis of African collection
1) Kariega 2) Cappelle Desprez
New Sr sources and several
mar...
Project outputs
PhD student trained and employed in wheat industry
QTL & markers already employed in MAS
Southern partners...
Acknowledgements
Funding
BBSRC-DFID
SA Winter Cereal Trust
National Research Foundation
Material
ARC-Small Grain Institute...
A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes
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A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes

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Renée Prins, Gloudi Agenbag, Zakkie Pretorius, Susanne Dreisigacker, Lesley Boyd

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A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes

  1. 1. A North-South partnership identifies genetic biodiversity for durable rust resistance in African wheat genotypes SARID project (UK: BBSRC-DFID) 2008-2012 Renée Prins Gloudi Agenbag Zakkie Pretorius Susanne Dreisigacker Lesley Boyd National Institute of Agricultural Botany
  2. 2. Project focus: Durable rust resistance Objectives: QTL mapping approach 1) Fine map YrAPR QTL on 2B & 4AL (Kariega) 2) Genetic analysis of Cappelle Desprez-derived YrAPR Association mapping approach 3) New sources of resistance Assess genetic diversity for stem and stripe rust resistances - JIC African wheat collection
  3. 3. Kariega Yr16DH70 (Cappelle-Desprez) Fine map QTL Identify QTL Susceptible parent Avocet S Palmiet Mapping population 254 DH 1020 F2 201 RIL Markers AFLP SSR DArT STS EST SSR DArT Phenotypic screen Greenhouse Field trials Field trials Linkage map Whole genome Limited coverage (BC) QTL map CIM/MQM CIM
  4. 4. Kariega: EST marker approach 5   BLAT  
  5. 5. Kariega: Chromosome 2BS QTL
  6. 6. Kariega: Chromosome 4AL QTL Slow rusting
  7. 7. CD-derived resistance (Yr16DH70) Theor Appl Genet 125: 109-120 (2012) R2 =23-53% (LAI & RT) wPt-743339 wPt-731381 wPt-733314 wPt-1722 wPt-5647 wPt-4197 tPt-1041 Xwmc407 Xgwm636 wPt-7721 wPt-0003 wPt-8490 wPt-740658 tPt-9405 Xwmc177 Xcfa2201 wPt-664251 wPt-5029 wPt-5498 tPt-3109 wPt-0553 wPt-1657 wPt-743211 wPt-5251 Xcfa2263 Xcfa2043 Xgwm294 wPt-7024 wPt-2293 wPt-3244 Xgwm312 Xwmc181a 2A QYr.ufs-2A Xgwm484 Xwmc453 Xcfd43 wPt-666389 wPt-667312 wPt-740836 Xgwm102 Xwmc18 Xwmc245 wPt-734322 wPt-664520 Xgwm539 wPt-3692 wPt-666518 Xcfd73 Xcfd233 Xwmc445 Xbarc228 Xwmc41 Xwmc181b Xbarc206 wPt-732882 wPt-6752 wPt-4691 wPt-671892 wPt-2160 wPt-730541 Xgwm349 Xwmc167 wPt-4559 wPt-9848 wPt-0153 Xcfd239 Xgwm311 Xgwm382 Xgwm301 Xbarc159 2D QYr.ufs-2D (Yr16) R2 =4.7-10.3% (LAI & RT)
  8. 8. Association analysis: plant materials and phenotypes Seedling test : Greenhouse 2010, RSA PTKST SDL~ seedling resistance Field trials: March 2009, Njoro, Kenya Sept. 2009 , Njoro, Kenya Oct. 2011, Greytown, RSA PTKST/TTKST SAI~ stem area infected RT ~reaction type SR phenotyping (110)   (8)   (38)   (12)   (2)   (45)   (49)   JIC African wheat collection (235) Ethiopia, Kenya, South Africa (RSA), Sudan, Tunisia, Morocco, Zambia Cultivars from RSA (39)
  9. 9. 0   10   20   30   40   50   60   70   80   90   100   1   5   10   20   30   40   50   60   70   no   score   Seedling and field data Stem area infected No.ofentries Njoro 2009 0   5   10   15   20   25   30   35   40   45   50   Greytown 2011 No.ofentries Stem area infected Range of ITs Range of stem rust severity
  10. 10. Association analyses y = Xα + Qβ + Kv + ε Statistical analyses: Q1: GLM with Q1 Q2: GLM with Q2 (PCA eigenvectors) K2: GLM with K2 Q1K1: MLM with the Q1 and K1 Q1K2: MLM with the Q1 and K2 Q2K1: MLM with the Q2 and K1 Q2K1 MLM with the Q2 and K2 Intra-chromosomal LD Population structure: model based clustering (Q1), PCA (Q2), kinship (K1 and K2) 0.0 0.2 0.4 0.6 0.8 1.0 0.00.20.40.60.81.0 SAI3a Observed p-value Cumulative%ofp-value K2 Q1 Q2 Q1K1 Q1K2 Q2K1 Q2K2 observed p-values Cumulative%ofp-values 0.0 0.2 0.4 0.6 0.8 1.0 0.00.20.40.60.81.0 K2 Q1 Q2 Q1K1 Q1K2 Q2K1 Q2K2 Genotypes 33 Gene-specific markers (12 Sr and Yr genes) -  Combining rare alleles in c, 155 retained marker alleles 3028 DArT markers (Wheat PstI(TaqI) _V3): -  Imputation with R:MissMDA package Version 1.2 -  Elimination of markers with: f<0.05, R2≥0.99 2185 final markers (1471 markers mapped on the Wheat Consensus Map provided by DArT PL) 0 2 4 6 8 10 0 2 4 6 8 10 12 Proportionofexplained variance(%) No. of principal component
  11. 11. Population structure DArT Gene-specific markers
  12. 12. MTAs: SDL~ seedling resistance - Multiple testing correction: False discovery rate (FDR) - R2 between 0.09 and 0.28 - Sr36 present in lines from Kenya, one line from RSA Stm773-2 (Sr36)
  13. 13. Next step: Validation of MTAs Two ‘novel’ Sr sources were identified for DH population development Linkage maps completed 2nd Field trial (2013)
  14. 14. Project outputs 3)Association analysis of African collection 1) Kariega 2) Cappelle Desprez New Sr sources and several marker trait associations 6AS   6AS   3BS   6AL  
  15. 15. Project outputs PhD student trained and employed in wheat industry QTL & markers already employed in MAS Southern partners- increased capacity building International conferences & team members visits Equipment New technologies Strengthen North-South team Foundation for next successful grant : BBSRC-SCPRID (2012-2016) Implementation of KASPar SNP technology in Africa (mid-2013)
  16. 16. Acknowledgements Funding BBSRC-DFID SA Winter Cereal Trust National Research Foundation Material ARC-Small Grain Institute Field Trials KARI-Njoro staff & Davinder Singh Pannar Sensako Technical assistance CenGen: D Liebenberg, T Chama, D Snyman, L Rademeyer & E Wessels UFS: C Bender & C Botha JIC: R Maccormack

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