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

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

3. 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

4. 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

5. Kariega: EST marker approach
5
BLAT

6. Kariega: Chromosome 2BS QTL

7. Kariega: Chromosome 4AL QTL
Slow rusting

8. 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)

9. 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)

10. 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

11. 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

12. Population structure
DArT Gene-specific markers

13. 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)

14. Next step: Validation of MTAs
Two ‘novel’ Sr sources were identified for DH population development
Linkage maps completed
2nd Field trial (2013)

15. 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

16. 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)

17. 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