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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
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
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)
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.
of e
ntri
es
Njoro 2009
0 5 10 15 20 25 30 35 40 45 50
Greytown 2011
No.
of e
ntri
es
Stem area infected
Range of ITs
Range of stem rust severity
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
0.0
0.2
0.4
0.6
0.8
1.0
SAI3a
Observed p-value
Cum
ulat
ive
% o
f p-v
alue
K2
Q1
Q2
Q1K1
Q1K2
Q2K1
Q2K2
observed p-values
Cum
ulat
ive
% o
f p-v
alue
s
0.0 0.2 0.4 0.6 0.8 1.0 0.
0 0.
2 0.
4 0.
6 0.
8 1.
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
Prop
ortio
n of
exp
lain
ed
varia
nce
(%)
No. of principal component
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 present in lines from Kenya, one line from RSA
Stm773-2 (Sr36)
Next step: Validation of MTAs Two ‘novel’ Sr sources were identified for DH population development Linkage maps completed 2nd Field trial (2013)
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
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)
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