Top Banner
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
17

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

May 11, 2015

Download

Education

Renée Prins, Gloudi Agenbag, Zakkie Pretorius, Susanne Dreisigacker, Lesley Boyd
Welcome message from author
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
Page 1: A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes

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

Page 2: A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes
Page 3: A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes

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

Page 4: A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes

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

Page 5: A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes

Kariega: EST marker approach

5  

BLAT  

Page 6: A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes

Kariega: Chromosome 2BS QTL

Page 7: A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes

Kariega: Chromosome 4AL QTL Slow rusting

Page 8: A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes

CD-derived resistance (Yr16DH70) Theor Appl Genet 125: 109-120 (2012)

R2 =23-53% (LAI & RT)

wPt-743339wPt-731381wPt-733314

wPt-1722 wPt-5647wPt-4197 tPt-1041

Xwmc407Xgwm636

wPt-7721 wPt-0003wPt-8490 wPt-740658

tPt-9405Xwmc177Xcfa2201

wPt-664251 wPt-5029wPt-5498 tPt-3109

wPt-0553wPt-1657 wPt-743211

wPt-5251Xcfa2263Xcfa2043

Xgwm294wPt-7024wPt-2293wPt-3244Xgwm312Xwmc181a

2AQYr.ufs-2A

Xgwm484Xwmc453 Xcfd43

wPt-666389wPt-667312wPt-740836Xgwm102Xwmc18Xwmc245

wPt-734322wPt-664520Xgwm539wPt-3692

wPt-666518Xcfd73Xcfd233

Xwmc445 Xbarc228Xwmc41 Xwmc181b

Xbarc206wPt-732882wPt-6752wPt-4691

wPt-671892wPt-2160

wPt-730541Xgwm349Xwmc167wPt-4559wPt-9848wPt-0153

Xcfd239 Xgwm311Xgwm382 Xgwm301

Xbarc159

2DQYr.ufs-2D (Yr16)

R2 =4.7-10.3% (LAI & RT)

Page 9: A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes

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)

Page 10: A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes

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

Page 11: A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes

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

Page 12: A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes

Population structure

DArT Gene-specific markers

Page 13: A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes

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)

Page 14: A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes

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

Page 15: A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes

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  

Page 16: A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes

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)

Page 17: A North-South partnership Identifies Genetic Biodiversity for Durable Rust Resistance in African Wheat Genotypes

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