Objective 1: Improve groundnut productivity for marginal environments

from Sub-Saharan Africa

EMBRAPA- UGA – ICRISAT – ISRA-Senegal – Malawi Nat. Prog. – Tanzania Nat. Prog

GCP-ARM – Lisbon – 27-30 Sept 2013

1: Diversity (disease / drought) 2: Molecular tools / SNPs 3: Disease QTL 4: Breeding (MABC / new pops) 5: Training 6: Data management

Rust

Rosette

Early leaf spots

Drought

A. hypogaea cv IAC Runner-886

BC-111

0102030405060708090

AixA

dBC

-5BC

-3BC

-136

BC-1

38BC

-203

BC-3

6BC

-33

BC-1

56BC

-6BC

-77

BC-1

57BC

-15

BC-3

0BC

-13

BC-1

70BC

-111

BC-1

45

Productivity (g)

%DLA *10

Rust: ICGV 02194, ICG 11426, ICGV 01276, ICGV 02286, and ICG 02446 Rosette: ICG 14705, ICG 13099, ICG 9449, and ICG 15405

ELS in ESA; ICG 6022, ICG 405, ICG 14466, ICG 6057, ICG 9449 and ICG 12509 ELS in WCA: ICG 6703; ICG 10036, ICG 10384 ICG 9449, ICG 12509, and ICG 11219

Wild germplasm

Cultivated germplasm

CSSL phenotyping in Senegal

Year Season Trial Traits

2011 off 2 water regimes 3 replications

Plant, seed and pod morphology, Yield components

2012 off 2 water regimes 3 replications

Plant, seeds and pod morphology Yield components

2012 rainy Nioro 3 replications

ELS

2013 rainy 3 locations Nioro (800mm) Bambey (550mm) Ndieul (300mm) 3 replications

Yield components

Subset of 80 CSSLs (Fleur 11 x AiAd)

42 QTLs over 4 traits

Same subset of 80 CSSLs - Icrisat Niger (2011) - Icrisat Malawi (2011) - Icrisat India (2011) - Embrapa (Dec 2012)

Activity 1: Genetic resources

Development of new populations at ISRA-CERAAS A. duranensis

A. ipaensis A. batizocoi A. valida

A. hypogaea Var Fleur11

ISATGR 278-18

F1 ISATGR 52B x Fleur11

X

Activity 1: Genetic resources

ABQTL (BC2F4) pop. ISATGR278-18 x Fleur11 22 BC1 plants identified out of ~500 plants checked Check of introgressions and recombinations on 14 l. groups 168 BC2 obtained from 22 BC1 x Fleur11♂ BC2F4 available in Oct. BC2F4:6 phenotyping in sep. 2014

Activity 1: Genetic resources

ABQTL (BC2F4) pop. ISATGR52B x Fleur11 F1 produced in 2012 / 112 BC1 currently identified. Target 192 BC1 for genetic map construction Ongoing backcrossing of 50 BC1 ➜ 400 BC2 in July BC2 ➜ BC2F2 Sep. – Dec. 2013

BR-BatSten1 = (A. batizocoiK9484 x A. stenospermaV10309)4x

BR-BatDur1 = (A. batizocoiK9484 x A. duranensis V14167)4x

BR-BatDur2 = (A. batizocoiK9484 x A. duranensis SeSn2848)4x

BR-IpaVillo1 = (A. ipaensis KG30076 x A. villosaV12812)4x

BR-GregSten1 = (A. gregoryiV6389 x A stenospermaV10309)4x

BR-IpaCor = (A. ipaensisKG30076 xA. correntina )4x

ALL RESISTANT TO RUST!!!!

New synthetics produced at EMBRAPA

60 lines from phase 1 re-evaluated across locations

ICG 12879 ICGV 02189 55-437 ICG 3140 ICG 4729 ICG 3584 ICGV 02038 ICGV 02266 ICGV 96466 ICGV 97182 ICG 4750 ICG 11088

47-10 ICG 14482 ICG 2772 ICG 5663 JL24 ICG 1834 ICG 12625 ICG 8106 ICGV 99001

ICGV02038, ICGV02189, ICGV 86124, ICGV 01276 and ICGV 97182) in good agronomic background identified by farmers on station are being used to generate new crosses to enhance drought and disease tolerance in sensitive varieties Activity 1: Genetic resources

R² = 0.65

-2

0

2

4

6

8

10

12

14

16

0.00 0.50 1.00 1.50 2.00 2.50 3.00

Pod

Yiel

d - W

S

Transpiration Efficiency

Postrainy season

Activity 1: Genetic resources

Sensitive

Tolerant

VPD response / Canopy development dynamics

Branching Leaf area LA under soil drying LA under high VPD

Development and use of KASPar genotyping assay

*used for MABC also; LLS: Late leaf spot; ELS: Early leaf spot; GRD: Groundnut rosette disease O/L: Oleic/ linoleic fatty acid; DR: Disease resistance

Total SNPs selected for KASPar assay 96

No. of validated markers on 94 genotypes 90

No. of polymorphic markers in reference set 72

Mean polymorphic information content (PIC) 0.32

Parental genotypes of mapping populations

Segregating traits Polymorphic markers

Polymorphism rate (%)

Interspecific mapping populations TMV 2 × TxAG 6 Agronomic traits 40 44.4 ICGV 87846 × ISATGR 265-5 Agronomic traits 36 40.0 ICG 0350 × ISATGR 184 Agronomic traits 37 41.1 ICG 0350 × ISATGR 9B Agronomic traits 36 40.0 ICG 0350 × ISATGR 5B Agronomic traits 44 48.9 ICG 0350 × ISATGR 90B Agronomic traits 36 40.0 Intraspecific mapping populations TG 26 × GPBD 4 Rust and LLS resistance 19 21.1 TAG 24 × GPBD 4* Rust and LLS resistance 18 20.0 ICG 11337 × JL 24 LLS resistance 22 24.4 ICGV 93437 × ICGV 95714 ELS resistance 20 22.2 Robut 33-1 × ICGV 95714 ELS resistance 23 25.6 ICGV 93437 × ICGV 91114 Rust resistance 9 10.0 ICGV 93437 × ICGVSM 95342 Rust resistance 23 25.6 ICGS 76 × CSMG 84-1 Drought tolerance 9 10.0 ICGS 44 × ICGS 76 Drought tolerance 5 5.6 TAG 24 × ICGV 86031 Drought tolerance 0 0.0 Chalimbana × ICGVSM 90704 Resistance to GRD 2 2.2 CG 7 × ICGVSM 90704 Resistance to GRD 6 6.7 ICGV 07368 × ICGV 06420 High & low oil content 12 13.3 ICGV 07166 × ICGV 06188 High & low oil content 10 11.1 ICGV 06420 × SunOleic 95A* O/L ratio 13 14.4 Intraspecific marker-assisted backcrossing (MABC) populations ICGV 91114 × GPBD 4 Rust resistance 15 16.7 JL 24 × GPBD 4 Rust resistance 17 18.9 ICGV 03042 × SunOleic 95A O/L ratio 12 13.3 ICGV 02411 × SunOleic 95A O/L ratio 15 16.7 ICGV 05141 × SunOleic 95A O/L ratio 12 13.3 ICGV 05100 × SunOleic 95A O/L ratio 10 11.1

Activity 2,3: Genomic resources

Details of different linkage maps

TAG 24 x ICGV 86031 (RIL-1)

ICGS 76 x CSMG 84-1 (RIL-2)

ICGS 44 x ICGS 76 (RIL-3)

TAG 24 x GPBD 4 (RIL-4)

TG 26 x GPBD 4 (RIL-5)

Marker loci mapped 191 119 83 188 181

Linkage groups 22 18 16 20 20

Marker loci/LG 2-19 2-14 2-10 2-17 2-15

Avg. marker loci/LG 8 7 5 9 8

Total map distance (cM) 1785 888 2203 1922 1964

Avg. distance/LG (cM) 81.15 59.2 110.1 96.1 85.4

Avg. inter-locus distance (cM)

9.54 11.88 15.47 10.23 9.9

Five genetic maps maps for 4x groundnut

TAG 2009, 118:729-739; TAG 2010, 121:971-984; Field Crops Res 2011, 122:49-59;

TAG 2011 122:1119-1132; Mol Breeding 2012, DOI 10.1007/s11032-011-9661-z; Mol Breeding 201 2, DOI 10.1007/s11032-011-9660-0.

LG_AhI

LG_AhII

LG_AhIII

LG_AhIV

LG_AhV

LG_AhVI

LG_AhVII

LG_AhVIII

LG_AhIX

LG_AhX

LG_AhXI

LG_AhXII

LG_AhXIII

LG_AhXIV

LG_AhXV

LG_AhXVI

LG_AhXVII

LG_AhXVIII

LG_AhXIX

LG_AhXX

Reference consensus genetic map

Marker loci mapped 897 Total map distance 3863.6 (cM) Map density 4.42 (cM)

Activity 2,3: Genomic resources

BC1 A. hypogaea × amphidiploid

CIRAD, France

RIL-1 A. hypogaea ICRISAT, India RIL-2 A. hypogaea ICRISAT, India RIL-3 A. hypogaea ICRISAT, India RIL-4 A. hypogaea ICRISAT, India RIL-5 A. hypogaea ICRISAT, India RIL-6 A. hypogaea GAAS, China RIL-7 A. hypogaea GAAS, China RIL-8 A. hypogaea GAAS, China RIL-9 A. hypogaea USDA-ARS, USA RIL-10 A. hypogaea USDA-ARS, USA TF5 A. hypogaea ×

amphidiploid EMBRAPA, Brazil

SKF2 A. hypogaea KDRI, Japan NYF2 A. hypogaea KDRI, Japan

High density consensus genetic map

Marker loci mapped 3,693

Total map distance (cM) 2,651

Map density (loci/cM) 1.39

Consensus QTL map for drought tolerance traits

Mol Breed 2012, 32:757-772

Cluster 6

Cluster 13

Cluster 11

Cluster 1

Cluster 12

Cluster 2

Cluster 7

Cluster 14

Cluster 16

Cluster 4

Cluster 5

Cluster 8

Cluster 9

Cluster 10

Cluster 3

Cluster 15

How yield and traits QTL co-map in cultivated peanut ?

QTL cluster for: Leaf expansion Leaf area Leaf conductance

Consensus QTL map for Rust and LLS resistance

Major QTL for LLS

Major QTL for rust

Common QTLs for LLS and rust

Mol Breed 2012, 32:773-788

Parental screening of mapping populations for disease resistance * Selected based on parental polymorphism # F6 RIL phenotyped for ELS

Populations Markers screened

Poly. markers

Disease resistance

Locations

ICGV 93437 X ICGVSM 95342* 1000 61 Rust resistance Malawi

ICGV 93437 X ICGV 94114 1000 56 Rust resistance Malawi

CG7 X ICGVSM 90704* 1000 119 GRD Malawi

CHALIMBANA X ICGVSM 90704 1000 84 GRD Malawi

ROBUT 33-1 X ICGV 95714* 1000 111 ELS Malawi

ICGV 93437 X ICGV 95714 1000 24 ELS Malawi

ICGV 86124 X ICG 7878 # 510 31 ELS Niamey

GRD : Groundnut rosette disease ELS : Early leaf spot

Marker-assisted breeding for rust resistance

Promising introgression lines are under replicated yield assessment trial

Cross Number of lines evaluated *

Lines with mean disease score of 2 *

ICGV 91114 x GPBD 4 57 25

JL 24 x GPBD 4 69 23

TAG 24 x GPBD 4 103 29

Some of the trainees • 3 scientists and 3 technicians trained in drought phenotyping and logisticics

of advancing breeding populations • Mr Adama Zongo ( PhD student from Burkina Faso) has undergone 3-

month training at ICRISAT Bamako and is currently being trained at Niamey for his thesis research on MAS for ELS.

• Mr. Richard Oteng Frimpong from SARI Ghana spent a month at the genomics centre of excellence at ICRISAT Center familiarising with the new tools and techniques and performed molecular characterisation of 50 advanced breeding lines introduced from ICRISAT Bamako

• Omar Halilou, Philippo Machamba trained on drought phenotyping • Etc…

Capacity building

Data Management Phenotypic and genotypic data mostly delivered See Patrick Okori’s presentation Monday pm

Acknowledgments: Partners, Farmers, TL 1 Team, GCP, BMGF

Thank you