TLM III: Improve groundnut productivity for marginal environments from sub-Saharan Africa – D...

Objective 1: Improve groundnut productivity for marginal environments

from Sub-Saharan Africa

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

Activity 1 Confirm disease/drought resistance/tolerance sources – Assess new diversity

Milestone 1 Confirmation of disease resistance and drought tolerance of at least 10 new genotypes

Milestone 2 Two new sources of disease resistance - new genetic material for breeding (either CSSL, AB line, synthetics)

Milestone 4 Pre-breeding material incorporating wild favourable alleles for future MARS.

Milestone 5 8 available synthetics tested for disease resistance; 1–2 AB-QTL populations with one synthetic amphidiploids.

Milestone 6 Database of phenotyping data for drought / knowledge of key traits for drought adaptation.

Milestone 7 A sub-set of 10 tolerant lines for TLII breeding / PVS trials.

M J J A S O N D J F M A M J J A S O N D J F M AActivity 1 5 1,2, 6 4

Year 3 Year 42012 2013 2013 2014

Activity 1: Genetic resources

Confirmation of the disease resistance and drought tolerance of at least 10 new genotypes identified from Phase I, and knowledge of the farmer acceptability of

all of these before their inclusion in the breeding scheme

Five lines (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

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 97183 ICG 4750

ICG 11088

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

Entries confirmed in 2011

In bold are confirmed tolerant in 2012 Repeat trial (2012-13)


Farmer acceptability of 10–20 new sources of disease resistance and drought tolerance tested PVS trials (in close collaboration with TLII).

Some lines tolerant to drought and foliar diseases were included in PVS trials in Mali and evaluated by a total of 1653 farmers in districts of Koutiala, Djijeni and Sanankoloba in Mali .

Pod and haulm yields are the most preferred traits.


New synthetics produced

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!!!!

Canopy Area – larger than parentals – - similar to peanut


Runner-886 AiAd

Introgression of disease resistance from A. duranensis Runner-886 susceptible agronomically adapted Synthetic AiAd resistant unadapted phenotype

end of season LS damage more resistant (not as resistant as new synthetics)

pod types

Runner-886 AiAd


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) Ndiol (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)


0100020003000400050006000

Yiel

d (k

g ha-1

)

Top and down yielding CSSLs along with 55-437 and Fleur11 under ww conditions

Pod yield-ww Haulm yield-ww

0

1000

2000

3000

4000

5000

6000

Yield (

kg ha-1 )

Top and down yielding CSSLs along with 55-437 and Fleur11 under ws conditions

Pod yield-ws Haulm yield-ws

00.10.20.30.40.50.60.7

HI

Harvest index (HI) of top and down yielding CSSLs along with 55-437 and Fleur11 under ww and ws conditions

HI-WW HI-WS

Evaluation of CSSL under WW and WS treatment in Niger

Some achieve higher yield than 55-437, a standard drought tolerant genotype


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 2 Develop SNP markers for cultivated groundnut

Milestone 8 One suitable method to identify SNPs.

Milestone 9 Genome-wide resource of SNPs useable towards a broadly applicable SNP, from an exploration of at least 8+8 contrasting genotypes.

M J J A S O N D J F M A M J J A S O N D J F M AActivity 2 9 9

Year 3 Year 42012 2013 2013 2014

M J J A S O N D J F M A M J J A S O N D J F M AActivity 3 12 10 11 12 13

Year 3 Year 42012 2013 2013 2014

Activity 3 Map disease resistance QTLs Anchor these QTL to the physical map

Milestone 10 4 populations phenotyped (1 per disease) for disease resistance

Milestone 11 QTLs for resistance to major groundnut diseases - QTL flanking markers deposited in MBP database.

Milestone 12 25 additional SSR markers in strategic regions of the groundnut genome containing disease resistance QTLs

Milestone 13 3 regions controlling disease resistance anchored on the groundnut physical map

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

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

Comprehensive association analysis in groundnut

524 marker-trait associations for 29 traits

PVE from 5.81-90.09%

Manuscript under preparation

154 SSRs and 15360 DArT features

51 traits (more than one season each) phenotyped on reference set

5 disease resistance 6 oil and nutritional quality 28 physiological traits 12 yield & yield components

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

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

Phenotyping of ICGV86031 x TAG24 RIL done in three environments

Purpose: combining field / lysimeter / pot based

targeted trait measurements

Development of two new populations for drought related traits in progress – now in F3 generation

Activity 4 Use MABC to introgress disease resistance QTL New breeding population for drought and disease towards MARS

Milestone 15 8 MABC materials introgressed with rust and rosette disease resistance QTLs in four FMPV backgrounds and transferred to TLII breeders in Year 4

Milestone 17 5 advanced backcross breeding materials with disease resistance tested in PVS trials.

Milestone 19 At least 4 new crosses (one per disease) developed and QTL identified for each disease between FMPV lines and new sources of disease resistance.

Milestone 20 At least 4 new crosses developed between advanced BC lines in FMPV background and new sources of drought tolerance from Activity 4, Phase I.

Milestone 21 Relevance of F4-family phenotyping for drought-related traits tested in at least one segregating population.

M J J A S O N D J F M A M J J A S O N D J F M AActivity 4 15 21 17 19,20 15 16

Year 3 Year 42012 2013 2013 2014

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

Activity 5 Strengthen capacity of NARS partners

Milestone 23

At least 2 NARS partners empowered to breed groundnut varieties with multiple attributes.

Milestone 24

3 scientists and 3 technicians trained in drought phenotyping and in the logistics of fast advancement of breeding populations.

Milestone 25

1 scientist and 1 technician from Malawian and Malian national programmes trained in DNA extraction and use of simple markers.

M J J A S O N D J F M A M J J A S O N D J F M AActivity 5 25 23,24 25

Year 3 Year 42012 2013 2013 2014

• 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 familiasing with the new tools and techniques and performed molecular characterisation of 50 advanced breeding lines introduced from ICRISAT Bamako

Activity 6 Management and storage of data Milestone 26 Marker genotyping data for groundnut reference collection

- At least 4 populations stored in public database and linked to the MBP.

Milestone 27 Phenotyping data of reference collection over 6 sites (India, Niger, Mali, Senegal, Tanzania and Malawi) and 6 years; RIL and MABC lines analysed and data stored in public database - Data from TLII trials added to this database.

M J J A S O N D J F M A M J J A S O N D J F M AActivity 6 26,27

Year 3 Year 42012 2013 2013 2014

Acknowledgments: Partners, Farmers, & TL 1 Team

Thank you

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