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

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  • 1. Objective 1: Improve groundnut productivity for marginal environments from Sub-Saharan Africa EMBRAPA- UGA – ICRISAT – ISRA-Senegal – CIRAD – Malawi Nat. Prog. – Tanzania Nat. Prog
  • 2. 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 A Activity 1 5 1,2, 6 4 Year 3 Year 4 2012 2013 2013 2014 Activity 1: Genetic resources
  • 3. 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
  • 4. 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) Activity 1: Genetic resources
  • 5. 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. Activity 1: Genetic resources
  • 6. 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 Activity 1: Genetic resources
  • 7. 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 Activity 1: Genetic resources
  • 8. 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) Activity 1: Genetic resources
  • 9. 0 1000 2000 3000 4000 5000 6000 Yield(kgha-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(kgha-1) Top and down yielding CSSLs along with 55 -437 and Fleur11 under ws conditions Pod yield- ws Haulm yield-ws 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 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 Activity 1: Genetic resources
  • 10. 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
  • 11. 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 A Activity 2 9 9 Year 3 Year 4 2012 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 A Activity 3 12 10 11 12 13 Year 3 Year 4 2012 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
  • 12. 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
  • 13. 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
  • 14. 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
  • 15. 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
  • 16. 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
  • 17. 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
  • 18. 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
  • 19. 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
  • 20. 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 A Activity 4 15 21 17 19,20 15 16 Year 3 Year 4 2012 2013 2013 2014
  • 21. 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
  • 22. 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 A Activity 5 25 23,24 25 Year 3 Year 4 2012 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
  • 23. 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 A Activity 6 26,27 Year 3 Year 4 2012 2013 2013 2014
  • 24. Acknowledgments: Partners, Farmers, & TL 1 Team Thank you

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