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2 Carmendevicente Tli


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2 Carmendevicente Tli

  1. 1. Tropical Legumes I Tropical Legumes II Annual Meeting 16–20 September 2009, Bamako, Mali
  2. 2. Outline • Overview of TLI phase I o Objectives, Activities o Partners o Achievements o Lessons • Transfer of TLI Outputs to TLII • Overview of TLI phase II o Rationale o Partners o Links with ongoing initiatives o New Activities o Integration between phase I and phase II o Predicted outputs for TLII in phase II
  3. 3. Overview of TLI phase I
  4. 4. Improving tropical legume productivity for marginal environments in sub-Saharan Africa (TLI) To develop the key genomic resources that are currently lacking in legumes (including cross-legume molecular markers for comparative genomics), identify molecular markers for traits of importance to resource- poor farmers (biotic stresses and drought tolerance), and improve “molecular” breeding capacities in sub- Saharan Africa 10 Million US$, 2007-2009, 1st May 2007
  5. 5. TLI Objectives 1, Improve groundnut productivity 2, Improve cowpea productivity 3, Improve common bean productivity 4, Improve chickpea productivity 5, Develop cross-species resources for comparative biology 6, Provide training and capacity building
  6. 6. TLI Activities ♦ Objectives 1 to 4 • Germplasm for genetic studies and breeding -- development + characterization • Generate genomic resources -- genetic studies and breeding • Molecular markers and genes for biotic stress resistance (crop specific) • Molecular markers and genes for drought tolerance • Fluctuating annual rainfall and uneven annual distribution • Enhancement of locally adapted germplasm -- target traits ♦ Objective 5 • Orthologous markers for cross genome analysis • Comparative analysis of the Arachis species complex • Genome divergence at orthologous loci ♦ Objective 6 • Project planning and training workshops • Support to local facilities
  7. 7. National Program Partner Institutions Groundnut Cowpea Bean Chickpea Capacity Building East Africa Ethiopia SARI EIAR EIAR University KARI, of KARI, Kenya Egerton Nairobi/KA Egerton University University RI 9 countries Naliendele Naliendele Research 14 institutions ECABREN 2 networks Tanzania Research LZARDI Station; ECABREN; ; ART Station ART; LZARDI West Africa Burkina Faso INERA INERA Cameroon IRAD IRAD Niger INRAN INRAN Senegal ISRA ISRA ISRA Southern Africa Chitedze Chitedze Research Malawi Research SABRN Station; SABRN Station Zimbabwe
  8. 8. Other Partner Institutions Cross species resources for Groundnut Cowpea Bean Chickpea comparative genomics University of University of ICRISAT California- CIAT ICRISAT California-Davis, USA Riverside, USA USDA/ Washington Catholic University of IITA RIKEN (Japan) State University, ICRISAT Brasilia, Brazil Pullman, USA University of University of University of University of California– EMBRAPA, Brazil California- Davis, California- Davis, California- Davis, Riverside, USA USA USA USA University of Georgia, Purdue University, University of CIAT USA USA Frankfurt, Germany DArT P/L, Australia DArT P/L, Australia IITA Instituto Agronomico NCPGR, India de Campinas, Brazil IIPR, India
  9. 9. Expected Outputs TLI phase I -Extensive evaluations of diverse germplasm -High-throughput genotyping systems -Trait specific genetic markers / marker–trait associations -Development and transferring of modern breeding tools - Building capability of NARS breeding programs
  10. 10. Achievements
  11. 11. Groundnut diversity studies Phenotyping of reference collection 1) Diseases •Malawi - ELS and rosette •Tanzania - rust and rosette •Mali and Senegal – LLS Altogether 19 sources of disease resistance identified 2) Drought Range of variation for pod yield (India) Highly contrasting drought -tolerant ICGVSM ICG12879 Germplasm (yield and trait based) was identified 87003 Florunner JL24 TMV2 ICG3421 ICG3746 and knowledge that farmer-preferred varieties 900 are highly sensitive to intermittent drought 800 has been obtained 700 600 Pod yield 500 400 300 200 100 0
  12. 12. Cowpea diversity studies  500 genotypes characterised for drought tolerance in Senegal, Burkina Faso, Nigeria and USA.  200 promising genotypes selected and evaluated for grain yield and drought tolerance traits. The same five ‘drought QTLs’ identified from genetic analysis of RIL populations -- robust QTL for to drought tolerance in many genetic backgrounds  Diversity analysis with 1536 SNP loci of breeding lines from IITA, Cameroon, Burkina Faso and California compared to IITA/GCP Reference Collection -- high degree of relatedness within breeding programmes
  13. 13. Common bean diversity studies Population structure of 200 genotypes of CIAT core collection well understood through molecular marker analysis (Blair et al. 2009)  useful for comparison of drought tolerance sources within each genepool  analyzed in Lattice design experiments with stratification by genepool origin and drought or irrigated treatments  phenotypic data for seed size, weight, height and length across genepools proven useful for association analysis with markers  sites in Ethiopia, Kenya, Malawi, Zimbabwe, Tanzania, Mozambique, Colombia used for testing of reference collection DJ1 DJ2 G M1 M2 NG1 NG2 P1 P2
  14. 14. Chickpea diversity studies  Phenotyping reference collection (300 lines) – two seasons - drought related traits e.g. root traits, HI, yield - insect resistance in both field and lab conditions - δ13C, SLA and SCMR  Interspecific population (131 RILs) - insect resistance  Two intraspecific populations ICC 4958 x ICC 1882 -264 RILs - root traits, HI, 13-C ICC 283 x ICC 8261- 281 RILs - root traits, HI Natural field conditions Detached leaf assay  The reference collection (305 lines) was evaluated for resistance to pod borer. About 25 genotypes were identified as being less susceptible. These lines were evaluated and selected for multi-site testing and breeding by National programmes.
  15. 15. Groundnut genomic resources  About 3,200 microsatellite markers are now available (only 300 at the beginning)  The first cultivated groundnut map completed (RIL between TAG24 and ICGV86031) T04 ISC04 T05 ISC05 T08WW PodWtWW08 T08WS PodWtWW08 TE04 SeedWtWW08 TEbis04 SeedWtWS08 TE05 HaulmWtWW08 TE08WS HaulmWtWW08 TE08WW SLAHar04 SLAPreTrt05 SLAPreTrt04 SLAHar05 SLA04 SLA05 LA04 LA05 SPADPreTrt04 SPADStresStrt04 SPAD7UndrStres04 SPAD005 SPAD505 SPAD1005 SPAD1505 Wateruse04 Initialbiomass04 Finalbiomass04 Deltabiomass04 Shootbiomass04 Delta13C04 TDM05 InitialDryWt05 DWINC05 ShootDWWW08 ShootDWWS08
  16. 16. Cowpea genomic resources  SNP discovery in EST covering 13 cowpea accessions, several RIL parents, African and broader germplasm accessions - 10,000 high confidence SNPs  Selection of 1536 SNP set (1 SNP per gene, high polymorphic information content in African breeding lines) ->90% of 1536 markers (1375) worked  Now exploring single-plex for customized breeding applications utilizing these validated SNPs  Creating a high-density consensus map Homozygotes AA Homozygotes BB Ilumina BeadStudio output for 1 SNP, 128 RIL Heterozygotes AB
  17. 17. Seven mapping populations genotyped and used to develop ~1,000 SNP consensus map 680cM; 11 LG; 1 marker/0.7cM - Muchero et al 2009, PNAS
  18. 18. Common bean genomic resources • SSR marker development based on multiple sources, such as small insert genomic libraries, ESTs and BAC end sequences. • SNP markers have been based on cDNA sequences from subtractive libraries for drought tolerant/susceptible genotypes, candidate genes and cross-legume sequences. ATA – rich SSR Source: Blair et al. (2008) Genome Small Insert - SSR Total : 417 SSRs discovered in 18,000 small insert clones from 3 libraries Source: Blair et al. (2009b) Genome EST-SSR Discovered through hybridization screening of 18,000 cDNA clones and sequencing of positive hits at 5’ and 3’ ends Source: Blair et al. (2009a) BMC Plant Bio CEL I and 768 Illumina arrays w/ Obj 5 Source: Galeano et al. (2009) Crop Sci
  19. 19. Chickpea genomic resources- large scale markers  1655 SSR markers were developed and 1416 of these were screened on parental genotypes of inter- and intra-specific mapping populations  An expanded DArT array with 15,360 clones was completed  The first Illumina® GoldenGate Assay (768 SNPs) developed and genotyping completed for reference mapping population (in collaboration with Obj 5) Genotyping data for ca. 2000 marker loci compiled on the international reference mapping population Varshney et al. 2009; COPB