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TLI 2012: Chickpea research progress

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Objective 4- CHICKPEA
5 Activities
Activity 1: Utilise genetic diversity to develop breeding
            and MAGIC populations (Harnessing diver...
Activity 1: Harnessing Diversity


Milestones:
1. 8 Parental genotypes for generating pre-breeding populations
   and MAGI...

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TLI 2012: Chickpea research progress

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TLI 2012: Chickpea research progress

  1. 1. Objective 4- CHICKPEA
  2. 2. 5 Activities Activity 1: Utilise genetic diversity to develop breeding and MAGIC populations (Harnessing diversity) Activity 2: Develop genomic resources for enhancing MABC and MARS activities (Genomic resources) Activity 3: Employ MABC and MARS activities to improve superior lines (Drought tolerance breeding) Activity 4: Strengthen capacity of NARS partners (Capacity building) Activity 5: Management and storage of data (Managing data)
  3. 3. Activity 1: Harnessing Diversity Milestones: 1. 8 Parental genotypes for generating pre-breeding populations and MAGIC populations identified Milestone completed 2. At least 2 pre-breeding populations (F2) generated 44 Pre-breeding populations were generated at ICRISAT, Kenya and Ethiopia 3. Phenotyping of pre-breeding populations completed and at least 10 pre- breeding lines identified for TLII (Milestone for year 4) 4. 500 MAGIC lines made available for trait mapping and identification of superior lines for drought tolerance (Milestone for year 3) 1200 F4 progenies from 8 parental lines from 28 2-ways, 14 4-ways and 7 8-ways crosses 5. Phenotyping data for drought-related traits made available on selected sets of at least 200 MAGIC lines for utilization in breeding and marker/gene discovery for drought tolerance (Milestone for year 4)
  4. 4. Progress under Activity 1
  5. 5. 17 Pre-breeding populations @ ICRISAT, Patancheru Cross Female parent Male parent Remarks ICCX-080093 ICC 4958 ICCV 92944 F5 seed harvested from 103 single plants ICCX-080165 ICC 14199 CRIL 2-17 F4 seed harvested ICCX-070097 ICCV 04512 ICCV 10 F4 population grown in ICCX-070100 ICCV 05530 ICCV 10 Aschochyta nurseries ICCX-080176 ICCX-070187 ICC 12475 F4 seed harvested ICCX-080180 ICCX-070189 ICC 12475 F4 seed harvested from 39 single plants ICCX-070119 ICCV 10 JAKI 9218 F6 seed harvested from 19 progenies ICCX-060029 JG 11 ICC 4958 F6 seed harvested from 45 progenies
  6. 6. 17 Pre-breeding populations @ ICRISAT, Patancheru Cross Female parent Male parent Remarks ICCX-070164 ICC 12475 ICC 1431 F6 seed harvested from 4 progenies ICCX-060037 Summary of pre-breeding populations harvested from 15 ICCV 04112 ICCV 10 F7 seed progenies and 1 line evaluated Crosses in F4 :4 in preliminary yield trail Crosses in 105 ICCX-060046 ICCV F : 1 ICC 9942 F7 seed harvested from 15 progenies and 1 line evaluated Crosses in F6 :9 in preliminary yield trail Crosses in F7 ICCX-060133 KAK 2 : 3 4958 3 F6 progeny bulks harvested ICC ICCX-060134 ICCV 92318 ICC 4958 4 F6 progeny bulks harvested ICCX-070024 ICCX-050037-F2-P3 ICC 4958 2 F6 progeny bulks harvested ICCX-070025 ICCX-050037-F2-P35 ICC 4958 7 F6 progenies harvested ICCX-060025 ICCV 10 ICCV 95334 3 lines in PYTS ICCX-060037 ICCV 04112 ICCV 10 6 F7 progenies harvested
  7. 7. 20 Pre-breeding populations @ ICRISAT, Nairobi Cross detail Remarks ICCRIL 03-0135 × 5 F2 single plants seed ICCRIL 04-0239 available for evaluation as F3 ICCRIL 04-0239 × ICCV 4958 2 F2 single plants seed available ICCV 4958 × ICCV 15333 5 F2 single plants seed available ICCV 15333 × ICCV 4958 4 F2 single plants seed available ICCRIL 04-0239 × 3 F2 single plants seed ICCV 03-0135 available ICCV 15333 × 7 F2 single plants seed ICCRIL 04-0239 available ICCRIL 03-0135 × ICCV 15333 9 F2 single plants seed available ICCV 960183-69 × ICCV 506 14 F2 single plants seed available ICCV 960183-69 × 1 F2 single plants seed ICCV 583311 available ICCV 583311 × ICCV 506 16 F2 single plants seed available ICCV 4958 × ICCRIL 03-0135 2 F2 single plants seed available
  8. 8. 20 Pre-breeding populations @ ICRISAT, Nairobi-con’t Cross Remarks ICCV 583311 × 16 F2 single plants seed ICCV 506 available for evaluation ICCV 4958 × 2 F2 single plants seed ICCRIL 03-0135 available for evaluation ICCV 1052 × 9 F2 single plants seed ICCRIL 04-0239 available for evaluation ICCV 1052 × 8 F2 single plants seed ICCV 4958 available for evaluation ICCV 1052 × 15 F2 single plants seed ICCV 15333 available for evaluation ICCRIL 03-0135 × 8 F2 single plants seed ICCV 4958 available for evaluation ICCV 4958 × 5 F2 single plants seed ICCRIL 04-0239 available for evaluation ICCV 506 × 13 F2 single plants seed ICCV 583311 available for evaluation ICCV 1052 × 7 F2 single plants seed ICCRIL 03-0135 available for evaluation Seed from 20 F2 ICCRIL 04-0239 × 3 F2 single plants seed crosses harvested ICCV 15333 available for evaluation
  9. 9. 5 Pre-breeding populations @ EU, Kenya  Three F2 crosses (ICCV 92944 × ICC 4958, ICCV 92944 x ICCV 97105 ICCV 00305 x ICCV 00108) have been harvested,  Will be advanced to F3 by Aug 2012  Two F3 crosses (ICCV 8261 x ICCV97105, ICCV 4958 x ICCV 97105) have been harvested  Will be advanced to F4 by Aug 2012
  10. 10. 2 Pre-breeding populations @ EIAR, Ethiopia  Two crosses, ICC 4958 × Habru, ICC 4958 × Ejere were made in 2009  At present these are in F3 generation through bulk advance  Single plant selection will be adopted  With in each population based on flower color 8 sub-population (2 from Habaru cross and 6 from Ejere) are being handled  In each sub population more than 10,000 seeds are harvested for next advance
  11. 11. For MAGIC populations Eight well performing elite chickpea lines (TLI & TLII) Parental line Remarks ICC 4958 Drought tolerant genotype found promising in Ethiopia, Kenya and India; drought tolerant parent of two mapping populations ICCV 10 Widely adapted drought tolerant cultivar found promising in India and Kenya JAKI 9218 Farmer-preferred cultivar in central and southern India JG 11 Farmer-preferred cultivar in southern India and also performing well in Kenya JG 130 Farmer-preferred cultivars from central India JG 16 Farmer-preferred cultivar in northern and central India ICCV 97105 Farmer-preferred elite line identified in Kenya and Tanzania ICCV 00108 Farmer-preferred elite line identified in Tanzania
  12. 12. Current status of MAGIC populations 8 parents: A) ICC 4958, B) JAKI 9218, C) JG 130, D) ICCV 00108, E) ICCV 97105, F) ICCV 10, G) JG 11, H) JG 16 28 2-ways Oct 09 – Feb 10 Field 14 4-ways Jun 10- Sep 10 Green house 7 8-ways Oct 10-Feb 11 Field F1s raised and selfed in green house Mar 11- Jun 11 F2s raised and selfed in green house Jun 11- Sep 11 SSD method 1200 F3 progenies raised in field Oct 11- Feb 12 SSD method 1200 F4 progenies raised in field Feb 12- May 12
  13. 13. Sharing the early generation of MAGIC lines 2-way These populations crosses already shared with 4 NARS partners in India (IIPR-Kanpur, JNKVV-Jabalpur, RAKCA-Sehore, RARS- Nandyal) and will be sent to NARS partners in Ethiopia and Kenya during March 2012 8-way F4 populations to be crosses shared during 2012-13
  14. 14. Activity 2: Genomic resources Milestones: 6. At least 768 informative SNPs for cultivated germplasm compiled Milestone completed 7. High-throughput and cost-effective SNP genotyping platform for at least 768 SNPs made available Milestone completed 8. At least 5 candidate genomic regions identified for developing local physical maps Efforts were initiated to develop genome-wide physical map for chickpea 9. Integrated QTL and physical map made available for selected 5 genomic regions Integrated QTL and physical maps developed for selected regions 10. Sequence data for selected BAC contigs for 5 genomic regions generated (Milestone for year 3) 11. 4 Additional markers from each of selected 5 QTL regions generated (Milestone for year 4)
  15. 15. Progress under Activity 2
  16. 16. Comprehensive genetic map LG8 LG2 LG1 Marker Loci: 1,291 Coverage: 845.56 cM LG7 LG3 LG4 LG5 LG6
  17. 17. Cost-effective Homozygote SNP assays Legume COSs Illumina/Solexa Allele specific Heterozygote 1G sequencing sequencing Homozygote KASPar assays designed for 2,468 SNPs 2,005 KASPar assays validated KASPar assays (625 CKAMs mapped) ADT score PIC value calculation ADT score >0.5 High PIC value 96-plex OPAs for Veracode assays BeadXpress system for BeadXpress
  18. 18. KASPar assays integrated in transcript map Markers mapped : 1328 Map distance : 788.6cM Hiremath et al. 2012 Average number of markers/LG : 166 Plant Biotech Jour Average inter-marker distance : 0.59cM
  19. 19. Towards genome-wide physical map Collaboration: NIPGR, India and UC-Davis, USA Fingerprinting statistics of different BAC-libraries Clones CAH library CAE library Old Total library 1st 2nd 1st 2nd 1st 2nd Clones 29,664 5,376 29,568 5,376 337 773 71,094 targeted (12X ) Clones with 28,492 5,160 28,272 5,240 319 765 68, 248 usable data Clones in FPC 18,285 3,502 22,571 3,926 319 765 49,368 Old library, 1st instance are the clones from which BES-SSR were developed Old library, 2nd instance are the RGH hybridizing clones
  20. 20. Statistics of physical map Collaboration: NIPGR, India and UC-Davis, USA Clone statistics in contigs: Total no. clones in 1,174 contigs 46,112 Range of clone in contigs 2 to 3,007 Average no. of clones in each contig 39.27 Genome coverage 8X Genome represented 615 Mb Band statistics in clones: Total no. of bands in clones 318,971 Average no. of bands in clones 271.69 Range of bands in clones 34 to 2,268 Minimum tiling path (MTP): Total no. of contigs 1,174 No of clones in MTP 4,290
  21. 21. Anchoring physical map with chickpea genetic maps Total number of BES-SSR markers integrated 259 Markers hitting singletons 25 Markers hitting contigs 234 Total number of contigs hit by markers 177 Contigs hit by 5 markers 1 Contigs hit by 4 markers 1 Contigs hit by 3 markers 6 Contigs hit by 2 markers 38 Contigs hit by single marker 131
  22. 22. BAC-contig close to drought related root trait QTL LG-04 Clone ID Contig Root trait QTL (No of clones ;Size in Mb) contribute >36% PV LG-04 CAH1015M17 Ctg198 (33, 4.29) Thudi et al. 2011, PLoS ONE
  23. 23. BAC-contigs covering genomic region for AB-QTL LG-02 Clone ID Contig (No. of clones; Size in Mb) LG-02 CAH1041C17 Ctg1390 (2, 0.26) 30.7 cM LG-02 16.5 cM ar3 ar1, ar2a R2 = 20 % CAH1041C17 Ctg1390 (2, 0.26) Iruela et al. 2007 CAH1034D19 Ctg14 (40, 5.2) Udupa and Baum et al. 2003 Thudi et al. 2011, PLoS ONE
  24. 24. Activity 3: Drought tolerance breeding Milestones: 12. Phenotyping data collected and appropriate phenotyping methodology(ies) selected based on detailed analysis of phenotyping data Appropriate phenotyping methodologies selected 13. At least 5 candidate markers for drought tolerance identified (Milestone for year 3) 14. At least 6 farmer-preferred varieties and donor genotypes identified Milestone completed 15. MABC programme being run by each NARS partner from Ethiopia and Kenya MABC program is being run by NARS partners in Ethiopia and Kenya 16. MABC products from Phase I evaluated by each NARS partner (Milestone for year 3) 17. At least 20 homozygous plants from BC3F2 progenies (MABC) of Phase II selected (Milestone for year 3) 18. 3 cycles of recombination completed for MARS (Milestone for year 3) 19. 2-4 farmer-preferred cultivars developed through MABC, and at least 10 superior lines improved for drought tolerance for SSA and Asia through MARS (Milestone for year 4) 20. At lest 2 breeding populations of TLII genotyped for drought and FW-resistance markers (Milestone for year 4) 25. A proposal to leverage funding for chickpea drought tolerance molecular breeding in South Asia approved by the Indian Government for a period of 3-4 years (200K/year) Milestone completed
  25. 25. Progress under Activity 3
  26. 26. Analysis of phenotyping data for drought tolerance (Milestone 12) ICC 4958 × ICC 1882 ICC 283 × ICC 8261 Reference set Trait Reps Year Location Reps Year Location Reps Year Location Root traits 3 2005, Patancheru 3 2006, Patancheru 3 2007, Patancheru 2007 2008 2008, 2009 Yield and HI 1 2005, Patancheru 1 2005, Patancheru 2 2008, EIAR related traits 2006, 2006, 2009 Eger Uni 2007 2007 IIPR Yield and HI 2 2008 Patancheru 2 2010 Patancheru - - - related traits Nandyal Nandyal, rainfed and Sehore Durgapura irrigated conditions 2009 Patancheru Nandyal, Durgapura, Hiryeur Transpiration 2 2008 Patancheru 2 2010 Patancheru 3 2008 Patancheru efficiency Nandyal Nandyal, 2009 Patancheru (δ13C) in Sehore Durgapura rainfed and High-quality genotyping data irrigated 2009 Patancheru for 1871 markers (from 1956) conditions Nandyal, Durgapura, -1072 DArTs, Hiryeur -764 SNPs (651 SNPs, 113 SNPs from 9 candidate genes) Data analysis completed -35 SSRs
  27. 27. Phenotyping on reference set- (i)  Reference set showed enormous diversity for reactions towards terminal drought  Large variations for root traits such as root length density, root dry weight, root volume, root surface area and root/shoot area  Large range variations were also detected for the transpiration efficiency related traits such as ∆13C, specific leaf area and the SPAD chlorophyll meter readings
  28. 28. Phenotyping on reference set- (ii)  ∆13C, SLA and SPAD chlorophyll meter readings - negatively and closely associated with the rate of partitioning  Phenotyping for the root traits and for the rate of partitioning account for a total trait based drought tolerance assessment and as a long term phenotyping strategy  Yield based phenotyping seems more appropriate and there is a need to continue to use this approach
  29. 29. Towards GWAS analysis.. A set of 85 DArT loci, equally distributed on chickpea genome ΔK/K indicate three subpopulations Group I Group II in reference set Group III
  30. 30. MTAs for root traits Trait No of Range of R2 (%) markers p value Root volume 9 8.9E-4 - 1.28E-5 4 - 13 Root dry weight 13 9.8E-4 - 3.63E-6 4 - 17 Rooting depth 1 8.80E-4 4 Root surface area 10 9.4E-4 - 1.1E-5 4 - 18 R-T ratio (%) 2 6.0E-4 - 5.2E-5 4 - 12 Root length 10 9.5E-4 - 4.8E-5 4-6 density
  31. 31. MTAs for phenological and yield related traits Traits No of P values R2 markers Days to flowering 14 9.7E-4 - 1.7E-5 4- 23 Days to maturity 28 9.8E-4 - 2.1E-5 4- 25 Seeds per pod 38 8.8E-4 - 1.3E-10 4- 26 Pods/plant 57 9.5E-4 - 4.3E-7 4- 18 100 seed weight 47 0.9E-4 - 5.6E-14 4- 42 Yield 28 0.9E-4- 3.3E-5 2- 15 Production 3 9.9E-4 -2.3 E-4 5 - 11 Biomass 9.6E-4 - 5.0E-8 4 - 17 Harvest index 15 9.6E-4 - 2.3E-5 4-9 Total dry matter 18 8.9 E-4 -7.15E-7 4 - 14 weight 13C 19 8.4E-4 - 1.72E-6 4 - 17 SPAD 1 2.70E-4 6 SLA 6 9.3E-4 - 4.3E-5 4 - 23
  32. 32. MABC for improving drought tolerance (TL I, Phase I) Crosses: 3 Cultivars x 2 Donors for root traits ↓ BC1: Cultivar x F1 ↓ JG 11 BC1F1 D BC 2:Cultivar x BC1F1 JG 11 x ICC 4958 O ↓ BC2F1 N Subjected to foreground and background selection E BC 3: Cultivar x BC2F1 As in BC2 ↓ BC3F1 Selected heterozygous plants for QTL-linked markers JG11 and over 90% genome of the recurrent parent ↓ ICC 4958 BC3F2 Select homozygous plants for QTL-linked markers Heterozygous ↓ for both alleles Seed multiplication BC3F3 ↓ Homozygous Multilocation evaluation BC3F4 lines for B alleles Homozygous for A allele
  33. 33. Phenotyping of MABC products in ROS BC3F3 lines phenotyped in ROS for assessing root traits
  34. 34. Enhanced root length MABC ICC 4958 products from ICC 4958 BC3F3 progenies JG11
  35. 35. Evaluation of MABC products (BC3F3) 1.7 Donor line Elite line MABC lines Root dry weight (g cylinder-1) 1.5 1.3 1.1 0.9 0.7 0.5 F2-P173 F2-P242 F2-P187 F2-P150 F2-P105 BC3F3s ICC 4958 ICC 1882 JG 11 Mean of 090013- 090013- 090013- 090013- 090013- ICCX- ICCX- ICCX- ICCX- ICCX- (2010) 0.50 Donor line Elite line MABC lines 0.45 0.40 RLD (cm cm-3) 0.35 0.30 0.25 0.20 (2010) F2-P105 F2-P187 F2-P216 F2-P242 F2-P173 4958 JG 11 BC3F3s Mean of 090013- 090013- 090013- 090013- 090013- ICC 1882 ICCX- ICCX- ICCX- ICCX- ICCX- ICC Vertical bars denote standard error of differences. The means were significantly different at 0.001 level and were based on 8 replicated cylinders with 2 plants in each cylinder)
  36. 36. Evaluation of MABC products (BC3F4)
  37. 37. Evaluation of BC3F4 lines in field conditions Evaluated under water-stressed and unstressed conditions at multi-locations (3 locations in India and 3 locations in Africa) during 2011/12
  38. 38. Evaluation of BC3F4 for grain yield (Nandyal)
  39. 39. Evaluation of BC3F4 for 100 seed weight (Nandyal)
  40. 40. MABC by NARS partners NARS partner Cross Generation Student/person involved EIAR, Ethiopia Ejere × ICC 4958 BC2F1 Musa Jarso EU, Kenya ICCV 97105 × ICC 4958 BC4F1 Serah Songok ICCV 95423 × ICC 4958 BC3F3 Mosses Oyier IIPR, India DCP92-3 × ICC 4958 BC1F1 KR Soren/ Subhojit Datta KWR108 × ICC 4958 BC2F1 KR Soren/ Subhojit Datta IARI, India Pusa 362 × ICC 4958 BC1F1 Shailesh Tripathi
  41. 41. MABC status in ICCV 95423 (Kenya) Crop Season Recurrent Donor parent •40-seeds sowed (October 2009) parent (RP) × (ICC 4958) •40-germinated (ICCV 95423) 1st cross Greenhouse •14 seeds harvested (April 2010) RP × F1 •6-seeds sowed,2-selected (True F1s) 1st Backcross Greenhouse •49 seeds harvested (July 2010) RP × BC1F1 •42-seeds sowed,10-selected (Foreground selection) 2nd Backcross Crop Season •89 seeds harvested (October 2010) RP × BC2F1 •42-seeds sowed, 6-selected (Foreground selection) 3rd Backcross Greenhouse •250 seeds harvested BC3F1 (April 2011) •96-seeds sowed, 37-selected (Foreground selection) Selfing •Remaining seeds to be sowed in this crop season of 2011 Greenhouse BC3F2 •150 seeds harvested(BC3F2) (July 2011) •96-seeds sowed. 7-1st selection (Foreground & background) Selfing >90% genome recovery Crop Season BC3F3 •Harvesting- on going (October 2011) •Seed multiplication
  42. 42. MABC status in ICCV 97105 (Kenya) Greenhouse Recurrent Donor parent 40-seeds sowed (Jan 2010) parents (RPs) × (ICC 4958) •39-germinated (ICCV 97105) 1st cross Greenhouse •23 seeds harvested (April 2010) RP × F1 •19-seeds sowed, 16 germinated and 5 selected 1st Backcross Breeding cage RP •42 seeds harvested BC1F1 (Dec 2010) × •32-seeds sowed, 27 seeds germinated 2nd Backcross •19-selected (Foreground selection) Crop Season •37 seeds harvested (April 2011) RP × BC2F1 •30-seeds sowed,17-selected (Foreground selection) 3rd Backcross Rain shelter •84 seeds harvested (April 2012) RP × BC3F1 •40 seeds sowed, 33 seeds germinated. Foreground 4th Backcross selection to be done in April 2012 to select BC3F1 Rain shelter April 2012) RP × BC4F1 30 seeds planted, only six germinated, to be confirmed for true heterozygosity.
  43. 43. MABC status in Ejere (Ethiopia)
  44. 44. NARS partners practicing modern breeding Serah Alice Robert Paul
  45. 45. NARS partners practicing modern breeding Musa Jarso marker analysis for MABC crosses Mosses oyier marker analysis for MABC crosses
  46. 46. MABC status in ICCV 10 (Indian project) Crop Season Recurrent Donor parent •40-seeds sowed (October 2009) parent (RP) (ICCV 10) × (ICC 4958) •37-germinated 1st cross Greenhouse (April 2010) RP × F1 •3-seeds harvested •3-seeds sowed,3-selected (True F1s) 1st Backcross Greenhouse (July 2010) RP × BC1F1 •69 seeds harvested •42-seeds sowed,12-selected (Foreground selection) 2nd Backcross Crop Season (October 2010) RP × BC2F1 •50 seeds harvested •25-seeds sowed,15-selected (Foreground selection) 3rd Backcross Greenhouse BC3F1 •250 seeds harvested (July 2011) •96-seeds sowed,31-selected (Foreground selection) Selfing Greenhouse BC3F2 •150 seeds harvested (July 2011) •96-plants,21-selected( Foreground & Background selection) Selfing >90%genome recovery Crop Season BC3F3 •Seed Multiplication (October 2011) BC3F4 Seeds available March 2012
  47. 47. MABC status @ IIPR (Indian project) KWR108 × ICC 4958 DCP92-3 × ICC 4958 (P1) (P2) MARKER : TA18 F1 (Off season 2011) F1 150bp Back 130bp cross BC1F1 Back BC1F1 cross BC2F1 10-May-12 47
  48. 48. MABC status @ IARI (Indian project) Off-season 2011 (June-Sept/Oct) Pusa 362 The true F1s harvested from main season were sown in pots in GH along with parents Hybridity of the F1s was checked using marker TAA170 and 5 heterozygotes were selected for making backcrosses. BC1F1 seeds (8) were sown in field in Nov 2011 along with recurrent parent (Pusa 362) for backcrossing Rabi 2011-12 FG selection for the linked polymorphic markers was done with TAA170, ICCM0249 and GA24. BC1F1 Pusa 362 5 BC1F1 heterozygotes showed presence of Pusa 362 alleles from both the parents BC2F1s subjected to FG and BG selection. (May/June 2012)
  49. 49. Marker-assisted recurrent selection (MARS) Parent 1 × Parent 2 JG 11 × ICC 04112 JG 130 × ICC 05107 Population development F1 Indian TLI F2 Single seed descent project Phase II 282 F3 progenies F3 Genotyping 70 marker 92 markers F3:4 282 progenies F3:5 QTL detection Multilocation phenotyping Kenya, Ethiopia and India Recombination 10 plants/family (A-H), 6 sets of 8 families/cross Rainfed and irrigated environments 1st Recombination cycle A B C D E F G H (2010-11) 2nd Recombination cycle F1 F1 F1 F1 3rd Recombination cycle F1 F1 QTL analysis completed F1 Population development F2 OptiMAS MARS lines for F3 F3:4 recombination cycles selected Multilocation phenotyping
  50. 50. Phenotyping of MARS population in Kenya & Ethiopia Ethiopia Kenya
  51. 51. MARS lines selected (JG 130 × ICCV 05107) Patancheru (weighted) 3000 2500 Seed Yield (kg/ha) 2000 1500 1000 IR 500 RF 0 Selected Lines Patancheru (un-weighted) 3000 2500 Seed Yield (kg/ha) 2000 1500 1000 IR 500 RF 0 Selected Lines Also selected for HI, biomass
  52. 52. MARS lines selected (JG 130 × ICCV 05107) Kenya (weighted) 3000 2500 Seed Yield (kg/ha) 2000 1500 1000 LR 500 SR 0 Selected Lines Kenya (un-weighted) 3000 2500 Seed Yield (kg/ha) 2000 1500 1000 LR 500 SR 0 Selected Lines Also selected for HI, biomass
  53. 53. MARS lines selected (JG 11 × ICCV 04112) Also for Biomass, HI
  54. 54. MARS lines selected (JG 11 × ICCV 04112) Also for Biomass, HI
  55. 55. Activity 4: Capacity building Milestones: 21. One modern breeding workshop organized for TLI and TLII breeders (Milestone for year 2) Milestone completed- 16 scientists (12 from five countries of Africa and 4 from four countries from Asia) trained in 4 week long workshop 22. 4 MSc and 2 PhD students trained in chickpea genomics and breeding activities (Milestone for year 4) PhD students Ms Serah Songok (Egerton University), Mr Musa Jarso (Addis Ababa University), Ms Alice Koskie (West Africa Centre for Crop Improvement) Mr Kebede Teshome (Haramaya University) MSc students Mr Abebe Sori (Haramaya University), Mr Moses Oyier (Egerton University), Mr Getachew Tilahun (Addis Ababa University).
  56. 56. Activity 5: Managing data Milestones: 23. At least 8 datasets comprising marker sequence data, marker genotyping data, mapping data and phenotyping data obtained in Phase I curated in appropriate databases 12 Datasets were curated on to IChIS, CMap, GDMS and local databases 24. At least 10 datasets comprising marker genotyping and/or phenotyping data on reference collection, mapping populations, MAGIC populations, MABC and MARS populations obtained in Phase II curated in appropriate databases (Milestone for year 4)
  57. 57. Links between TLI and TLII Drought tolerant MAGIC lines will be very useful for the TLII community Access to a larger number of informative SSR and SNP markers associated with drought tolerance Better phenotyping methodologies selected can be transferred to TLII for use in breeding programmes MABC products being transferred to TLII  Cost-effective SSR, DArT and SNP genotyping platform for fingerprinting TLII breeding lines
  58. 58. Take home message….  44 pre-breeding populations and 1200 F4 MAGIC progenies developed  Cost-effective KASPar/ Veracode assays developed, SNPs integrated in genetic map and published open access articles; efforts are underway to link QTLs to physical map  Phenotyping data analysis completed and GWAS study initiated  BC3F4 lines from Phase I evaluated under multi-location trials and several MABC programme being run by NARS partners and MARS cycles are underway; PhD and MSc students undertaking molecular breeding work  Several datasets from Phase I already curated
  59. 59. Many thanks to all contributors • ICRISAT, Patancheru,India: Pooran Gaur, Krishnamurthy L Mahendar Thudi, Trushar Shah, SivaKumar, A Rathore, Rachit Saxena, Prasad Peteti, Manish Roorkiwal, Pavana Hiremath • ICRISAT, Nairobi, Kenya: NVPR Ganga Rao, Said Silim • EIAR, Addis Ababa, Ethiopia: Asnake Fikre, Musa Jarso • Egerton University, Kenya: Paul Kimurto, Richard Mulwa, Serah Songok, Mosses Oyier • IIPR, India: N Nadarajan, S Datta, KR Soren • IARI, India: Shailesh Tripathi, Ch Bharadwaj • UC-Davis, USA: Mingcheng Luo and Doug Cook • NIPGR, India: Sabhyata Bhatia, AK Tyagi
  60. 60. VI International Conference on Legume Genetics and Genomics (VI ICLGG) Hyderabad Marriott Hotel & Convention Center, Hyderabad, India October 2-7, 2012 Featured Speakers: David Bertioli, Catholic Uni, Brazil Doug Cook, UC-Davis, USA Martin Crespi, ISV-CNRS, France Conference Topics: Jeff Doyle, Cornell Uni, USA Peter Gresshoff, Queensland Uni, Australia • Next generation genomics Valérie Geffroy, Paris Uni-Sud, France CLL Gowda, ICRISAT, India • Nutrition Georgina Hernández, UNAM, Mexico T J Higgins, CSIRO, Australia • Development Sachiko Isobe, KDRI, Japan • Evolution and Diversity Scott Jackson, Purdue Uni, USA Eva Kondorosi, IPG-Szeged, Hungary • Symbiosis Günter Kahl, FrankfurtUni, Germany Suk-Ha Lee, Seoul National Uni, Korea • Abiotic Stress Da Luo, Sun Yat Sen Uni, China Greg May, NCGR, USA • Pathogenesis and disease Henry Nguyen, Missouri Uni, USA resistance N Nadarajan, IIPR, India Giles Oldroyd, JIC, UK • Translational genomics Karam Singh, CSIRO/UWA, Australia • Genomics-assisted breeding Richard Thompson, INRA-Dijon, France Ana Torres, IFAPA, Spain • Harnessing germplasm resources Michael Udvardi, Noble Foundation, USA Carroll Vance, Minnesotta Uni, USA Bert Vandenberg, Saskatchewan Uni, Canada … and many more ! www.icrisat.org/gt-bt/VI-ICLGG/Homepage.htm ICLGG2012@gmail.com; r.k.varshney@cgiar.org

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