TL-I Phase II        GCP

    WORK PLAN
         for
Objective 4- chickpea
Collaborating Scientists
                   and Institutions                                GCP

 ICRISAT, India- Rajeev ...
Activity 1                   Activity 2          Activity 3            Activity 4                  Activity 5             ...
Activity 1
                                                 GCP

                   Characterization
                   of...
Activity 1                                  Activity 2          Activity 3            Activity 4                  Activity...
Scheme for MAGIC populations
                                                                            GCP

Parental lin...
Timeline for development of
                MAGIC population                                         GCP
Activity         ...
Activity 2 in TLI
              Large scale markers and              GCP

              high-density genetic map




     ...
High-throughput & cost-
            effective marker genotyping                  GCP




Integrated with Molecular Breedin...
Diagnostic markers for
               accelerating molecular breeding
                                             GCP
   ...
Activity 1                                   Activity 2             Activity 3            Activity 4                  Acti...
Phase I- Activity:
Marker discovery for insect resistance
                                    GCP
Natural field conditions...
Scheme for AB-QTL approach
                                                                                    GCP
       ...
Activity 1                                  Activity 2                     Activity 3                      Activity 4     ...
Phase I- Activity 4:
Large scale drought phenotyping
                              GCP




                               ...
Activity 1                                   Activity 2                     Activity 3                      Activity 4    ...
Expected outputs
                                                 GCP


1. TE phenotyping reference collection and
   ICC ...
TL-I Activity 6
Crosses:
                 MABC for Donors for root traits
                   3 Cultivars x 2
             ...
MABC for drought tolerance
            by NARS partners                                     GCP

            Selection of ...
MABC by NARS partners
                                                                                           GCP
     ...
TL-I Activity 6
           MARS for drought tolerance                               GCP



Five good-by-good crosses invol...
Development of MARS
                                  populations continued                                             GC...
Activity 1                                   Activity 2                     Activity 3                      Activity 4    ...
New Activity- trait package
                                                 GCP



                   Genotyping
        ...
Activity 6: Capacity-building
                                                     GCP

Sub-activities:

Strengthening inf...
Activity 1                                   Activity 2                     Activity 3                      Activity 4    ...
Data storage & Management
                                                GCP




  Molecular Breeding Platform

  Datab...
Activity 1                                   Activity 2                     Activity 3                      Activity 4    ...
In summary…
                                                 GCP


  Phase II proposal is based on achievements of
   Pha...
GCP
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38 Rajeev Varshney Tli Objective4 Phase Ii Work Plan

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38 Rajeev Varshney Tli Objective4 Phase Ii Work Plan

  1. 1. TL-I Phase II GCP WORK PLAN for Objective 4- chickpea
  2. 2. Collaborating Scientists and Institutions GCP  ICRISAT, India- Rajeev Varshney, Pooran Gaur, HC Sharma, L Krishnamurthy, Nalini Mallikarjuna, Mahendar Thudi, Siva K. Chamarthi  ICRISAT, Kenya- NVPR Ganga Rao, Said N. Silim  Egerton University, Kenya - Paul Kimurto, Richard Mulwa  Ethiopian Institute of Agricultural Research (EIAR), Ethiopia- Asnake Fikre  Indian Institute of Pulse Research (IIPR) Kanpur, India- Sushil K Chaturvedi, SD Mahapatra,Aditya Pratap  University of California-Davis, USA- Doug Cook, Ming Cheng Luo  DArT Pty Ltd., Yaramulla, Australia- Andrzej Killian
  3. 3. Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7 Reference Enriched BAC end Interspecific Intraspecific Elite lines collection libraries sequences population population 2007 Trait mapping Trait mapping & Ethiopia India, Kenya Phenotyping GCP MARS SSRs MABC X Phase I DArTs Major effect Introgression Minor effect QTLs F3 25-50 Genetic QTLs Genotyping contrast lines SNPs maps BC3F2 Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers Harnessing Diversity Biotic stress Data managemnet resources Capacity Building Abiotic stress Genomic resistance resistance Molecular breeding
  4. 4. Activity 1 GCP Characterization of diversity - extensive phenotyping Pre-breeding population MAGIC population Harnessing diversity
  5. 5. Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7 Reference Enriched BAC end Interspecific Intraspecific Elite lines collection libraries sequences population population 2007 Trait mapping Trait mapping & Ethiopia India, Kenya Phenotyping GCP MARS SSRs MABC X Phase I DArTs Major effect Introgression Minor effect QTLs F3 25-50 Genetic QTLs Genotyping contrast lines SNPs maps BC3F2 Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers 2010 Pre- breed. populations (GCP central registry & Data management MAGIC populations Phase II phenotyping Subset of ICGGC) MAGIC lines phenotyping SUPERIOR LINES Phenotypic data, Markergenotyping data 2014
  6. 6. Scheme for MAGIC populations GCP Parental line Remarks ICC 4958 Drought-tolerant genotype found to be promising in Ethiopia, Kenya and India; drought-tolerant parent of two mapping populations ICCV 10 Widely adapted drought-tolerant cultivar found to be 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 Cavanagh et al. 2008
  7. 7. Timeline for development of MAGIC population GCP Activity Timeline Make 28 one-way crosses Oct 2009–Feb 2010 Confirm hybrids by genotyping and make 14 four-way Mar 2010–Jun 2010 crosses Confirm hybrids by genotyping and make 7 eight-way Jun 2010–Sep 2010 crosses Grow F1s Oct 2011–Feb 2011 Grow F2 (n=500 minimum) Mar 2011– Jun 2011 •  MAGIC lines with enhanced drought tolerance Grow F4 (SSD) Jun 2011–Sep 2011 •  Fine resolution mapping population Grow F5 (SSD) Oct 2011– Feb 2012 Grow F6 (SSD) Mar 2012–Jun 2012 Grow F7 (SSD) Jun 2012– Sep 2012 Grow F8 progenies for seed bulking Oct 2012– Feb 2013 Genotyping of selected MAGIC populations Jan 2013–June 2013 Selection of subset of MAGIC lines based on June 2013- Sept 2013 SNP genotyping/haplotype data
  8. 8. Activity 2 in TLI Large scale markers and GCP high-density genetic map LG 8 Total marker loci - 1821 Inter-marker distance- 2.48cM LG 2 LG 7 LG 1 LG 3 LG 4 LG 5 LG 6
  9. 9. High-throughput & cost- effective marker genotyping GCP Integrated with Molecular Breeding Platform for facilitating molecular breeding in high-throughput and cost-effective manner e.g. - genotyping of MAGIC population - genotyping of AB- population - genotyping of MABC population - genotyping of MARS population
  10. 10. Diagnostic markers for accelerating molecular breeding GCP Marker needs to be Polymorphic in D x R Linkage group 5 -  0 genotypes tested 3 harboring hot spot -  50% success for drought related QTLs in TL-I (Act 4) - 4 markers Candidate QTLs Genetic map CaM0856 ICCM0249 TAA170 STMS11 GA24 Physical map Additional markers BACs
  11. 11. Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7 Reference Enriched BAC end Interspecific Intraspecific Elite lines collection libraries sequences population population 2007 Trait mapping Trait mapping & Ethiopia India, Kenya Phenotyping GCP MARS SSRs MABC X Phase I DArTs Major effect Introgression Minor effect QTLs F3 25-50 Genetic QTLs Genotyping contrast lines SNPs maps BC3F2 Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers 2010 SNP resources & genotyping platform Pre- breed. populations High density genetic maps (GCP central registry & Data management MAGIC populations BAC contigs Phase II phenotyping sequencing NGS Subset of ICGGC) MAGIC lines phenotyping SSR markers SUPERIOR LINES Phenotypic data, Marker/ BAC end sequences 2014
  12. 12. Phase I- Activity: Marker discovery for insect resistance GCP Natural field conditions Detached leaf assay - No natural variation in cultivated germplasm - QTL discovery based on interspecific mapping population didn’t yield appropriate QTLs
  13. 13. Scheme for AB-QTL approach GCP JG11 × PI 489777 Nov 2010 - Mar 2011 (Cultivated) (Wild) F1 Jun 2011 - Oct 2011 JG 11 × BC1F1 Nov 2011 - Mar 2012 JG 11 × BC2F1 Jun 2012 – Oct 2012 × BC2F2 (Genotyping) Nov 2012 - Mar 2013 QTL Analysis × BC2F2:3 (Phenotyping) Jun 2013 – Oct 2013 Identification and charecterisation of ABCLs Nov 2013 - Mar 2013
  14. 14. Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7 Reference Enriched BAC end Interspecific Intraspecific Elite lines collection libraries sequences population population 2007 Trait mapping Trait mapping & Ethiopia India, Kenya Phenotyping GCP MARS SSRs MABC X Phase I DArTs Major effect Introgression Minor effect QTLs F3 25-50 Genetic QTLs Genotyping contrast lines SNPs maps BC3F2 Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers 2010 SNP resources JG 11 × PI 489777 & genotyping platform Expectations Pre- breed. AB-QTL app - Candidate markers and QTLs populations High density Validation genetic maps (GCP central registry & of QTLs - ABCLs with enhanced resistance to insect resistance Data management MAGIC populations BAC contigs Phase II - Validation of insect resistance QTL phenotyping sequencing NGS Subset of ICGGC) MAGIC lines ABCLs phenotyping SSR markers AB-QTLs SUPERIOR LINES Phenotypic data, Marker/ BAC end sequences, QTLs, QTLs-associated markers 2014
  15. 15. Phase I- Activity 4: Large scale drought phenotyping GCP -  000 cylinder 2 (1.2 m long, 20 cm dm) -  Root traits -  Yield -  Harvest index -  CID -  OID WUE/ TE phenotyping needs to be undertaken
  16. 16. Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7 Reference Enriched BAC end Interspecific Intraspecific Elite lines collection libraries sequences population population 2007 Trait mapping Trait mapping & Ethiopia India, Kenya Phenotyping GCP MARS SSRs MABC X Phase I DArTs Major effect Introgression Minor effect QTLs F3 25-50 Genetic QTLs Genotyping contrast lines SNPs maps BC3F2 Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers 2010 SNP resources JG 11 × PI 489777 & genotyping platform Pre- AB-QTL app breed. populations WUE, TE Phenotyping High density Validation genetic maps (GCP central registry & of QTLs Data management MAGIC populations BAC contigs Phase II phenotyping sequencing NGS Subset of Identification of ICGGC) MAGIC lines superior lines for ABCLs phenotyping SSR drought tolerance markers AB-QTLs SUPERIOR LINES Phenotypic data, Marker/ BAC end sequences, QTLs, QTLs-associated markers 2014
  17. 17. Expected outputs GCP 1. TE phenotyping reference collection and ICC 4958 × ICC 1882 mapping population 2. Metadata analysis on all set of phenotyping data- best phenotyping methodology 3. Superior lines with enhanced drought tolerance 4. Validation of drought QTL in elite chickpea lines
  18. 18. TL-I Activity 6 Crosses: MABC for Donors for root traits 3 Cultivars x 2 drought tolerance GCP Donors BC1: Cultivar x F1 ↓ BC1F1 BC 2: Cultivar x BC1F1 ↓ BC2F1 Subjected to foreground and background selection BC3: Cultivar x BC2F1 Cultivars As in BC 2 ↓ BC3F1 Selected heterozygous plants for QTL-linked markers and over 90% genome of the recurrent parent JG 11 ↓ BC3F2 2009-2010 Select homozygous plants for QTL-linked markers ↓ BC3F3 Seed multiplication Chefe KAK 2 ↓ Multilocation evaluation BC3F4 lines
  19. 19. MABC for drought tolerance by NARS partners GCP Selection of cultivars ICCV 97105: Farmer-preferred desi chickpea elite line identified in Kenya and Tanzania through farmer-participatory varietal selection (FPVS) trials conducted in phase I of TLII. This is being proposed for release in Kenya and Tanzania. Ejere: Farmer-preferred kabuli chickpea cultivar identified in Ethiopia through FPVS trials conducted in phase I of TLII. DCP-92-3: Most-popular desi chickpea cultivar in north-eastern India ICC 4958: Well known drought-tolerant genotype with deep and vigorous root system. It is a drought tolerant parent of two mapping populations for root traits. It has also performed well in Ethiopia, Kenya and India
  20. 20. MABC by NARS partners GCP Egerton University, DZARC–Debre IIPR, Kanpur, Njoro, Kenya Ziet, Ethiopia India ICCV 97105 × ICC Ejere × ICC 4958 DCP 92-3 × ICC 4958 4958 Make cross Oct 2009–Mar Oct 2009–Mar Nov 2009 – Mar 2010 2010 2010 Grow F1 and make BC1 Apr 2010–Aug 10 Apr 2010–Aug Jun 2010–Oct 2010 2010 Grow BC1F1, foreground and Oct 2010–Mar Oct 2010–Mar Nov 2010–Mar background selection, make BC2 2011 2011 2011 Grow BC2F1, foreground and Apr 2011–Aug 11 Apr 2011–Aug Jun 2011–Oct background selection, make BC3 2011 2011 Grow BC3F1, foreground and Oct 2011–Mar 12 Oct 2011–Mar Nov 2011–Mar background selection, self selected 2012 2012 plants Grow BC3F2, select homozygous Apr 2012–Aug Apr 2012– Aug Jun 2012–Oct plants for QTL-linked markers, 2012 2012 2012 self selected plants Grow BC3F3 progenies for seed Oct 2012–Mar Oct 2012–Mar Nov 2012–Mar multiplication 2013 2013 2013 Multilocation evaluation of BC3F4 Apr 2013 –Aug Apr 2013–Aug Nov 2013–Mar progenies 2013 2013 2014
  21. 21. TL-I Activity 6 MARS for drought tolerance GCP Five good-by-good crosses involving cultivars from Africa and Asia Set 1 (2 crosses) Set-2 (3 crosses) 2008/09 Genotyping of F3 plants F2 grown F4 (Seed mutiplication) Genotyping of F3 plants Multilocation evaluation F4 (Seed mutiplication) of F5 progenies and QTL analysis Selection and inter-crossing Multilocation evaluation of F3s of F5 progenies and 2009/10 QTL analysis
  22. 22. Development of MARS populations continued GCP Parent 1 × Parent 2 Population development F1 F2 Single seed descent F3 282 F3 progenies Genotyping F3:4 282 progenies F3:5 QTL detection Multilocation phenotyping 10 plants/family (A-H), 6 sets of 8 families/cross Recombination 1 st Recombination cycle A B C D E F G H 2nd Recombination cycle F1 F1 F1 F1 3rd Recombination cycle F1 F1 F1 F2 development F3 Population F3:4 Multilocation phenotyping
  23. 23. Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7 Reference Enriched BAC end Interspecific Intraspecific Elite lines collection libraries sequences population population 2007 Trait mapping Trait mapping & Ethiopia India, Kenya Phenotyping GCP MARS SSRs MABC X Phase I DArTs Major effect Introgression Minor effect QTLs F3 25-50 Genetic QTLs Genotyping contrast lines SNPs maps BC3F2 Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers phenotyping Multilocation 2010 SNP resources JG 11 × PI 489777 F5 & genotyping (NARS) MABC platform Pre- AB-QTL app breed. populations WUE, TE Phenotyping cycles Recombination High density Validation genetic maps (GCP central registry & of QTLs BC3F4 Molecular Data management MAGIC populations BAC contigs Breeding Phase II phenotyping Multilocation phenotyping Platform sequencing NGS phenotyping Multilocation Subset of Selection of ICGGC) MAGIC lines phenotyping ABCLs phenotyping SSR methodology(ies) BC3F2 markers AB-QTLs SUPERIOR LINES Phenotypic data, Marker/ BAC end sequences, QTLs, QTLs-associated markers, Next generation breeders trained 2014
  24. 24. New Activity- trait package GCP Genotyping MBP Development Markers for of populations Marker screening FW resistance for root trait QTL - Act 5.2 of and FW resistance CMBN TL II associated markers Govt of India (TL I) MBP Phenotyping
  25. 25. Activity 6: Capacity-building GCP Sub-activities: Strengthening infrastructure in collaboration with Activity 3 of Objective 5 Organization of a modern breeding workshop for TL-I & TL-II breeders of chickpea Six MSc and three PhD students trained in chickpea genomics and breeding activities
  26. 26. Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7 Reference Enriched BAC end Interspecific Intraspecific Elite lines collection libraries sequences population population 2007 Trait mapping Trait mapping & Ethiopia India, Kenya Phenotyping GCP MARS SSRs MABC X Phase I DArTs Major effect Introgression Minor effect QTLs F3 25-50 Genetic QTLs Genotyping contrast lines SNPs maps BC3F2 Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers phenotyping Multilocation 2010 SNP resources JG 11 × PI 489777 F5 & genotyping (NARS) MABC platform Pre- AB-QTL app Infrastructure Strengthening breed. populations WUE, TE Phenotyping cycles Recombination High density Validation genetic maps (GCP central registry & of QTLs BC3F4 Data management MAGIC populations BAC contigs Phase II phenotyping Multilocation phenotyping studentship sequencing NGS phenotyping Multilocation PhD Subset of Selection of ICGGC) MAGIC lines phenotyping ABCLs phenotyping SSR methodology(ies) BC3F2 markers AB-QTLs SUPERIOR LINES Phenotypic data, Marker/ BAC end sequences, QTLs, QTLs-associated markers, Next generation breeders trained 2014
  27. 27. Data storage & Management GCP   Molecular Breeding Platform   Databases within ICRISAT (Activity 2/ Obj 5)   GCP Central Registry   International Chickpea Genetics & Genomics Consortium (ICGGC)
  28. 28. Activity 1 Activity 2 Activity 3 Activity 4 Activity 5 Activity 6 Activity 7 Reference Enriched BAC end Interspecific Intraspecific Elite lines collection libraries sequences population population 2007 Trait mapping Trait mapping & Ethiopia India, Kenya Phenotyping GCP MARS SSRs MABC X Phase I DArTs Major effect Introgression Minor effect QTLs F3 25-50 Genetic QTLs Genotyping contrast lines SNPs maps BC3F2 Phenotypic data, Marker/ BAC end sequences, Marker genotyping/ QTLs,QTLs-associated markers phenotyping Multilocation 2010 SNP resources JG 11 × PI 489777 F5 & genotyping (NARS) MABC platform Pre- AB-QTL app Infrastructure Strengthening breed. populations WUE, TE Phenotyping cycles Recombination High density Validation genetic maps (GCP central registry & of QTLs BC3F4 Data management MAGIC populations BAC contigs Phase II phenotyping Multilocation phenotyping studentship sequencing NGS phenotyping Multilocation PhD Subset of Selection of ICGGC) MAGIC lines phenotyping ABCLs phenotyping SSR methodology(ies) BC3F2 markers AB-QTLs SUPERIOR LINES Phenotypic data, Marker/ BAC end sequences, QTLs, QTLs-associated markers, Next generation breeders trained 2014
  29. 29. In summary… GCP   Phase II proposal is based on achievements of Phase I of TLI and requirements of TL II and heavily interacted with Mol Breed Platform   All activities are downstream application oriented   Flexible- open for more suggestions from TL II   Diagnostic markers for drought and insect res.   Superior lines (MAGIC, ABCLs, MABCs, MARS) for drought tolerance and insect resistance   Mol breeding being undertaken by NARS
  30. 30. GCP

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