Objective 4- CHICKPEA

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)

Milestones: 1. 8 Parental genotypes for generating pre-breeding populations and MAGIC populations identified COMPLETED

2. At least 2 pre-breeding populations (F2) generated (Milestone for year 2) Pre-breeding populations will be advanced

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 lines will be advanced to F6 and genotyped

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)

Activity 1: Harnessing Diversity

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Breeding populations to be advanced (Milestone 2)

Crosses made in India: 17 Crosses in F4 : 4 Crosses in F5 : 1 Crosses in F6 : 9 Crosses in F7 : 3 Crosses made in ICRISAT Nirobi: 20 Crosses in F2 : 20 Crosses made in EU Kenya: 2 Crosses in F2 : 2 Crosses made in EIAR Ethiopea: 5 Crosses in F2 : 2 Crosses in F3 : 3

MAGIC populations to be advanced (Milestone 4)

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

F1s raised and selfed in green house Mar 11- Jun 11

SSD method

SSD method

14 4-ways Jun 10- Sep 10 Green house

7 8-ways Oct 10-Feb 11 Field

F2s raised and selfed in green house Jun 11- Sep 11

1200 F3 progenies raised in field Oct 11- Feb 12

1200 F4 progenies raised in field Feb 12- May 12

1200 F5 progenies will be raised in field Jun 12- Sep 12

1200 F6 progenies will be raised in field Oct 12- Feb 13

SSD method

SSD method SNP genotyping

Milestones: 6. At least 768 informative SNPs for cultivated germplasm compiled 7. High-throughput and cost-effective SNP genotyping platform for at least

768 SNPs made available 8. At least 5 candidate genomic regions identified for developing local physical

maps 9. Integrated QTL and physical map made available for selected 5

genomic 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 3)

Activity 2: Genomic resources

COMPLETED

COMPLETED

COMPLETED

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Efforts were initiated to develop genome-wide physical map for chickpea

Sequencing of BAC contigs and development of markers (Milestone 10 and 11)

Genome assembly to be available in next four months

With the help of genetic map, sequence from BAC ends, together with genome assembly new markers will be developed for target QTL regions

Milestones: 12. Phenotyping data collected and appropriate phenotyping methodology(ies) selected based

on detailed analysis of phenotyping data (Milestone for year 2) Detailed phenotyping analysis will be conducted and appropriate 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 COMPLETED 15. MABC programme being run by each NARS partner from Ethiopia, Kenya and India

(Milestone for year 2) MABC to be run by NARS 16. MABC products from Phase I evaluated by each NARS partner (Milestone for year 3) MABC to be evaluated by NARS 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) 1st cycle of recombination initiated 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 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) COMPLETED

Activity 3: Drought Tolerance Breeding

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At least 5 candidate markers for drought tolerance identified

(Milestone 13)

Based on genome-wide association mapping and

mining the genome sequence, candidate markers

associated with drought tolerance will be

identified

NARS partner

Cross Plan (2012-13)

EIAR, Ethiopia

Ejere × ICC 4958

BC3F3 seeds will be harvested

Arerti x ICC 4958 Seed miltiplication of 16 BC3F3 lines

EU, Kenya ICCV 97105 × ICC 4958 BC3F3 seeds will be harvested

ICCV 95423 × ICC 4958 6 BC3F4 lines will be evaluated

IIPR & IARI, India

ICCV 10 × ICC 4958

20 BC3F4 lines will be evaluated

IIPR, India DCP92-3 × ICC 4958 BC3F1 seeds will be harvested

KWR108 × ICC 4958 BC2F1 seeds will be harvested

IARI, India Pusa 362 × ICC 4958 BC3F1 seeds will be harvested

MABC by NARS (Milestone 15)

Evaluation of MABC lines of phase 1

(Milestone 16)

Activity Location

BC3F5 lines of JG 11 × ICC 4958 (22 lines)

EIAR, Ethiopia Egerton University, Kenya ICRISAT, Nairobi ICRISAT, Patancheru TL II partners

BC3F5 lines of 1. Chefe × ICC 4958 (8 lines) 2. KAK2 × ICC 4958 (2 lines)

EIAR, Ethiopia Egerton University, Kenya ICRISAT, Patancheru TL II partners

Recombination cycles planned for MARS (Milestone 18)

JG 130 X ICCV 05107- Egerton Uni, Kenya; IIPR, India JG 11 X ICCV 04112- EIAR, Ethiopia; IARI, India

B A C D E F H G × × × ×

AB CD EG GH × ×

ADCD EFGH ×

ABCDEFGH

10 seeds sown for each line Recombination cycle I Min 20 seeds from each cross Marker analysis- select 10 seed and sow Recombination cycle II Min 100-200 seeds Harvested from each Cross Marker analysis- select 10 seed and sow Recombination cycle III

Select best lines based on allele from all 8 lines Self heterozygous lines Select best lines based on evaluation

Milestones: 21. One modern breeding workshop organized for TLI and TLII breeders COMPLETED 22. 4 MSc and 2 PhD students trained in chickpea genomics and breeding activities (Milestone for year 4) Work of 4 PhD and 2 MSc students will be continued

Activity 4: Capacity building

Kenya: - Ms Serah Songok, PhD student, Eger Uni (Supervisors: P Kimurto, R Mulwa, RK Varshney)

- Ms Alice Koskie, PhD student, WACCI (Supervisors: JK Kedawi, P Kimurto and PM Gaur)

- Mr Moses Oyier, MSc student, Eger Uni (Supervisors: P Kimurto, R Mulwa, RK Varshney)

Ethiopia: - Mr Musa Jarso, PhD student, Addis Ababa Uni (Supervisors: Prof Endeshaw, A Fikre, RK Varshney)

- Mr Kebede Teshome, PhD student, Haramaya Uni (Supervisors: F Mekbib, RK Varshney, PM Gaur)

- Mr Getachew Tilahun, Addis Ababa Uni (Supervisors: A Fikre, RK Varshney )

Modern molecular breeders for NARS (Milestone 12)

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

COMPLETED 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)

Thanks a lot!