Gene discovery

Specific goals : Identification and validation of candidate genes conferring tolerance to abiotic stress and resistance to diseases. 

Outputs:

1. Drought responsive expressed sequence tags (ESTs) for chickpea
2. Fusarium wilt responsive ESTs for pigeonpea
3. Integration of candidate genes and transcription factors in chickpea
4. Allelic diversity at candidate genes in chickpea and pigeonpea
5. TILLING (Targeted Local Lesions In Genome) populations for pearl millet and chickpea

Ongoing projects on genome or EST sequencing for many model and crop species, and the characterization of their genes, has led to a shift in emphasis from analyzing sequences to understanding gene function. At ICRISAT, we are working in close collaboration with several advanced research institutes (ARIs) and national agricultural research systems (NARS) to generate characterization and validation of candidate genes. Also, we are interested in applying functional genomics approaches in the identification of the genes involved in the biotic and abiotic stress tolerance in our mandated crops.

Generation of expressed sequence tags (ESTs) in chickpea

The root tissues of drought tolerant (ICC 4958) and sensitive (ICC 1882) chickpea genotypes grown under controlled growth conditions and challenged by drought are being targeted for generating the ESTs. In case of pigeonpea, ESTs are being generated from the root tissues of Fusarium wilt resistant (ICPL 20102) and susceptible (ICP 2376) pigeonpea plants treated with the Fusarium udum inoculums, grown under glasshouse conditions.

Integration of candidate genes to genetic maps

Unigenes or candidate genes and transcription factors identified through functional genomics experiments for abiotic stress tolerance and biotic stress resistances are being targeted for their integration into genetic maps of respective species.

Allelic diversity at candidate genes in chickpea and pigeonpea

On the one hand, candidate genes like DREB2A, ASR, Sucrose Synthetase, ERECTA are being targeted to identify the homologues across the seven crop species including three cereals (barley, sorghum and rice), two legume species (chickpea and common bean) and two root and tuber crop species (potato and cassava). On the other hand, orthologous candidate genes are planned to sequence across the reference collection in collaborative mode involving several CG centres and ARIs. Sequence data thus obtained for chickpea and sorghum will be analyzed to understand the nucleotide diversity, population structure and to explore the association mapping.

In the case of pigeonpea, a set of 16 genotypes representing seven Cajanus species are being used with conserved orthologous sequence (COS) markers for analysis of sequence diversity in pigeonpea to understand the evolution of diversity across the Cajanus species. This is also being used for the development of single nucleotide polymorphism (SNP) markers.

Generation of TILLING populations

With an objective of validating the candidate genes, TILLING populations are being generated for pearl millet (inbred line P1449-2-P1) and chickpea (accession no. ICC 4958). The chemical mutagen ethyl methane sulfonate (EMS) has been selected to develop these TILLING populations, as it generates mostly SNPs in genes and can be controlled to produce a high density of point mutations causing a variety of lesions, including nonsense and missense mutations.

For further details contact :Rajeev Varshney