The 3000 Chickpea Genome Sequencing Initiative for Mining Superior Allelles for Crop Improvement.

Chickpea (Cicer arietinum) is the second most important food legume globally, which plays a key role in ensuring the nutritional food security. Average chickpea productivity is less than 1 t /ha as the crops is exposed to several biotic and abiotic stresses in marginal environments. In order to ensure nutritional food security in developing countries, it is essential to develop the superior chickpea varieties with enhanced yield. With an objective to mine the superior alleles, ICRISAT along with its partners has initiated efforts to re-sequence global chickpea composite collection comprising of 3,000 diverse chickpea lines. All these 3,000 lines are being re-sequenced using whole genome resequencing approach with a minimum depth of 10X. Re-sequence data is being aligned to the reference genome for variant detection and construction of HapMap. In parallel, all these 3,000 lines are being phenotyped at 6 different locations in India for yield and yield related traits. Phenotyping data along with re-sequencing data will be used for identification of superior alleles using genome-wide association studies (GWAS). By now, we have already re-sequenced >500 chickpea lines at a depth of 5X to 13X. In total 1.8 Tb sequence data have been generated and ~5 million SNPs have been identifed. Some efforts using the phenotyping data and re-sequencing data on a set of 300 lines (the ‘reference set’) have been made to conduct GWAS and several marker-trait associations have been identified. In summary, the initiative will serve a base for large scale discovery of superior alleles that will accelerate chickpea improvement programs at international level.