Re-Sequencing of 429 Lines for Understanding Drought and Heat Tolerance Mechanisms in Chickpea (Cicer arietinum L.)

Chickpea (Cicer arietinum L.) is an important food legume crop, particularly for the arid regions, providing one of the most balanced nutritional compositions. Current global yield average of chickpea is less than 1 t ha^–1 due to several biotic and abiotic stresses. Recently after completion of chickpea draft genome efforts were initiated to use the genome sequence for chickpea improvement. In order to exploit the genome sequence for chickpea improvement ~400 chickpea lines including 300 lines from chickpea reference set and 100 elite chickpea varieties have been sequenced using whole genome re-sequencing approach on Illumina HiSeq 2500 at 5X to 13X coverage. In total 1.8 Tb sequence data were generated and aligned to draft chickpea genome for variant calling and structural variation analysis. Structural variation analysis revealed ~4.7 million SNPs, >500 K each of Indels and CNVs. In addition, linkage disequilibrium analysis using sliding window approach in TASSEL with a minimum allele frequency (MAF) of 0.2 was also performed. Furthermore, analysis on genetic diversity, gene loss, domestication and selection sweep is underway. Phenotyping data for high priority traits for breeding is being compiled and will be used for genome-wide association analysis as well as genetic architecture, evolution and domestication studies for identification of superior/novel alleles contributing to the trait of interest. Detailed results will be presented in the conference.