Genome Sequence Diversity Pattern and Trends in 140 Elite Cultivars of Chickpea (Cicer arietinum)

Chickpea (Cicer arietinum L., 2n=16), a self-pollinated, diploid annual species which ranks second worldwide as a food legume crop is primarily a crop of developing countries contributing to a larger part of human food and animal feed in these areas. Because of exposure of the crop to range of biotic and abiotic stresses, crop productivity is <1 ton per hectare. Molecular breeding approaches have been quite challenging for crop improvement because of a very narrow genetic diversity in the elite genepool. With an objective to understand genome architecture and genome dynamics in the elite cultivars of chickpea, a non-redundant set of 140 cultivars that includes 82 varieties released in India were subjected to whole genome re-sequencing (WGRS) on Illumina HiSeq 2000 platform. 5X-12X (with an average 7.3X) coverage WGRS data were generated for 129 lines and RAD sequence data (0.80X) were generated on 11 lines. Alignment of sequence data to the draft genome sequence of chickpea (Varshney et al. 2013, Nature Biotechnology 31:240-246) has provided >1.3 Million SNPs in genome, >108 K in mRNA and >42 K in CDS regions. Comprehensive analysis on structural variations (SNPs, Indels, PAVs, CNVs), LD decay, temporal diversity in terms of released varieties in different decades, as well as market type (desi and kabuli) and phylogenetic analysis will be presented. In addition, based on haplotypes for 140 lines, a detailed hapmap of chickpea will be presented. These data will be useful to understand diversity pattern as well as tag the genomic regions for traits of interest to breeders that may be applied for facilitating chickpea breeding.