Spatial and Temporal Genome Diversity in Chickpea

Chickpea (Cicer arietinum L., 2n=16) is the second most important food legume crop in the world. It contributes to a larger part of human food and animal feed in developing countries. Due to exposure of the crop to range of biotic and abiotic stresses, the crop productivity, however, is <1 ton per hectare. Furthermore, because of a very narrow genetic diversity in the elite genepool, molecular breeding approaches have also not been in routine for crop improvement in chickpea. With an objective to estimate variations and linkage disequilibrium (LD) in elite germplasm, a non-redundant set of 129 varieties released in 12 countries (Australia, Bangladesh, Spain, Canada, USA, Ethiopia, India, Nepal, Kenya, Tanzania, Myanmar and Sudan) were subjected to whole genome re-sequencing (WGRS). While 5X-12X (with an average 7.3X) coverage WGRS data were generated for 129 lines. Alignment of sequence data for these cultivars with 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. By using these structural variations (SNPs, Indels, PAVs, CNVs), a comprehensive analysis has been undertaken on LD decay, spatial and temporal diversity in terms of released varieties in different decades, as well as market type (desi and kabuli). In addition, a first generation HapMap for chickpea has been developed that provides a resource of large-scale variations for facilitating chickpea breeding.