Whole Genome Re-Sequencing Reveals Genome Wide Variations Among Parental Lines of Mapping Populations in Chickpea

Whole genome re-sequencing approach has been adopted in chickpea (Cicer arietinum), the second most important grain legume, for understanding genome-wide variations that can be utilized for chickpea improvement through molecular breeding. Towards this direction a set of 35 select chickpea inbred genotypes representing parental lines of 16 mapping populations segregating abiotic (drought, heat, salinity), biotic stresses (Fusarium wilt, Ascochyta blight, Botrytis grey mould, Helicoverpa pod borer) and nutritionally important (protein content) traits were used in the present study. A total of 3.41 trillion base pairs of data, generated on 35 select inbred genotypes of chickpea, comprising 91.62 million 150-bp reads, with an average sequencing depth of ~8× for each line.  On an average 92.19% reads from each genotype could be aligned to chickpea reference genome with 82.18% coverage. The number of reads from each genotype aligned on to reference genome varied from 12,765,493 to 87,487,094, while uniquely aligned reads varied from 7,778,952 to 40,072,407. A total of 144,888 unique SNPs and 9,349 indels were detected while comparing with the chickpea reference genome based on CDC Frontier. The total number of SNPs widely varied from one inbred line to the other with a range of 111,583 (Arerti) to 1,001,744 (IG 72953). Highest number of SNP were identified on Ca4 pseudomolecule. Copy number variations (CNV) such as gene deletions and duplications have been identified across the chickpea parental lines, which were minimum in PI 489777 (1 gene deletion) to maximum in JG 74 (1497). Genome-wide SNPs, copy number variations and structural variations identified in different mapping populations are a valuable resource in genetic research and helpful in locating genes/genomic segments responsible for economically important traits.