Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.)

Mahendar Thudi et al., 'Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.)', BMC Plant Biology, vol. 16(S1), pp.53-64, Springer Nature, 2016

Background: Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poorfarmers in South Asia and Sub-Saharan Africa. In order to harness the untapped genetic potential available forchickpea improvement, we re-sequenced 35 chickpea genotypes representing parental lines of 16 mappingpopulations segregating for abiotic (drought, heat, salinity), biotic stresses (Fusarium wilt, Ascochyta blight,Botrytis grey mould, Helicoverpa armigera) and nutritionally important (protein content) traits using wholegenome re-sequencing approach.Results: A total of 192.19 Gb data, generated on 35 genotypes of chickpea, comprising 973.13 million reads,with an average sequencing depth of ~10 X for each line. On an average 92.18 % reads from each genotypewere aligned to the chickpea reference genome with 82.17 % coverage. A total of 2,058,566 unique single nucleotidepolymorphisms (SNPs) and 292,588 Indels were detected while comparing with the reference chickpea genome.Highest number of SNPs were identified on the Ca4 pseudomolecule. In addition, copy number variations (CNVs) suchas gene deletions and duplications were identified across the chickpea parental genotypes, which were minimum in PI489777 (1 gene deletion) and maximum in JG 74 (1,497). A total of 164,856 line specific variations (144,888 SNPs and19,968 Indels) with the highest percentage were identified in coding regions in ICC 1496 (21 %) followed by ICCV97105 (12 %). Of 539 miscellaneous variations, 339, 138 and 62 were inter-chromosomal variations (CTX), intrachromosomalvariations (ITX) and inversions (INV) respectively.Conclusion: Genome-wide SNPs, Indels, CNVs, PAVs, and miscellaneous variations identified in different mappingpopulations are a valuable resource in genetic research and helpful in locating genes/genomic segments responsiblefor economically important traits. Further, the genome-wide variations identified in the present study can be used fordeveloping high density SNP arrays for genetics and breeding applications