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Abstract
BackgroundChickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in South Asia and Sub-Saharan Africa. In order to harness the untapped genetic potential available for chickpea improvement, we re-sequenced 35 chickpea genotypes representing parental lines of 16 mapping populations segregating for abiotic (drought, heat, salinity), biotic stresses (Fusarium wilt, Ascochyta blight, Botrytis grey mould, Helicoverpa armigera) and nutritionally important (protein content) traits using whole genome re-sequencing approach.ResultsA 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 genotype were aligned to the chickpea reference genome with 82.17 % coverage. A total of 2,058,566 unique single nucleotide polymorphisms (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) such as gene deletions and duplications were identified across the chickpea parental genotypes, which were minimum in PI 489777 (1 gene deletion) and maximum in JG 74 (1,497). A total of 164,856 line specific variations (144,888 SNPs and 19,968 Indels) with the highest percentage were identified in coding regions in ICC 1496 (21 %) followed by ICCV 97105 (12 %). Of 539 miscellaneous variations, 339, 138 and 62 were inter-chromosomal variations (CTX), intra-chromosomal variations (ITX) and inversions (INV) respectively.ConclusionGenome-wide SNPs, Indels, CNVs, PAVs, and miscellaneous 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. Further, the genome-wide variations identified in the present study can be used for developing high density SNP arrays for genetics and breeding applications.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0690-3) contains supplementary material, which is available to authorized users.
Highlights
Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in South Asia and Sub-Saharan Africa
To dissect complex biotic and abiotic stresses, several bi-parental mapping populations and generation mapping populations like multi-parent advanced generation intercross (MAGIC) population are being used at ICRISAT
Few thousand simple sequence repeat (SSR) markers are available for trait mapping in chickpea, limited polymorphism among parental lines of bi-parental mapping population has been hindering the trait mapping efforts to reach to the candidate genes responsible for the traits of interest [7]
Summary
Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in South Asia and Sub-Saharan Africa. Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated mostly on residual soil moisture in the arid and semi-arid regions of the world It is a self-pollinated crop and cross pollination is a rare event (0–1 %) [1]. Chickpea has its origin in southeastern Turkey, and after its domestication, from a closely related wild species C. reticulatum Ladizinsky, in the Middle East this crop progressed further throughout the Mediterranean region, India and Ethiopia [2, 3]. It is a rich source of protein to vegetarian diets, especially in India. Despite being the largest producer, India imports chickpea from several countries e.g. Australia, Turkey, Mexico, USA, Canada etc
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