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

Thudi, M and Khan, A W and Kumar, V and Gaur, P M and Katta, K and Garg, V and Roorkiwal, M and Samineni, S and Varshney, R K (2016) Whole genome re-sequencing reveals genome-wide variations among parental lines of 16 mapping populations in chickpea (Cicer arietinum L.). BMC Plant Biology, 16 (10). pp. 53-64. ISSN 1471-2229

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Background: Chickpea (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. 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 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), intrachromosomal variations (ITX) and inversions (INV) respectively. Conclusion: Genome-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.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Chickpea, Resequencing, Copy number variations, Mapping population, Genomics
Subjects: Mandate crops > Chickpea
Others > Genetics and Genomics
Depositing User: Mr Ramesh K
Date Deposited: 10 Feb 2016 08:41
Last Modified: 21 Oct 2016 09:31
URI: http://oar.icrisat.org/id/eprint/9311
Official URL: http://dx.doi.org/10.1186/s12870-015-0690-3
Acknowledgement: We greatly appreciate support from the CGIAR Research Program on Grain Legumes, ICRISAT, India, for publication of this article. This article has been published as part of BMC Plant Biology Volume 16 Supplement 1, 2015: Selected articles from PlantGen 2015 conference: Plant biology. The full contents of the supplement are available online at http://​www.​biomedcentral.​com/​bmcplantbiol/supplements/16/S1. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes, ICRISAT, India. ICRISAT is a member of CGIAR Consortium.
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