First-generation HapMap in Cajanus spp. reveals untapped variations in parental lines of mapping populations

Kumar, V and Khan, A W and Saxena, R K and Garg, V and Varshney, R K (2016) First-generation HapMap in Cajanus spp. reveals untapped variations in parental lines of mapping populations. Plant Biotechnology Journal, 14 (08). pp. 1673-1681. ISSN 1467-7652

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Whole genome re-sequencing (WGRS) was conducted on a panel of 20 Cajanus spp. accessions (crossing parentals of recombinant inbred lines, introgression lines, multiparent advanced generation intercross and nested association mapping population) comprising of two wild species and 18 cultivated species accessions. A total of 791.77 million paired-end reads were generated with an effective mapping depth of ~12X per accession. Analysis of WGRS data provided 5 465 676 genome-wide variations including 4 686 422 SNPs and 779 254 InDels across the accessions. Large structural variations in the form of copy number variations (2598) and presence and absence variations (970) were also identified. Additionally, 2 630 904 accession-specific variations comprising of 2 278 571 SNPs (86.6%), 166 243 deletions (6.3%) and 186 090 insertions (7.1%) were also reported. Identified polymorphic sites in this study provide the first-generation HapMap in Cajanus spp. which will be useful in mapping the genomic regions responsible for important traits.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Deletions, Insertions, Nextgeneration sequencing, Pigeonpea, Single-nucleotide polymorphism, Whole genome re-sequencing, Mapping, Genomics
Subjects: Mandate crops > Pigeonpea
Depositing User: Mr Ramesh K
Date Deposited: 05 Feb 2016 10:06
Last Modified: 05 Jan 2017 16:08
Official URL:
Acknowledgement: The authors are thankful to the United States Agency for International Development (USAID) (Grant ID: RFA/RFP # BFSG- 11-00002), Biotechnology Industry Partnership Programme (BIPP) and Department of Biotechnology of Government of India for funding various projects related to pigeonpea genomics and molecular breeding projects at ICRISAT that has made this study possible. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes. ICRISAT is a member of the CGIAR Consortium.
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