CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea

D. Doddamani; A.W. Khan; M.A.V.S.K. Katta; G. Agarwal; M. Thudi; P. Ruperao; D. Edwards; R.K. Varshney

doi:10.1093/database/bav078

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CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea

Journal article

Open access

Peer reviewed

CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea

D. Doddamani, A.W. Khan, M.A.V.S.K. Katta, G. Agarwal, M. Thudi, P. Ruperao, D. Edwards and R.K. Varshney

Database, Vol.2015, Art. bav078

2015

DOI: https://doi.org/10.1093/database/bav078

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Abstract

Molecular markers are valuable tools for breeders to help accelerate crop improvement. High throughput sequencing technologies facilitate the discovery of large-scale variations such as single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). Sequencing of chickpea genome along with re-sequencing of several chickpea lines has enabled the discovery of 4.4 million variations including SNPs and InDels. Here we report a repository of 1.9 million variations (SNPs and InDels) anchored on eight pseudomolecules in a custom database, referred as CicArVarDB that can be accessed at http://cicarvardb.icrisat.org/ . It includes an easy interface for users to select variations around specific regions associated with quantitative trait loci, with embedded webBLAST search and JBrowse visualisation. We hope that this database will be immensely useful for the chickpea research community for both advancing genetics research as well as breeding applications for crop improvement.

Details

Title: CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea
Authors/Creators: D. Doddamani (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
A.W. Khan (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
M.A.V.S.K. Katta (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
G. Agarwal (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
M. Thudi (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
P. Ruperao (Author/Creator) - The University of Queensland
D. Edwards (Author/Creator) - The University of Western Australia
R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
Publication Details: Database, Vol.2015, Art. bav078
Publisher: Oxford University Press
Identifiers: 991005544097807891
Copyright: © 2015 The Authors.
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Mathematical & Computational Biology
ESI research areas: Biology & Biochemistry