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

Doddamani, D and Khan, A W and Katta, M A V S K and Agarwal, G and Thudi, M and Ruperao, P and Edwards, D and Varshney, R K (2015) CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea. Database. 01-07. ISSN 1758-0463

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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.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Chickpea; CicArVarDB; Genomics; Genetics Research; SNP database; InDel database; Crop Improvement
Subjects: Mandate crops > Chickpea
Depositing User: Mr Ramesh K
Date Deposited: 25 Aug 2015 03:58
Last Modified: 21 Oct 2016 06:30
URI: http://oar.icrisat.org/id/eprint/8954
Official URL: http://dx.doi.org/10.1093/database/bav078
Projects: UNSPECIFIED
Funders: CGIAR Generation Challenge Programme and Australia -India Strategic Research Fund (AISRF)
Acknowledgement: Authors are thankful to the CGIAR Generation Challenge Programme and Australia–India Strategic Research Fund (AISRF) for financial support. Thanks are also due to Manish Roorkiwal and Pooran Gaur for their contribution and help in different experiments. This work has been undertaken as part of the CGIAR Research Program on Grain Legumes. ICRISAT is a member of the CGIAR Consortium. Authors are thankful to the CGIAR Generation Challenge Programme and Australia -India Strategic Research Fund (AISRF) for financial support. Funding for open access charge: Authors are thankful to Australia–India Strategic Research Fund (AISRF) for financial support.
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