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; Pradeep Ruperao; Dave Edwards; Rajeev K. Varshney

doi:10.1093/database/bav078

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, Pradeep Ruperao, Dave Edwards, Rajeev K. Varshney

Institute of Agriculture

Research output: Contribution to journal › Article › peer-review

22 Citations (Scopus)

Abstract

© The Author(s) 2015. Published by Oxford University Press. 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.

Original language	English
Article number	bav078
Number of pages	7
Journal	Database
Volume	2015
DOIs	https://doi.org/10.1093/database/bav078
Publication status	Published - Aug 2015

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10.1093/database/bav078Licence: CC BY

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title = "CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea",

abstract = "{\textcopyright} The Author(s) 2015. Published by Oxford University Press. 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.",

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T1 - CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea

AU - Doddamani, D.

AU - Khan, A.W.

AU - Katta, M.A.V.S.K.

AU - Agarwal, G.

AU - Thudi, M.

AU - Ruperao, Pradeep

AU - Edwards, Dave

AU - Varshney, Rajeev K.

PY - 2015/8

Y1 - 2015/8

N2 - © The Author(s) 2015. Published by Oxford University Press. 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.

AB - © The Author(s) 2015. Published by Oxford University Press. 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.

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

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