CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea.
Open Access
- 18 August 2015
- journal article
- dataset
- Published by Oxford University Press (OUP) in Database: The Journal of Biological Databases and Curation
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. Database URL:http://cicarvardb.icrisat.org.Keywords
This publication has 34 references indexed in Scilit:
- Discovery of Single Nucleotide Polymorphisms in Complex Genomes Using SGSautoSNPBiology, 2012
- Impact of Genomic Technologies on Chickpea Breeding StrategiesAgronomy, 2012
- High-Throughput SNP Discovery and Genotyping for Constructing a Saturated Linkage Map of Chickpea (Cicer arietinum L.)DNA Research, 2012
- Large‐scale development of cost‐effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumesPlant Biotechnology Journal, 2012
- Large‐scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi‐arid tropics of Asia and AfricaPlant Biotechnology Journal, 2011
- UniProt Knowledgebase: a hub of integrated protein dataDatabase: The Journal of Biological Databases and Curation, 2011
- Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genomeTheoretical and Applied Genetics, 2010
- Next-generation sequencing technologies and their implications for crop genetics and breedingTrends in Biotechnology, 2009
- AutoSNPdb: an annotated single nucleotide polymorphism database for crop plantsNucleic Acids Research, 2008
- Basic Local Alignment Search ToolJournal of Molecular Biology, 1990