CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea.
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.
Research Program Grain Legumes, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502 324, Telangana State, India.
Dadakhalandar
D
Doddamani
Research Program Grain Legumes, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502 324, Telangana State, India.
Aamir W
AW
Khan
Research Program Grain Legumes, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502 324, Telangana State, India.
Mohan A V S K
MA
Katta
Research Program Grain Legumes, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502 324, Telangana State, India.
Gaurav
G
Agarwal
Research Program Grain Legumes, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502 324, Telangana State, India.
Mahendar
M
Thudi
School of Agriculture and Food Sciences, University of Queensland, St Lucia, Queensland, Australia 4072, School of Plant Biology, The University of Western Australia, Perth, Western Australia, Australia 6009 and.
Pradeep
P
Ruperao
School of Plant Biology, The University of Western Australia, Perth, Western Australia, Australia 6009 and Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia 6009.
David
D
Edwards
Research Program Grain Legumes, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502 324, Telangana State, India, School of Plant Biology, The University of Western Australia, Perth, Western Australia, Australia 6009 and r.k.varshney@cgiar.org.
Rajeev K
RK
Varshney
D029863:Cicer / Q000235:genetics*; D018556:Crops, Agricultural / Q000235:genetics*; D030561:Databases, Nucleic Acid; D054643:INDEL Mutation; D000069600:Plant Breeding; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA / Q000295:instrumentation / Q000379:methods