CicArVarDB: Chickpea Variation Database

Chickpea contributes significantly in the semi-arid tropics in terms of food and fodder. It's productivity and yield are severely hampered by biotic and abiotic stresses. Molecular markers such as single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) implemented through breeding approaches can offer a solution to the hindrance. Advances in modern sequencing technologies like genome sequencing, whole genome re-sequencing (WGRS) and genotyping by sequencing (GBS) have potential to produce large number of molecular markers. With an objective to catalogue variations identified from the WGRS and restriction site–associated DNA sequencing of total 90 genotypes CicArVarDB has been developed (http://cicarvardb.icrisat.org). This database is user friendly and provides possibility to user for choosing variations including SNPs, small insertions and deletions (1-10 base pairs) from a targeted region. Web BLAST is also implemented in the database to search the presence of markers in a user provided query sequence. The database is also configured with the genome browser 'JBrowse' which enables user to visualize the quality of reads, mapping quality and a piece of evidence for the presence of a marker in the genome. The database has been designed to help user and support the application of existing genomic resources to strengthened chickpea varietal improvement programs.