SNP-Seek Resource for Rice Research

The 3,000 rice genome project generated a large dataset of genomic variation to the world’s most important crop. We identified ~40M SNPs using BWA aligner and GATK variant calling on five reference genomes of rice, representing the major variety groups: Nipponbare (jap), IR 64 (ind), 93-11(ind), DJ 123 (aus) and Kasalath (aus). The results are accessible through the Rice SNP-Seek website (http://snp-seek.irri.org) or by web-services with defined APIs. SNP-Seek provides legacy phenotypic and passport data for all the sequenced varieties from the International Rice Genebank Information System at IRRI and incorporates gene models from several rice annotation projects.

Inside SNP-Seek, the massive genotypic data are stored as HDF5 files for fast retrieval, while the germplasm, phenotypic and genomics data are in RDMS using the CHADO schema, allowing the use of controlled terms from biological ontologies as query constraints. Several visualization tools are embedded including: JBrowse for SNPs, indels and genes; VISTA for the genome alignments; phylogenetic tree and MDS plots to explore the evolutionary relationships between the varieties; allele frequency chart and the genotype matrix viewer. A list manager for SNPs, varieties and genes allows the user to pass results as constraints in their queries. The SNP Annotator can add traits, ontology terms, functional effects and interactions to the markers in a list. In this demo we will present the data and features of the Rice SNP-Seek Database, and show typical use cases focusing on allele-mining and breeding applications.