Consideration of O. Rufipogon Diversity with a SNP Database

Speciation process from Oryza rufipogon, the most closely related wild relatives, to cultivated rice Oryza sativa, has been revealed by employing comprehensive NGS genotyping of a broad variety of O. rufipogon accessions. With the phenotypic information of those accessions, they will be served as an excellent resource of genotypes and phenotypes for future rice functional genomics and efficient breeding by the means of GWAS and Genomic Prediction methodologies. Here we aim to comprehensively integrate our previous outcome and newly determined genotype information onto a united repository. We have been constructing an SNP database serving the variant information with seamless connection to Oryzabase, an integrated rice science database published and maintained by National Institute of Genetics, Japan.

The database consists of genotype information of 446 O. rufipogon accessions derived by imputation method and 17 accessions by imputation-free middle depth (~20x) sequencing. In order to inspect the molecular evolutionary significance, dN, dS, and dN/dS ratio of all gene models were also computed and stored. In addition, SnpEff results were included as functional annotations of the variants. A couple of variant viewers were implemented, “Graphic View” as a conventional genome viewer interface and “Tabular View” as a text-based browser for precise inspection of each variant one by one. The portable PED/MAP download function was also available.

In this presentation, the current status and the future direction of the SNP database will be reported and discussed.