Home - IC4R Rice Variation Database

Rice (species in gen. Oryza) is not only an important model organism for monocots but also the most widely consumed staple food for a large part of the world's human population (about 2.5 billion people). Recently, thousands of rice accessions have been re-sequenced, in which single nucleotide polymorphism (SNP) is an important molecular marker for rice breeding. So we collected almost all the public available re-sequenced rice accessions (5152), and identified about 18M SNPs against Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecule using unified standard SNP-calling pipeline

Here we provide detailed annotation information of variations, including SNP consequence, gene function, etc.. It was also hyper-linked to other databases (e.g. dbSNP).  We curated the SNP effects by integrating available genotype-to-phenotype association results.  We developed a powerful 'Search Engine' and a multi-track 'Browser' for users to obtain desired information.  Also, we developed three practical online tools, RiceClustwl, Population Genetic Analysis and Gene Haplotype Analysis, for users to do advanced data mining and analysis. 

Release Notes

  • We curate the SNP effects by integrating available genotype-to-phenotype association results.
  • We develop a powerful 'Search Engine' and a multi-track 'Browser' for users to obtain desired information.
  • We develop three practical online tools (RiceClustwl, Population Genetic Analysis, Gene Haplotype Analysis) for users to do some advanced data mining and analysis.

Recent publications

  • Crowell, S. et al. Genome-wide association and high-resolution phenotyping link Oryza sativa panicle traits to numerous trait-specific QTL clusters. Nat. Commun. 7, 10527 (2016).
  • Yano, K. et al. Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice. Nat. Genet. advance online publication, (2016). [more...]
  • Spindel, J. E. et al. Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement. Heredity 116, 395?408 (2016).
  • Li, G. et al. Genome-Wide Sequencing of 41 Rice (Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation. Mol. Plant 0, (2016).
  • Wang, H. et al. The Power of Inbreeding: NGS Based GWAS of Rice Reveals Convergent Evolution during Rice Domestication. Mol. Plant doi:10.1016/j.molp.2016.04.018