Ricebase: A BreedBase implementation for rice with tools for gene discovery and marker development.

Authors: Edwards, Jeremy

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/16/2019
Publication Date: 1/14/2020
Citation: Edwards, J. 2020. Ricebase: A BreedBase implementation for rice with tools for gene discovery and marker development. International Plant and Animal Genome Conference, San Diego, California, January 11-15, 2020. Abstract W155. Electronic Publication.

Interpretive Summary:

Technical Abstract: Ricebase is an integrative genomic database for rice that bridges the gap between the “big data” of rice genomics and the practical needs of rice breeders and researchers. There are numerous rice genomic data sets and published genotype-phenotype associations available to use in developing of marker assisted selection (MAS) tools for breeders. However, the amount of data and the organization of the data are obstacles that restrict one from making full use of these information resources. Finding and combining information from diverse sources for simultaneous evaluation is challenging because of varying data structures and a lack of a common coordinate system to facilitate comparison. Ricebase overcomes the information overload by curating information that is particularly relevant to rice breeding from multiple sources using a well-structured database schema and a common coordinate system based on the reference genome assembly. The Ricebase implementation of BreedBase focuses on connections between germplasm, genetic diversity and molecular markers that are relevant to rice improvement. Data types stored include accession records, pedigrees, phenotypes, genotypes, and molecular markers. Ricebase uses the genome browser JBrowse to display the locations of various genomic features on chromosome coordinates from the MSU7/IRGSP-1.0 assembled rice genome as zoom-able and scroll-able tracks. These browser tracks include the sequence itself, annotated genes, SNPs, SSRs, and QTLs. SSR marker positions are displayed on genome browser tracks along with combined SNPs from the 700K HDRA and 3,000 rice genome resequencing studies, providing continuity between past and current marker technologies. Ricebase has recently been updated to present the results of recent biparental and genome-wide association (GWA) mapping studies as tracks identifying genomic regions associated with the traits. Currently, genome browser tracks are available for biparental QTL mapping of chalk and fissure resistance, and GWA-QTL mapping of salt tolerance, cold tolerance, grain quality, and yield components. Genome browser track features are clickable to bring up links to additional information about the feature, relationships to other features, and database records. For example, SSRs link to accessions that are genotyped with the SSR and their allele states, and QTLs link to literature citations and reported candidate genes.