|Mueller, Lukas - Boyce Thompson Institute|
Submitted to: Database: The Journal of Biological Databases and Curation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/23/2016
Publication Date: 8/10/2016
Citation: Edwards, J., Baldo, A.M., Mueller, L.A. 2016. Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees, and whole-genome-based data. Database: The Journal of Biological Databases and Curation. 2016:baw107.
Interpretive Summary: Rice researchers have relied on various types of molecular markers over time for marker assisted breeding and genetic discovery. The scientific literature and associated data sets link those molecular markers with particular traits and historic information about rice varieties. It is difficult to connect all of the different molecular marker types that have been used. Ricebase connects molecular marker information using a common coordinate system in a searchable and browseable interface. This is important for rice geneticists and breeders because it allows them to navigate between old and new molecular marker data in a user-friendly way, and provides opportunities to make new genetic discoveries by exploring their results in the context of surrounding genes and genomic diversity.
Technical Abstract: Ricebase (http://ricebase.org) is an integrative genomic database for rice (Oryza sativa) with an emphasis on combining data sets in a way that maintains the key links between past and current genetic studies. Ricebase includes DNA sequence data, gene annotations, nucleotide variation data, and molecular marker fragment size data. Rice research has benefitted from early adoption and extensive use of simple sequence repeat (SSR) markers; however the majority of rice SSR markers were developed prior to the latest rice pseudomolecule assembly. Interpretation of new research using SNPs in the context of literature citing SSRs requires a common coordinate system. A new pipeline, using a stepwise relaxation of stringency, was used to map SSR primers onto the latest rice pseudomolecule assembly. The SSR markers and experimentally assayed amplicon sizes are presented in a relational database with a web-based front end, and are available as a track loaded in a genome browser with links connecting the browser and database. The combined capabilities of Ricebase link genetic markers, genome context, allele states across rice germplasm, and potentially user curated phenotypic interpretations as a community resource for genetic discovery and applied breeding in rice.