Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 10, 2009
Publication Date: December 15, 2009
Citation: Grant, D.M., Nelson, R., Cannon, S.B., Shoemaker, R.C. 2009. SoyBase, The USDA-ARS Soybean Genetics and Genomics Database. Nucleic Acids Research. Doi: 10.1093/nar/gkp798. Interpretive Summary: The recent decade has seen a huge increase in the acquisition of genetic and genomic data for many crop species. No where has this been more evident than for soybean where the whole genome sequence has recently been generated and assembled. Managing and visualizing this vast array of information requires a specialized and manually curated database. In this manuscript, the authors report on the development and status of SoyBase, a USDA-ARS-supported genetic and genomic database. The database contains data on more than 90 unique soybean traits acquired over nearly 20 years of research. This data is embedded in the genetic and physical map, including the assembled genome sequence. SoyBase provides visualization and analysis tools to study the data. This database is critical to soybean breeders, molecular geneticists and students. Access to SoyBase will speed the improvement of soybean traits by breeders, aid in the development of hypotheses for geneticists and provide speedy access to information for students. All of this will result increased knowledge and better soybeans with improved characteristics.
Technical Abstract: SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. The quantitative trait loci (QTL) represent more than 18 years of QTL mapping of more than 90 unique traits. SoyBase also contains the well-annotated “Williams 82” genomic sequence and associated data-mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. SoyBase is the repository for controlled vocabularies for soybean growth, development and trait terms, which are also linked to the more general plant ontologies. SoyBase can be accessed at http://soybase.org.