A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database

Authors: Brown, Anne; CONNORS, SHAWN - US Department Of Agriculture (USDA); Huang, Wei; WILKEY, ANDREW - Iowa State University; Grant, David; Weeks, Nathan; Cannon, Steven; Graham, Michelle; Nelson, Rex

Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/23/2020
Publication Date: 12/2/2020
Citation: Brown, A.V., Connors, S., Huang, W., Wilkey, A., Grant, D.M., Weeks, N.T., Cannon, S.B., Graham, M.A., Nelson, R. 2020. A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Research. 49(D1):D1496-D1501. https://doi.org/10.1093/nar/gkaa1107.
DOI: https://doi.org/10.1093/nar/gkaa1107

Interpretive Summary: Developing new crop varieties to deal with challenges such as new pathogen strains or environmental challenges requires information about the genetic basis for plant responses to these stresses. To fulfill the needs of soybean breeders and researchers, the USDA-ARS maintains the SoyBase online database as a central repository for genetic and genomic data and related resources for soybean. In addition to genetic and genomic data, SoyBase is also a center for distribution of announcements of meetings, soybean genetics committee reports and job openings for the soybean breeding and research community. Availability of this online resource to researchers and breeders is important for development of improved soybean cultivars, benefitting farmers and consumers.

Technical Abstract: SoyBase, the USDA’s genetic and genomics database, holds professionally curated soybean genetic and genomic data, which is integrated and made accessible to researchers and breeders. The site holds several reference genome assemblies, as well as genetic maps, thousands of mapped traits, expression and epigenetic data, pedigree information, and extensive variant and genotyping data sets. SoyBase displays include genetic, genomic, and epigenetic maps of the soybean genome. Gene expression data is presented in the genome viewer as heat maps and pictorial and tabular displays in gene report pages. Millions of sequence variants have been added, representing variations across various collections of cultivars. This variation data is explorable using new interactive tools to visualize the distribution of those variants across the genome, between selected accessions. SoyBase holds several reference-quality soybean genome assemblies, accessible via various query tools and browsers, including a new visualization system for exploring the soybean pan-genome. SoyBase also serves as a nexus of announcements pertinent to the greater soybean research community. The database also includes a soybean-specific anatomic and biochemical trait ontology. The database can be accessed at https://soybase.org.