GrainGenes: A data-rich repository for small grains genetics and genomics

Authors: YAO, ERIC - University Of California; BLAKE, VICTORIA - Montana State University; COOPER, LAUREL - Oregon State University; WIGHT, CHARLENE - Agri Food - Canada; MICHEL, STEVE - Oregon State University; CAGIRICI, H - Oak Ridge Institute For Science And Education (ORISE); Lazo, Gerard; Birkett, Clayton; WARING, DAVID - Cornell University; Jannink, Jean-Luc; HOLMES, IAN - University Of California; WATERS, AMANDA - Pepsico; EICKHOLT, DAVID - Pepsico; Sen, Taner

Submitted to: Database: The Journal of Biological Databases and Curation
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/26/2022
Publication Date: 5/22/2022
Citation: Yao, E., Blake, V.C., Cooper, L., Wight, C.P., Michel, S., Cagirici, H.B., Lazo, G.R., Birkett, C., Waring, D.J., Jannink, J., Holmes, I., Waters, A.J., Eickholt, D.P., Sen, T.Z. 2022. GrainGenes: A data-rich repository for small grains genetics and genomics. Database: The Journal of Biological Databases and Curation. 2022. Article baac034. https://doi.org/10.1093/database/baac034.
DOI: https://doi.org/10.1093/database/baac034

Interpretive Summary: GrainGenes (https://wheat.pw.usda.gov) is an international centralized repository ensuring long-term sustainability for curated, peer-reviewed datasets of interest to researchers working on wheat, barley, rye, and oat. GrainGenes houses and manages genomic, genetic, germplasm, and phenotypic datasets through a relational database accessed through a dynamically-generated web interface for facilitated data discovery. Since 1992, the GrainGenes resource has continuously served geneticists and breeders in both the public and private sectors globally. Several new datasets were curated into the database along with new visualization and search tools. Four training videos were prepared and shared through a YouTube channel to guide users through the tools and resources at GrainGenes.

Technical Abstract: As one of the U.S Department of Agriculture, Agricultural Research Service (USDA-ARS) flagship databases, GrainGenes (https://wheat.pw.usda.gov) serves the data and community needs of globally-distributed small grains researchers for the genetic improvement of the Triticeae family and Avena species that include wheat, barley, rye, and oat. GrainGenes accomplishes its mission by continually enriching its cross-linked data content following the FAIR (Findable, Accessible, Interoperable, Re-usable) principles, enhancing and maintaining an intuitive web interface, creating tools to enable easy data access, and establishing data connections within and between GrainGenes and other biological databases to facilitate knowledge discovery. GrainGenes operates within the biological database community, collaborates with curators and genome sequencing groups, and contributes to the AgBioData Consortium and the International Wheat Initiative through the Wheat Information System. Interactive and linked content is paramount for successful biological databases and GrainGenes now has 2,917 manually curated gene records, including 289 genes and 254 alleles from the Wheat Gene Catalogue. There are over 4.8 million gene models in 51 genome browser assemblies, 6,273 quantitative trait loci, and over 1.4 million genetic loci on 4,756 genetic and physical maps contained within 443 mapping sets, complete with standardized metadata. Most notably, 50 new genome browsers that include outputs from the Wheat and Barley Pangenome projects have been created. We provide an example of an eQTL (expression quantitative trait loci) track on the IWGSC Chinese Spring wheat browser to demonstrate how genome browser tracks can be adapted for different data types. To help users benefit more from its data, GrainGenes created four tutorials available on YouTube. GrainGenes is executing its vision of service by continuously responding to the needs of the global small grains community by creating a centralized, long-term, interconnected data repository.