GrainGenes: Genetics, Genomes, and Pangenomes

Authors: Yao, Eric; BLAKE, VICTORIA - Montana State University; SHARMA, PARVA - University Of Maryland; PORETSKY, ELLY - Oak Ridge Institute For Science And Education (ORISE); MICHEL, STEVE - Volunteer; Birkett, Clayton; WARING, DAVID - Cornell University; Jannink, Jean Luc; Gu, Yong; TIWARI, VIJAY - University Of Maryland; Lazo, Gerard; Sen, Taner

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/10/2025
Publication Date: 12/16/2025
Citation: Yao, E., Blake, V., Sharma, P.K., Poretsky, E., Michel, S., Birkett, C.L., Waring, D.J., Jannink, J., Gu, Y.Q., Tiwari, V.K., Lazo, G.R., Sen, T.Z. 2025. GrainGenes: Genetics, Genomes, and Pangenomes. Genetics. 232(4)Article iyaf270. https://doi.org/10.1093/genetics/iyaf270.
DOI: https://doi.org/10.1093/genetics/iyaf270

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 to help geneticists and breeders develop wheat, barley, rye, and oat plants with desired agronomic traits against abiotic and biotic stresses such as diseases that cost American farmers millions of dollars per year.

Technical Abstract: As one of the flagship databases of the U.S. Department of Agriculture, GrainGenes is positioned at the critical juncture of agricultural data crossroads. GrainGenes (https://graingenes.org; https://wheat.pw.usda.gov) is a centralized location for curated data and web-based tools for wheat, barley, rye, and oat in the service of a global user base. Since 1992, GrainGenes has been serving plant researchers in their quest to improve traits, including biotic and abiotic resistance, as well as high nutrition content. Starting with genetic markers and maps, GrainGenes has evolved to acquire genomic sequences, assemblies, and annotations, leading to an ever increasing number of pangenomes. Over the years, new web-based tools and capabilities were added to the website to increase the access and utility of peer-reviewed datasets for researchers, plant geneticists and breeders at various stages of their careers, from high school students to emeritus professors. Here we provide a comprehensive vista of GrainGenes curated content and customized tools so that through researchers, growers, and farmers, animals are fed with high-quality feed, and an ever-growing human population has enough to eat and drink nutritious food and food products.