Skip to main content
ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #436569
Research Project: Championing Improvement of Sorghum and Other Agriculturally Important Species through Data Stewardship and Functional Dissection of Complex Traits

Location: Plant, Soil and Nutrition Research

Title: GramenePlants: Advancing Plant Pan-Genome Resources for an AI-Ready Future

Author
item Gladman, Nicholas
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item WEI, XUEHONG - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item VAN BUREN, PETER - Cold Spring Harbor Laboratory
item OLSON, AUDRA - Cold Spring Harbor Laboratory
item KIM, SUYUN - Cold Spring Harbor Laboratory
item Ware, Doreen
item BRAYNEN, JANEEN - Cold Spring Harbor Laboratory

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 6/15/2026
Publication Date: 6/15/2026
Citation: Gladman, N.P., Olson, A., Kumari, S., Wei, X., Chougule, K., Lu, Z., Van Buren, P., Olson, A., Kim, S., Ware, D., Braynen, J. 2026. GramenePlants: Advancing Plant Pan-Genome Resources for an AI-Ready Future. Meeting Abstract. National Association for Plant Breeding (NAPB) annual meeting.

Interpretive Summary:

Technical Abstract: Since 2001, Gramene has supported comparative plant genomics, genetics, breeding, and evolution. With a global user base, it provides integrated access to genome annotations, variation, pathways, regulatory networks, and expression data across coordinated platforms. Rebranded as GramenePlants, Release 69 includes 233 reference genomes, curated pathways for 139 species, and extensive variation data. Recent updates add expression visualization tools, a literature-curated gene function catalog, and large-scale phenomics data for trait discovery. The enhanced Germplasm tab links loss-of-function alleles to public germplasm repositories. Crop pan-genome resources—including GrameneMaize, GrameneOryza, GrameneGrapevine, and SorghumBase—enable exploration of structural and presence/absence variation. Integration of standard SNP identifiers (rsIDs) and collaborations with the US National Plant Germplasm System (NPGS) and Breeding Insight have created useful database resources as well as community products in addition to enhancing reproducibility and alignment with FAIR data principles. Looking forward, Gramene supports the community through FAIR data training and by developing next-generation AI tools, including a Model Context Protocol (MCP) server to make integrated gene search data accessible to AI agents. A core strategic priority is making all integrated data ‘AI-ready’ to empower researchers and breeders to leverage advanced analytics for predictive biology. Together, GramenePlants and its crop-specific portals provide a scalable, community-driven infrastructure for advancing plant genomics research into the era of artificial intelligence.