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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 #428897
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: Unifying Rice Diversity: The GrameneOryza 2025 Pan-Genome Platform for Research and Community Engagement

Author
item WEI, SHARON - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item Gladman, Nicholas
item ZHANG, LIFANG - Cold Spring Harbor Laboratory
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item Ware, Doreen
item KIM, SUYUN - Cold Spring Harbor Laboratory
item DOOLING, KATE - Cold Spring Harbor Laboratory
item OLSON, CHRISTOPHER - Cold Spring Harbor Laboratory
item ASSMANN, SARAH - Pennsylvania State University
item DYER, SARAH - Embl-Ebi
item JAISWAL, PANKAJ - Oregon State University

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 8/23/2025
Publication Date: 8/23/2025
Citation: Wei, S., Chougule, K., Lu, Z., Olson, A., Tello-Ruiz, M., Gladman, N.P., Zhang, L., Kumar, V., Kumari, S., Ware, D., Kim, S., Dooling, K., Olson, C., Assmann, S., Dyer, S., Jaiswal, P. 2025. Unifying Rice Diversity: The GrameneOryza 2025 Pan-Genome Platform for Research and Community Engagement . Meeting Abstract. 2025 International Symposium on Rice Functional Genomics (ISRFG).

Interpretive Summary:

Technical Abstract: Gramene Plants (www.gramene.org), a comparative genome browser for plants, was established 21 years ago following the landmark sequencing of the first complete crop genome, Oryza sativa Japonica. In response to the growing number of sequenced rice genomes, Gramene Plants launched the GrameneOryza' pan-genome portal (oryza. gramene.org) in 2008. Developed in collaboration with AGI, MSU, USDA-ARS, IRRI, RAP-DB, I-OMAP, and PanOryza, the platform supports rice genomics and breeding through integrated tools for comprehensive term-based search, sequence alignment, gene annotation, expression data, gene trees, function projection, synteny mapping, genetic markers, germplasm resources, and community curation. In the era of pan-genomes, GrameneOryza currently hosts 28 wild and domesticated Oryza genomes, many of which are of the highest assembly quality, including those from the MAGIC16 panel?. The platform also aligns with FAIR principles, aiming to make data Findable. Accessible. Interoperable, and Reusable. The latest release (R8) incorporates 68 million rsIDs from EVA^ release 6 into its variation module. SNPs and genotypes from global studies (e.g., 3K-RGP, USDA Mini-Core, World and Japanese Rice Collections) are integrated, with gene consequences predicted. This enables the Gramene Search Interface to identify germplasms carving loss-of-function alleles and direct users to stock center websites for seed acquisition. New features, such as Oryza CLIMtools, allow users to explore genotvpe-environment associations across curated germplasm. GrameneOryza continues to support community engagement through data stewardship, training, and feedback coordination.