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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 #419340
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: GrameneOryza 2024: A Collaborative Pan-Genome Resource for Rice Diversity, Knowledge Discovery, and Community Engagement

Author
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item OLSON, ANREW - 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 - Cold Spring Harbor Laboratory
item DYER, SARAH - Embl-Ebi
item JAISWAL, PANKAJ - Oregon State University

Submitted to: International Symposium on Rice Germplasm Evaluation and Enhancement
Publication Type: Abstract Only
Publication Acceptance Date: 9/20/2024
Publication Date: 9/9/2024
Citation: Chougule, K., Wei, S., Lu, Z., Olson, A., Tello-Ruiz, M.K., Gladman, N.P., Zhang, L., Kumar, V., Kumari, S., Ware, D., Kim, S., Dooling, K., Olson, C., Assmann, S., Dyer, S., Jaiswal, P. 2024. GrameneOryza 2024: A Collaborative Pan-Genome Resource for Rice Diversity, Knowledge Discovery, and Community Engagement. International Symposium on Rice Germplasm Evaluation and Enhancement. International Symposium on Rice Functional Genomics Conference, September 9, 2024.

Interpretive Summary:

Technical Abstract: The first complete genome sequence of rice (Oryza sativa) was published in 2002, marking the first crop genome to be sequenced. This milestone laid the groundwork for the Gramene database (http://www.gramene.org), which initially served as the sole comparative genome mapping resource for grasses and has provided access to rice genome diversity for over 20 years. Numerous rice genomes with various agriculturally important traits have since been sequenced, culminating in the development of the pan-genome site GrameneOryza (https://oryza.gramene.org) in 2008. In collaboration with institutions like AGI, MSU, USDA-ARS, and consortia such as IRRI, RAPDB, I-OMAP, and PanOryza, GrameneOryza has advanced rice genomics by offering tools for comparative genomics, including sequence alignment, gene annotation, genetic marker information, gene trees, gene function projections, and synteny maps. It also integrates with other plant databases to enhance its utility. GrameneOryza features 28 Oryza genomes, including domesticated African rice, the MAGIC16 collection, short life cycle KitaakeX, and heirloom US Carolina Gold Rice. Release 8 includes 31M SNPs from EVA, 6.5M SNPs from the USDA Mini-Core Collection, and 12M SNPs from the World Rice and Japanese Rice Collections, along with expression and pathway information on reference IRGSP1. The inclusion of Oryza CLIMtools provides access to environment-genome associations and correlations for a large pool of curated Oryza genotypes. New Germplasm and Sequences tabs offer quick access to germplasm with loss-of-function alleles, gene, transcript, and protein sequences. GrameneOryza coordinates data stewardship, training, and feedback with the community and is funded by 8062-21000-051-000D.