Gramene Oryza Release 8 unveils new pan-genes and SNP data from USDA and NARO Core Collections

The GrameneOryza team is thrilled to unveil its eighth data release, a significant upgrade to this rice pan-genomics resource. This data build introduces new pan-gene identifiers for Oryza sativa Japonica Nipponbare from the NSF-funded PanOryza Project (DBI #2029854), and integrates standard rsIDs from the European Variation Archive (EVA) for 27 million SNPs. The update also includes new core collections datasets  from the United States Department of Agriculture (USDA) and the Japanese National Agriculture and Food Research Organization (NARO), expanding genetic variation data by over 18 million SNPs:

• USDA Rice Mini-Core Collection (URMC) - 6.5 million SNPs, 190 accessions (Kumar et al, 2021)

• World Rice Core (NARO-WRC) - 12 million SNPs, 68 accessions (Tanaka et al, 2020a)

• Rice Core Collection of Japanese Landraces (NARO-JRC) - 12 million SNPs, 50 accessions (Tanaka et al, 2020b)

New features in Release 8.0 include a “Sequences” tab for easy access to gene, transcript, and protein sequences, and a “Germplasm” tab that lists germplasm with putative loss-of-function (LOF) or protein-truncating variants (PTV) per gene in over 3,500 rice accessions, with direct links to major rice germplasm repositories (e.g., IRRI and GRIN-Global). Additionally, the “Papers” tab now allows researchers and breeders to suggest gene functions based on experimental evidence, enhancing collaborative research efforts. This release further includes an incremental update of curated gene annotations and new chromatin signatures of plant regulatory elements.

Core funding for the project is provided by the Agricultural Research Service of the U.S. Department of Agriculture (USDA ARS 8062-21000-051-00D). We are grateful for their continued support to drive advancements in rice genomics. 

For more details and to access the updated database, visit the release notes at GrameneOryza (https://oryza.gramene.org).