Gramene Oryza PanGenome 6.0 is out with curated RAP-DB and NCBI's geneRIFs, searchable QTLs, and 76 million MAGIC16 SNPs

Submitted by marcela.karey on Sat, 01/14/2023 - 13:47

Oryza PanGenome Release 6.0

Released: January 2023

Gramene's Oryza portal (https://oryza.gramene.org) is a pan-genome resource for rice. In its sixth release, find functional curation data for over 4000 RAP-DB genes and NCBI's geneRIFs. This information is linked to relevant publications and other reference databases, and may be found under the Xrefs tab and a new Papers tab in the Search results, see for example: GFR1 or Os10g0508100. In addition, over 20,000 QTLs from Gramene's legacy QTLs database and the Q-Taro database have been made searchable, search for example: chalkiness or grain shattering. Approximately 19 million SNPs called per each of four Magic16 genomes from the 3000 rice genome project were called by Dr. Rod Wing's group from resequencing reads using GATK4 software:

Core funding for the project was provided by the Agricultural Research Service of the U.S. Department of Agriculture (USDA ARS 8062-21000-041-00D) and NSF-DBI CIBR-BBSRC award #2029854.