Gramene Oryza PanGenome 7.0 is out with a new Oryza CLIMtools portal!

Oryza PanGenome Release 7.0

Released: August 2023

Gramene's Oryza portal (https://oryza.gramene.org) is a pan-genome resource for rice. In its seventh release, we are introducing the Oryza CLIMtools portal to study Environment x Genome x Phenotype Associations in rice. We also feature new 3K SNP data for four Magic16 genomes: ARC 10497, Zhenshan 97, Liu Xu, and N22 (see * below), and have updated the gene names of all Magic16 genomes. Gene functional annotations from RAP-DB (Sept. 2022) and GeneRIF from curated scientific literature were also updated.

Browse the approximately 19 million SNPs per each of eight Magic16 genomes from the 3000 rice genome project called anew by Dr. Rod Wing's group from resequencing reads using GATK4 software:

• Oryza sativa Japonica Nipponbare
• O. sativa Xian/Indica-adm var. Minghui 63
• O. sativa Xian/Indica-1B1 var. IR64
• O. sativa Geng/Japonica-trop1 var. Azucena
• O. sativa circum-Basmati var. ARC 10497*
• O. sativa Xian/Indica-1A var. Zhenshan 97*
• O. sativa Xian/Indica-3B2 var. Liu Xu*
• O. sativa circum-Aus1 var. N22*

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.