SorghumBase release 3 is out with over 17 million new variants including naturally occurring SNPs and chemically induced point mutations
The SorghumBase Team is pleased to announce the third release of SorghumBase (https://www.sorghumbase.org/) (see release notes #3) with its genome browser providing access to information on 18 reference genomes and 30,475 gene family trees, and QTL data for 220 traits. This release features over 17 million new genetic variants, including naturally occurring SNPs (nearly 13 million naturally occurring SNPs in 499 sorghum accessions from Lozano et al (2021) and chemically induced point mutations (over 2.5 million variations identified in 486 sorghum accessions in the M3 generation of an EMS-mutagenized sorghum population reported by Addo-Quaye et al (2018). In addition, over 1.7 million EMS-induced mutations in the 252 M4 mutant pools previously described by Jiao et al (2016) were recalled for this set.
The 3.0 release of SorghumBase also includes improved performance and layouts for the News, Publications and Events pages. In addition, our publications database has grown to 325 papers, six of which have been highlighted in recent news posts.
In the current release, Sorghum bicolor BTx623 genes are associated with expression and pathway information. Baseline gene expression data was drawn from seven sorghum datasets curated and processed by the EMBL-EBI Expression Atlas. Pathway information is based on Gramene’s Plant Reactome pathways with associations to 1,248 sorghum genes from 269 orthology-based pathways projections (from manually curated rice pathways). Please see SorghumBase R3 release notes for additional information.
The SorghumBase pangenome database (https://www.sorghumbase.org) is a curated, open-source, integrated data resource for comparative functional genomics of sorghum varieties. The genome databases were built in direct collaboration with the Gramene and Ensembl Plants projects. Other data sets were facilitated via collaborations with the Expression Atlas, the Sorghum QTL Atlas, and the Plant Reactome databases.
Core funding for the project is provided by the Agricultural Research Service of the U.S. Department of Agriculture (USDA-ARS 8062-21000-041-00D). Please let us know if you have any questions or suggestions.