SorghumBase release 6 is out with BTx623 v5.1 and over 40 million new SNP and EMS variants
The SorghumBase Team is pleased to announce the sixth release of SorghumBase (https://www.sorghumbase.org) (see release notes #6).
The current release includes the assembly version 5.1 of the Sorghum bicolor BTx623 genome from JGI’s Phytozome (restricted by the Ft Lauderdale Accord).
This release also includes over 40 million new sorghum variants: 8.6M EMS-induced mutations in 890 samples of BTx623, and 32.5M SNPs from Tx2783, a sugarcane aphid (SCA)-resistant Sorghum Association Panel (SAP) accession. In addition, we are releasing a downloadable list of 1.6 million predicted loss-of-function variants from BTx623 (naturally occurring SNPs and EMS-induced mutations) that includes flanking sequences, which can be used for genetic marker primer design (KASP, CAPS, rhPCR). This stable flat file is accessible through the SorghumBase FTP site (ftp.sorghumbase.org)
To support the functional annotation of sorghum genes, we are featuring a new Papers tab in the gene search results, which lists PubMed-indexed papers associated with curated genes from NCBI’s GeneRIF and RAP-DB. This feature, together with indexing of nearly 13K QTLs associated with 330 traits, makes it possible to search associated Trait Ontology (TO) and Plant Ontology (PO) terms in SorghumBase. To support curation of gene structure, we have also added links to the Gene Tree Curation Tool to the “Homology Results” tab of all BTx623 genes.
Our publications database has grown to 739 papers, 53 of which have been highlighted in recent News posts, and is searchable by author, keywords, pubmed ID, or any other text within the title or abstract. Please check the upcoming Events page for the latest conferences, meetings, webinars, etc. relevant to the sorghum research community. You are always welcome to Contact Us if you are interested in hosting a training event, would like to collaborate with the SorghumBase team or to have any questions, comments or concerns.
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).
