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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #427972
Research Project: Championing Improvement of Sorghum and Other Agriculturally Important Species through Data Stewardship and Functional Dissection of Complex Traits

Location: Plant, Soil and Nutrition Research

Title: SorghumBase is a Knowledgebase for Sorghum Genomic Data and Community Interaction

Author
item BRAYNEN, JANEEN - Cold Spring Harbor Laboratory
item Gladman, Nicholas
item GLADMAN, NICHOLAS - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item OLSON, AUDRA - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item Ware, Doreen
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item VAN BUREN, PETER - Cold Spring Harbor Laboratory

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 7/26/2025
Publication Date: 7/26/2025
Citation: Braynen, J., Gladman, N.P., Gladman, N., Chougule, K., Wei, S., Lu, Z., Tello-Ruiz, M., Olson, A., Kumari, S., Ware, D., Kumar, V., Van Buren, P. 2025. SorghumBase is a Knowledgebase for Sorghum Genomic Data and Community Interaction. Meeting Abstract. American Society of Plant Biologists - Plant Biology 2025 Meeting.

Interpretive Summary:

Technical Abstract: SorghumBase (https://www.sorghumbase.org) is a USDA-ARS funded database. It serves as a central KnowledgeBase for sorghum stakeholders with a focus on genomic, phenomic, and community event data. SorghumBase prioritizes the curation of data on genomes associated with valuable agricultural traits such as disease resistance, grain quality, and drought resilience. The most recent release (Release 9) includes fast pan-genome annotations with representative models from extensive gene families derived from 88 sorghum genome assemblies. Release 9 also features over 78 million genetic variants, 4.2 million gene annotations, and 44,841 phylogenetic gene trees. Noteworthy additions include 12 new sorghum genomes including two high-quality BTx623 reference genome assemblies, gene annotations for 46 expired Plant Variety Protection Act (ex-PVP) breeding lines, and standard SNP identifiers (rsIDs) for 70 sorghum genomes along with the database’s outgroups: maize, rice, and Arabidopsis. Interoperability continues to be strengthened via our cooperation with EMBL-EBI’s Gene Expression Atlas, Plant Reactome, BAR eFP Browser, and OZ Sorghum QTL Atlas. Other new features like the Germplasm tab highlight germplasm with natural and EMS-induced protein-truncating variants in gene models (functionally null genes). Combined with the incorporation of 41 million rsIDs from the European Variation Archive that are mapped to over 3,000 GWAS hits from a meta-analysis of 25 studies, this genotype-phenotype integration provides powerful insights for translational research. All data is accessible via a genome browser and FTP for download, in accordance with AgBioData’s FAIR principles to enhance usability. SorghumBase is funded by the USDA-ARS grant 8062-21000-051-000D.