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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 #417535
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 2024: Building Partnerships and Integrating Genetic Knowledge for the Sorghum Community

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

Submitted to: American Society of Plant Biologists Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 6/22/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: SorghumBase (https://www.sorghumbase.org) is a USDA-ARS funded resource for curated multi-omics and genetic datasets. SorghumBase collaborates with stakeholders to coordinate and support stewardship of sorghum genomics data, establishing best practices in data management. We have identified genomes associated with high-value traits, disease resistance, grain quality, and drought tolerance, and developed reference assemblies for these accessions. Gene model identification and mapping are performed via a fast pan-genome annotation approach using representative pan-gene models selected from gene families. SorghumBase release 7 hosts 29 sorghum genome sequences, including both v3 and v5 assemblies of the reference genome BTx623, 59 million genetic variations, 1,055,435 gene annotations, 42,926 phylogenetic gene trees, and 972 selected scientific publications. It integrates curated data from the EMBL-EBI Gene Expression Atlas, BAR eFP Browsers, Plant Reactome pathways database, and QTL Atlas (OZ Sorghum). These features are anchored to the BTx623 v3 assembly and can be projected to other genomes. We work with the AgBioData community to develop data and metadata standards, supporting biocuration of population studies and expression data in line with FAIR principles. Recent updates include incorporating rsIDs from the European Variation Archive, mapping 41 million rsIDs, and linking these to over 3,000 GWAS hits from a meta-analysis of 25 studies. A new germplasm tab has been added to the search interface, listing germplasms with protein-truncating variants, enhancing the resource's usability for translational biology. Data is available for query and download via our genome browser and FTP site. Supported by USDA-ARS #8062-21000-041-00D.