Skip to main content
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 #414841
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: Public Genetic and Genomic Database for the Sorghum Research and Breeding Community

Author
item TELLO-RUIZ, MARCELA - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - 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 VAN BUREN, PETER - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item Ware, Doreen
item Gladman, Nicholas

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 4/2/2024
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-omic and genetic datasets. SorghumBase works closely with stakeholders to coordinate and support stewardship of sorghum genomics data, while establishing best-practices on data management. Together, we have identified genomes that are important to a variety of sorghum programs including breeding germplasm, disease resistance lines (anthracnose and grain mold), and mapping and diversity populations; this includes 12 lines that have undergone recent sequencing and annotation. Gene model identification and mapping are performed via a pan-genome annotation pipeline using all genetic elements that have currently been identified in all sorghum reference genomes. We maintain a database of scientific publications, genome sequences, genetic variation, gene structure annotations, and comparative genomic analyses integrated with curated data from the Gene Expression Atlas at EBI, BAR eFP Browsers, Plant Reactome database, and QTL Atlas at OZ Sorghum; all using the BTx623 genome as an anchor for these features and as a common link to other Gramene databases. Community coordination aims to improve reference structural gene annotations and develop standards for nomenclature and support biocuration of population studies, expression analyses and gene functions to ensure SorghumBase is a FAIR (Findable, Accessible, Interoperable, Reusable) data resource. As such, data available for bulk query and download include genome data that is accessible via our FTP site and gene expression information through the integrated Gene Expression Atlas. Supported by USDA-ARS #8062-21000-041-00D.