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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 #428860
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: A Knowledgebase for Sorghum Genomics, Phenomics, and Stakeholder Engagement

Author
item Gladman, Nicholas
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item TELLO-RUIZ, MARCELLA - Cold Spring Harbor Laboratory
item VAN BUREN, PETER - Cold Spring Harbor Laboratory
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item ZHANG, LIFANG - Cold Spring Harbor Laboratory
item OLSON, AUDRA - Cold Spring Harbor Laboratory
item KIM, CATHERINE - Cold Spring Harbor Laboratory
item BRAYNEN, JANEEN - Cold Spring Harbor Laboratory
item Hayes, Chad
item Xin, Zhanguo
item Klein, Robert
item Rooney, William
item PROVART, NICHOLAS - University Of Toronto
item PASHA, ASHER - University Of Toronto
item O'MEARA, ABIGAIL - Cold Spring Harbor Laboratory
item SHAKOOR, NADIA - Donald Danforth Plant Science Center
item MICHAEL, TODD - Salk Institute
item Harrison, Melanie
item Ware, Doreen

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/18/2026
Publication Date: 1/19/2026
Citation: Gladman, N.P., Olson, A., Kumari, S., Wei, S., Chougule, K., Lu, Z., Tello-Ruiz, M.K., Van Buren, P., Kumar, V., Zhang, L., Olson, A., Kim, C., Braynen, J., Hayes, C.M., Xin, Z., Klein, R.R., Rooney, W.L., Provart, N., Pasha, A., O'Meara, A., Shakoor, N., Michael, T.P., Harrison, M.L., Ware, D. 2026. SorghumBase: A Knowledgebase for Sorghum Genomics, Phenomics, and Stakeholder Engagement. Genetics. https://doi.org/10.1093/genetics/iyaf266.
DOI: https://doi.org/10.1093/genetics/iyaf266

Interpretive Summary: SorghumBase is an online resource created to support scientists and others working with sorghum, a globally important grain and bioenergy crop. It brings together a wide range of sorghum-related data—such as genetics, traits, and research findings—into one easy-to-use platform. The goal is to make this information easier to find, access, and share so researchers can work more efficiently and collaboratively. The latest version of SorghumBase includes data from 88 sorghum varieties, information on over 100 million genetic differences, and tools to explore genes, traits, and plant performance. It also offers updates on sorghum research, funding opportunities, and training materials to help users stay connected and informed. Overall, SorghumBase acts as a central hub to support innovation and teamwork in the sorghum research community.

Technical Abstract: Centralizing valuable community data and resources into a user-friendly interface and accessible repository has become essential for agricultural science; embracing Findable Accessible, Interoperable, and Reusable (FAIR) principles is now standard for effective databases. SorghumBase (https://www.sorghumbase.org), is a knowledgebase designed for the sorghum research community. The SorghumBase team curates genomic, transcriptomic, variation, and phenotypic information and aggregates community events, providing rich visualizations and bulk data access. The modular framework of the database is built with open-access software to yield a robust, modifiable, and sustainable data infrastructure. Release 9 of SorghumBase includes: 1) 88 sorghum reference genomes and an updated pan-gene index, 2) over 100 million variants have been mapped onto the two genomes BTx623 and Tx2783, 3) assignment of 41 million Reference Cluster SNP identifiers (rsIDs) from BTx623 across the pan-genome, 4) updated gene search homology, gene expression, and germplasm visualizations and features, 5) added and standardized 234 phenotypic data from 40 community-generated GWAS studies and 148 traits from the Sorghum QTL Atlas (Oz Sorghum), 6) improved news, funding, and a research content management system for community access and interaction, 7) outreach materials including training documents and videos, and 8) community engagement initiatives through training and working groups. SorghumBase serves as a hub for sorghum data and stakeholder engagement while promoting community standards to drive research and multi-omics breeding approaches.