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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 #389929
Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

Title: SorghumBase: a web-based portal for sorghum genetic information and community advancement

Author
item GLADMAN, NICHOLAS - Cold Spring Harbor Laboratory
item OLSON, ANDREW - Cold Spring Harbor Laboratory
item WEI, SHARON - Cold Spring Harbor Laboratory
item CHOGULE, KAPEEL - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item TELLO0RUIZ, MARCELA - Cold Spring Harbor Laboratory
item MEIJS, IVAR - Cold Spring Harbor Laboratory
item VAN BUREN, PETER - Cold Spring Harbor Laboratory
item JIAO, YINPING - Texas Tech University
item WANG, BO - Cold Spring Harbor Laboratory
item KUMAR, VIVEK - Cold Spring Harbor Laboratory
item KUMARI, SUNITA - Cold Spring Harbor Laboratory
item ZHANG, LIFANG - Cold Spring Harbor Laboratory
item Burke, John
item Chen, Junping
item Burow, Gloria
item Hayes, Chad
item Emendack, Yves
item Xin, Zhanguo
item Ware, Doreen

Submitted to: Planta
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/27/2021
Publication Date: 1/11/2022
Citation: Gladman, N., Olson, A., Wei, S., Chogule, K., Lu, Z., Tello0ruiz, M., Meijs, I., Van Buren, P., Jiao, Y., Wang, B., Kumar, V., Kumari, S., Zhang, L., Burke, J.J., Chen, J., Burow, G.B., Hayes, C.M., Emendack, Y., Xin, Z., Ware, D. 2022. SorghumBase: a web-based portal for sorghum genetic information and community advancement. Planta. 255:35. https://doi.org/10.1007/s00425-022-03821-6.
DOI: https://doi.org/10.1007/s00425-022-03821-6

Interpretive Summary: This publication serves as an announcement for the release of SorghumBase. SorghumBase is a web-based modular portal that serves to host current and future publicly-available genetic and genomic data for the agriculturally important crop Sorghum bicolor. This web resource addresses the lack of a central hub for sorghum producers, breeders, and other researchers to access publicly-available data that would be useful to them in developing improved sorghum germplasm. The current SorghumBase platform has amalgamated most of the useful genomic data currently available, but can also serve as a community-driven tool for including future genomic and genetic data as those come out. It also will build up resources that are more targeted for the breeding community in coming releases.

Technical Abstract: Public research and development in agriculture rely on proper data and resource sharing within the stakeholder community. For plant breeders, agronomists, molecular biologists, geneticists, and bioinformaticians, centralizing desirable data into a user-friendly hub for crop systems is essential for successful collaborations and breakthroughs in germplasm development. Here, we present the SorghumBase web portal (https://www.sorghumbase.org), a resource for the sorghum research community. SorghumBase hosts a wide range of sorghum genomic information in a modular framework, built with open-source software, to provide a sustainable platform. This initial release of SorghumBase includes: 1) five sorghum reference genome assemblies in a pan-genome browser; 2) genetic variant information for natural diversity panels and ethyl methanesulfonate (EMS)-induced mutant populations; 3) search interface and integrated views of various data types; 4) links supporting interconnectivity with other repositories including genebank, QTL, and gene expression databases; and 5) a content management system to support access to community news and training materials. SorghumBase offers sorghum investigators improved data collation and access that will facilitate the growth of a robust research community to support genomics-assisted breeding.