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

Gladman, Nicholas, Olson, Andrew, Wei, Sharon, Chougule, Kapeel, Lu, Zhenyuan, Tello-Ruiz, Marcela, Meijs, Ivar, Van Buren, Peter, Jiao, Yinping, Wang, Bo, Kumar, Vivek, Kumari, Sunita, Zhang, Lifang, Burke, John, Chen, Junping, Burow, Gloria, Hayes, Chad, Emendack, Yves, Xin, Zhanguo, Ware, Doreen (January 2022) SorghumBase: a web-based portal for sorghum genetic information and community advancement. Planta: an international journal of plant biology, 255 (2). p. 35. ISSN 0032-0935

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URL: https://www.ncbi.nlm.nih.gov/pubmed/35015132
DOI: 10.1007/s00425-022-03821-6

Abstract

MAIN CONCLUSION: SorghumBase provides a community portal that integrates genetic, genomic, and breeding resources for sorghum germplasm improvement. Public research and development in agriculture rely on proper data and resource sharing within stakeholder communities. 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.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > databases
bioinformatics > genomics and proteomics > analysis and processing > reference assembly
organism description > plant > sorghum
CSHL Authors:
Communities: CSHL labs > Ware lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 11 January 2022
Date Deposited: 12 Jan 2022 14:52
Last Modified: 26 Jan 2022 15:33
PMCID: PMC8752523
URI: https://repository.cshl.edu/id/eprint/40475

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