Planta publication describing SorghumBase
The recent Planta article represents the first manuscript on SorghumBase, an open access community portal funded by the USDA and developed at Cold Spring Harbor Laboratory focused on sorghum genomic and genetic resources. Valuable feedback on the conceptualization and the site’s usability was provided by John Burke, Junping Chen, Gloria Burow, Chad Hayes, Yves Emendack, and Zhanguo Xin.
The manuscript covers the initial release of the SorghumBase knowledgebase with five sorghum genomes (BTx623, Rio, RTx430, RTx436, and Tx2783), SNP and structural variation data, EMS mutations, and QTLs, adhering to FAIR data sharing principles, and walks the user through an example of how to use the general search and visualization to find a sorghum gene or gene ortholog from another species using a common name or the INDSC-conforming gene ID (SORBI_3…).
Nick Gladman, USDA Research Plant Molecular Geneticist at Cold Spring Harbor Laboratory said on the importance of having a dedicated database for sorghum that “SorghumBase provides a dedicated resource for all sorghum investigators. With continued community engagement, we hope to build out even greater functionality for breeders and molecular biology researchers.”
For a complete description of data and featured contents in the first release of SorghumBase, see the Initial Release Notes. At the time of this publication, the SorghumBase site has increased by 13 new sorghum reference genomes (see Release 2 Notes).
This work was a collaborative effort with the sorghum research community, ARS and university scientists, and resource managers. Core funding for the project is provided by the Agricultural Research Service of the U.S. Department of Agriculture (USDA ARS 59-8062-9-002).
The article may be accessed for free from https://rdcu.be/cEOSE, where readers are able to use Enhanced PDF features including annotation tools, one-click supplements, citation file exports and article metrics.
How to cite SorghumBase: Gladman N, Olson A, Wei S, Chougule K, Lu Z, Tello-Ruiz M, Meijs I, Van Buren P, Jiao Y, Wang B, Kumar V, Kumari S, Zhang L, Burke J, Chen J, Burow G, Hayes C, Emendack Y, Xin Z, Ware D. SorghumBase: a web-based portal for sorghum genetic information and community advancement. Planta [Internet]. 2022 Jan 11;255(2):35. Available from: http://dx.doi.org/10.1007/s00425-022-03821-6 PMID: 35015132.
