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

Nicholas Gladman; Andrew Olson; Sharon Wei; Kapeel Chougule; Zhenyuan Lu; Marcela Tello-Ruiz; Ivar Meijs; Peter Van Buren; Yinping Jiao; Bo Wang; Vivek Kumar; Sunita Kumari; Lifang Zhang; John Burke; Junping Chen; Gloria Burow; Chad Hayes; Yves Emendack; Zhanguo Xin; Doreen Ware

doi:10.1007/s00425-022-03821-6

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

Nicholas Gladman, Andrew Olson, Sharon Wei, Kapeel Chougule, Zhenyuan Lu, Marcela Tello-Ruiz, Ivar Meijs, Peter Van Buren, Yinping Jiao, Bo Wang, Vivek Kumar, Sunita Kumari, Lifang Zhang, John Burke, Junping Chen, Gloria Burow, Chad Hayes, Yves Emendack, Zhanguo Xin, Doreen Ware

Plant & Soil Science

Research output: Contribution to journal › Article › peer-review

11 Scopus citations

Abstract

Main conclusion: SorghumBase provides a community portal that integrates genetic, genomic, and breeding resources for sorghum germplasm improvement. Abstract: 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.

Original language	English
Article number	35
Journal	Planta
Volume	255
Issue number	2
DOIs	https://doi.org/10.1007/s00425-022-03821-6
State	Published - Feb 2022

Keywords

Breeding
Genetic
Genomic
Molecular
Resource
Sorghum

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10.1007/s00425-022-03821-6

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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. (2022). SorghumBase: a web-based portal for sorghum genetic information and community advancement. Planta, 255(2), Article 35. https://doi.org/10.1007/s00425-022-03821-6

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title = "SorghumBase: a web-based portal for sorghum genetic information and community advancement",

abstract = "Main conclusion: SorghumBase provides a community portal that integrates genetic, genomic, and breeding resources for sorghum germplasm improvement. Abstract: 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.",

keywords = "Breeding, Genetic, Genomic, Molecular, Resource, Sorghum",

author = "Nicholas Gladman and Andrew Olson and Sharon Wei and Kapeel Chougule and Zhenyuan Lu and Marcela Tello-Ruiz and Ivar Meijs and {Van Buren}, Peter and Yinping Jiao and Bo Wang and Vivek Kumar and Sunita Kumari and Lifang Zhang and John Burke and Junping Chen and Gloria Burow and Chad Hayes and Yves Emendack and Zhanguo Xin and Doreen Ware",

note = "Publisher Copyright: {\textcopyright} 2022, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.",

year = "2022",

month = feb,

doi = "10.1007/s00425-022-03821-6",

language = "English",

volume = "255",

journal = "Planta",

issn = "0032-0935",

number = "2",

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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 2022, 'SorghumBase: a web-based portal for sorghum genetic information and community advancement', Planta, vol. 255, no. 2, 35. https://doi.org/10.1007/s00425-022-03821-6

TY - JOUR

T1 - SorghumBase

T2 - a web-based portal for sorghum genetic information and community advancement

AU - Gladman, Nicholas

AU - Olson, Andrew

AU - Wei, Sharon

AU - Chougule, Kapeel

AU - Lu, Zhenyuan

AU - Tello-Ruiz, Marcela

AU - Meijs, Ivar

AU - Van Buren, Peter

AU - Jiao, Yinping

AU - Wang, Bo

AU - Kumar, Vivek

AU - Kumari, Sunita

AU - Zhang, Lifang

AU - Burke, John

AU - Chen, Junping

AU - Burow, Gloria

AU - Hayes, Chad

AU - Emendack, Yves

AU - Xin, Zhanguo

AU - Ware, Doreen

PY - 2022/2

Y1 - 2022/2

N2 - Main conclusion: SorghumBase provides a community portal that integrates genetic, genomic, and breeding resources for sorghum germplasm improvement. Abstract: 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.

AB - Main conclusion: SorghumBase provides a community portal that integrates genetic, genomic, and breeding resources for sorghum germplasm improvement. Abstract: 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.

KW - Breeding

KW - Genetic

KW - Genomic

KW - Molecular

KW - Resource

KW - Sorghum

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U2 - 10.1007/s00425-022-03821-6

DO - 10.1007/s00425-022-03821-6

M3 - Article

C2 - 35015132

AN - SCOPUS:85122924699

SN - 0032-0935

VL - 255

JO - Planta

JF - Planta

IS - 2

M1 - 35

ER -

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

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