SorghumBase: a web-based portal for sorghum genetic information and community advancement
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,...
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| Veröffentlicht in: | Planta 2022-02, Vol.255 (2), p.35-35, Article 35 |
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| creator | 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 |
| description | 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. |
| doi_str_mv | 10.1007/s00425-022-03821-6 |
| format | Article |
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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.</description><identifier>ISSN: 0032-0935</identifier><identifier>EISSN: 1432-2048</identifier><identifier>DOI: 10.1007/s00425-022-03821-6</identifier><identifier>PMID: 35015132</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Agricultural development ; Agricultural research ; Agriculture ; Biomedical and Life Sciences ; Content management systems ; Databases, Genetic ; Ecology ; Edible Grain ; Ethyl methanesulfonate ; Forestry ; Gene expression ; Genetic diversity ; Genetic variance ; Genome, Plant - genetics ; Genomes ; Genomics ; Germplasm ; Internet ; Life Sciences ; Plant Breeding ; Plant communities ; Plant Sciences ; Quantitative trait loci ; R&D ; Research & development ; Short Communication ; Sorghum ; Sorghum - genetics</subject><ispartof>Planta, 2022-02, Vol.255 (2), p.35-35, Article 35</ispartof><rights>This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply 2022</rights><rights>2022. This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.</rights><rights>This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply 2022. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c540t-547bd4bcb4a0e69571d3c5d9498e3a1669653b3fa9815debd7f291554c603d3</citedby><cites>FETCH-LOGICAL-c540t-547bd4bcb4a0e69571d3c5d9498e3a1669653b3fa9815debd7f291554c603d3</cites><orcidid>0000-0002-8125-3821</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00425-022-03821-6$$EPDF$$P50$$Gspringer$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00425-022-03821-6$$EHTML$$P50$$Gspringer$$Hfree_for_read</linktohtml><link.rule.ids>230,314,780,784,885,27923,27924,41487,42556,51318</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35015132$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Gladman, Nicholas</creatorcontrib><creatorcontrib>Olson, Andrew</creatorcontrib><creatorcontrib>Wei, Sharon</creatorcontrib><creatorcontrib>Chougule, Kapeel</creatorcontrib><creatorcontrib>Lu, Zhenyuan</creatorcontrib><creatorcontrib>Tello-Ruiz, Marcela</creatorcontrib><creatorcontrib>Meijs, Ivar</creatorcontrib><creatorcontrib>Van Buren, Peter</creatorcontrib><creatorcontrib>Jiao, Yinping</creatorcontrib><creatorcontrib>Wang, Bo</creatorcontrib><creatorcontrib>Kumar, Vivek</creatorcontrib><creatorcontrib>Kumari, Sunita</creatorcontrib><creatorcontrib>Zhang, Lifang</creatorcontrib><creatorcontrib>Burke, John</creatorcontrib><creatorcontrib>Chen, Junping</creatorcontrib><creatorcontrib>Burow, Gloria</creatorcontrib><creatorcontrib>Hayes, Chad</creatorcontrib><creatorcontrib>Emendack, Yves</creatorcontrib><creatorcontrib>Xin, Zhanguo</creatorcontrib><creatorcontrib>Ware, Doreen</creatorcontrib><title>SorghumBase: a web-based portal for sorghum genetic information and community advancement</title><title>Planta</title><addtitle>Planta</addtitle><addtitle>Planta</addtitle><description>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.</description><subject>Agricultural development</subject><subject>Agricultural research</subject><subject>Agriculture</subject><subject>Biomedical and Life Sciences</subject><subject>Content management systems</subject><subject>Databases, Genetic</subject><subject>Ecology</subject><subject>Edible Grain</subject><subject>Ethyl methanesulfonate</subject><subject>Forestry</subject><subject>Gene expression</subject><subject>Genetic diversity</subject><subject>Genetic variance</subject><subject>Genome, Plant - genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Germplasm</subject><subject>Internet</subject><subject>Life Sciences</subject><subject>Plant Breeding</subject><subject>Plant communities</subject><subject>Plant Sciences</subject><subject>Quantitative trait loci</subject><subject>R&D</subject><subject>Research & development</subject><subject>Short Communication</subject><subject>Sorghum</subject><subject>Sorghum - 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genetics</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Germplasm</topic><topic>Internet</topic><topic>Life Sciences</topic><topic>Plant Breeding</topic><topic>Plant communities</topic><topic>Plant Sciences</topic><topic>Quantitative trait loci</topic><topic>R&D</topic><topic>Research & development</topic><topic>Short Communication</topic><topic>Sorghum</topic><topic>Sorghum - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Gladman, Nicholas</creatorcontrib><creatorcontrib>Olson, Andrew</creatorcontrib><creatorcontrib>Wei, Sharon</creatorcontrib><creatorcontrib>Chougule, Kapeel</creatorcontrib><creatorcontrib>Lu, Zhenyuan</creatorcontrib><creatorcontrib>Tello-Ruiz, Marcela</creatorcontrib><creatorcontrib>Meijs, Ivar</creatorcontrib><creatorcontrib>Van Buren, Peter</creatorcontrib><creatorcontrib>Jiao, Yinping</creatorcontrib><creatorcontrib>Wang, Bo</creatorcontrib><creatorcontrib>Kumar, Vivek</creatorcontrib><creatorcontrib>Kumari, Sunita</creatorcontrib><creatorcontrib>Zhang, Lifang</creatorcontrib><creatorcontrib>Burke, John</creatorcontrib><creatorcontrib>Chen, Junping</creatorcontrib><creatorcontrib>Burow, Gloria</creatorcontrib><creatorcontrib>Hayes, Chad</creatorcontrib><creatorcontrib>Emendack, Yves</creatorcontrib><creatorcontrib>Xin, Zhanguo</creatorcontrib><creatorcontrib>Ware, Doreen</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Planta</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gladman, Nicholas</au><au>Olson, Andrew</au><au>Wei, Sharon</au><au>Chougule, Kapeel</au><au>Lu, Zhenyuan</au><au>Tello-Ruiz, Marcela</au><au>Meijs, Ivar</au><au>Van Buren, Peter</au><au>Jiao, Yinping</au><au>Wang, Bo</au><au>Kumar, Vivek</au><au>Kumari, Sunita</au><au>Zhang, Lifang</au><au>Burke, John</au><au>Chen, Junping</au><au>Burow, Gloria</au><au>Hayes, Chad</au><au>Emendack, Yves</au><au>Xin, Zhanguo</au><au>Ware, Doreen</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>SorghumBase: a web-based portal for sorghum genetic information and community advancement</atitle><jtitle>Planta</jtitle><stitle>Planta</stitle><addtitle>Planta</addtitle><date>2022-02-01</date><risdate>2022</risdate><volume>255</volume><issue>2</issue><spage>35</spage><epage>35</epage><pages>35-35</pages><artnum>35</artnum><issn>0032-0935</issn><eissn>1432-2048</eissn><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.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>35015132</pmid><doi>10.1007/s00425-022-03821-6</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0002-8125-3821</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
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| ispartof | Planta, 2022-02, Vol.255 (2), p.35-35, Article 35 |
| issn | 0032-0935 1432-2048 |
| language | eng |
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| source | MEDLINE; SpringerLink Journals - AutoHoldings |
| subjects | Agricultural development Agricultural research Agriculture Biomedical and Life Sciences Content management systems Databases, Genetic Ecology Edible Grain Ethyl methanesulfonate Forestry Gene expression Genetic diversity Genetic variance Genome, Plant - genetics Genomes Genomics Germplasm Internet Life Sciences Plant Breeding Plant communities Plant Sciences Quantitative trait loci R&D Research & development Short Communication Sorghum Sorghum - genetics |
| title | SorghumBase: a web-based portal for sorghum genetic information and community advancement |
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