{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1360011143963365632.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.1111/pbi.13000"}},{"identifier":{"@type":"URI","@value":"https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fpbi.13000"}},{"identifier":{"@type":"URI","@value":"https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.13000"}},{"identifier":{"@type":"URI","@value":"https://onlinelibrary.wiley.com/doi/full-xml/10.1111/pbi.13000"}},{"identifier":{"@type":"URI","@value":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1111%2Fpbi.13000"}}],"dc:title":[{"@value":"Gene regulatory networks for lignin biosynthesis in switchgrass <i>(Panicum virgatum</i>)"}],"description":[{"type":"abstract","notation":[{"@value":"<jats:title>Summary</jats:title><jats:p>Cell wall recalcitrance is the major challenge to improving saccharification efficiency in converting lignocellulose into biofuels. However, information regarding the transcriptional regulation of secondary cell wall biogenesis remains poor in switchgrass (<jats:italic>Panicum virgatum</jats:italic>), which has been selected as a biofuel crop in the United States. In this study, we present a combination of computational and experimental approaches to develop gene regulatory networks for lignin formation in switchgrass. To screen transcription factors (<jats:styled-content style=\"fixed-case\">TF</jats:styled-content>s) involved in lignin biosynthesis, we developed a modified method to perform co‐expression network analysis using 14 lignin biosynthesis genes as bait (target) genes. The switchgrass lignin co‐expression network was further extended by adding 14 <jats:styled-content style=\"fixed-case\">TF</jats:styled-content>s identified in this study, and seven <jats:styled-content style=\"fixed-case\">TF</jats:styled-content>s identified in previous studies, as bait genes. Six <jats:styled-content style=\"fixed-case\">TF</jats:styled-content>s (Pv<jats:styled-content style=\"fixed-case\">MYB</jats:styled-content>58/63, Pv<jats:styled-content style=\"fixed-case\">MYB</jats:styled-content>42/85, Pv<jats:styled-content style=\"fixed-case\">MYB</jats:styled-content>4, Pv<jats:styled-content style=\"fixed-case\">WRKY</jats:styled-content>12, Pv<jats:styled-content style=\"fixed-case\">SND</jats:styled-content>2 and Pv<jats:styled-content style=\"fixed-case\">SWN</jats:styled-content>2) were targeted to generate overexpressing and/or down‐regulated transgenic switchgrass lines. The alteration of lignin content, cell wall composition and/or plant growth in the transgenic plants supported the role of the <jats:styled-content style=\"fixed-case\">TF</jats:styled-content>s in controlling secondary wall formation. <jats:styled-content style=\"fixed-case\">RNA</jats:styled-content>‐seq analysis of four of the transgenic switchgrass lines revealed downstream target genes of the secondary wall‐related <jats:styled-content style=\"fixed-case\">TF</jats:styled-content>s and crosstalk with other biological pathways. <jats:italic>In vitro</jats:italic> transactivation assays further confirmed the regulation of specific lignin pathway genes by four of the <jats:styled-content style=\"fixed-case\">TF</jats:styled-content>s. Our meta‐analysis provides a hierarchical network of <jats:styled-content style=\"fixed-case\">TF</jats:styled-content>s and their potential target genes for future manipulation of secondary cell wall formation for lignin modification in switchgrass.</jats:p>"}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1380011143963365639","@type":"Researcher","foaf:name":[{"@value":"Xiaolan Rao"}],"jpcoar:affiliationName":[{"@value":"BioDiscovery Institute and Department of Biological Sciences University of North Texas Denton TX USA"},{"@value":"BioEnergy Science Center (BESC) Oak Ridge National Laboratory Oak Ridge TN USA"}]},{"@id":"https://cir.nii.ac.jp/crid/1380011143963365637","@type":"Researcher","foaf:name":[{"@value":"Xin Chen"}],"jpcoar:affiliationName":[{"@value":"Center for Applied Mathematics Tianjin University Tianjin China"}]},{"@id":"https://cir.nii.ac.jp/crid/1380011143963365636","@type":"Researcher","foaf:name":[{"@value":"Hui Shen"}],"jpcoar:affiliationName":[{"@value":"BioDiscovery Institute and Department of Biological Sciences University of North Texas Denton TX USA"},{"@value":"BioEnergy Science Center (BESC) Oak Ridge National Laboratory Oak Ridge TN USA"}]},{"@id":"https://cir.nii.ac.jp/crid/1380011143963365760","@type":"Researcher","foaf:name":[{"@value":"Qin Ma"}],"jpcoar:affiliationName":[{"@value":"Department of Agronomy, Horticulture, and Plant Science and Department of Mathematics and Statistics South Dakota State University Brookings SD USA"}]},{"@id":"https://cir.nii.ac.jp/crid/1380011143963365641","@type":"Researcher","foaf:name":[{"@value":"Guifen Li"}],"jpcoar:affiliationName":[{"@value":"Noble Research Institute Ardmore OK USA"}]},{"@id":"https://cir.nii.ac.jp/crid/1380011143963365638","@type":"Researcher","foaf:name":[{"@value":"Yuhong Tang"}],"jpcoar:affiliationName":[{"@value":"BioEnergy Science Center (BESC) Oak Ridge National Laboratory Oak Ridge TN USA"},{"@value":"Noble Research Institute Ardmore OK USA"}]},{"@id":"https://cir.nii.ac.jp/crid/1380011143963365633","@type":"Researcher","foaf:name":[{"@value":"Maria Pena"}],"jpcoar:affiliationName":[{"@value":"BioEnergy Science Center (BESC) Oak Ridge National Laboratory Oak Ridge TN USA"},{"@value":"Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology University of Georgia Athens GA USA"}]},{"@id":"https://cir.nii.ac.jp/crid/1380011143963365640","@type":"Researcher","foaf:name":[{"@value":"William York"}],"jpcoar:affiliationName":[{"@value":"BioEnergy Science Center (BESC) Oak Ridge National Laboratory Oak Ridge TN USA"},{"@value":"Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology University of Georgia Athens GA USA"}]},{"@id":"https://cir.nii.ac.jp/crid/1380011143963365761","@type":"Researcher","foaf:name":[{"@value":"Taylor P. Frazier"}],"jpcoar:affiliationName":[{"@value":"Department of Plant Sciences University of Tennessee Knoxville TN USA"}]},{"@id":"https://cir.nii.ac.jp/crid/1380011143963365632","@type":"Researcher","foaf:name":[{"@value":"Scott Lenaghan"}],"jpcoar:affiliationName":[{"@value":"Department of Food Science University of Tennessee Knoxville TN USA"}]},{"@id":"https://cir.nii.ac.jp/crid/1380011143963365634","@type":"Researcher","foaf:name":[{"@value":"Xirong Xiao"}],"jpcoar:affiliationName":[{"@value":"BioDiscovery Institute and Department of Biological Sciences University of North Texas Denton TX USA"}]},{"@id":"https://cir.nii.ac.jp/crid/1380011143963365642","@type":"Researcher","foaf:name":[{"@value":"Fang Chen"}],"jpcoar:affiliationName":[{"@value":"BioDiscovery Institute and Department of Biological Sciences University of North Texas Denton TX USA"},{"@value":"BioEnergy Science Center (BESC) Oak Ridge National Laboratory Oak Ridge TN USA"},{"@value":"Center for Bioenergy Innovation (CBI) Oak Ridge National Laboratory Oak Ridge TN USA"}]},{"@id":"https://cir.nii.ac.jp/crid/1380011143963365635","@type":"Researcher","foaf:name":[{"@value":"Richard A. Dixon"}],"jpcoar:affiliationName":[{"@value":"BioDiscovery Institute and Department of Biological Sciences University of North Texas Denton TX USA"},{"@value":"BioEnergy Science Center (BESC) Oak Ridge National Laboratory Oak Ridge TN USA"},{"@value":"Center for Bioenergy Innovation (CBI) Oak Ridge National Laboratory Oak Ridge TN USA"}]}],"publication":{"publicationIdentifier":[{"@type":"PISSN","@value":"14677644"},{"@type":"EISSN","@value":"14677652"}],"prism:publicationName":[{"@value":"Plant Biotechnology Journal"}],"dc:publisher":[{"@value":"Wiley"}],"prism:publicationDate":"2018-09-17","prism:volume":"17","prism:number":"3","prism:startingPage":"580","prism:endingPage":"593"},"reviewed":"false","dc:rights":["http://creativecommons.org/licenses/by/4.0/","http://creativecommons.org/licenses/by/4.0/"],"url":[{"@id":"https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fpbi.13000"},{"@id":"https://onlinelibrary.wiley.com/doi/pdf/10.1111/pbi.13000"},{"@id":"https://onlinelibrary.wiley.com/doi/full-xml/10.1111/pbi.13000"},{"@id":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1111%2Fpbi.13000"}],"createdAt":"2018-08-22","modifiedAt":"2023-09-14","relatedProduct":[{"@id":"https://cir.nii.ac.jp/crid/1050286428521875072","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Fiber‐specific regulation of lignin biosynthesis improves biomass quality in Populus"},{"@value":"Fibre‐specific regulation of lignin biosynthesis improves biomass quality in <i>Populus</i>"},{"@value":"Fiber-specific regulation of lignin biosynthesis improves biomass quality in Populus"},{"@value":"Fibre-specific regulation of lignin biosynthesis improves biomass quality in Populus"}]},{"@id":"https://cir.nii.ac.jp/crid/1050287297269461376","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"MYB-mediated regulation of lignin biosynthesis in grasses"}]},{"@id":"https://cir.nii.ac.jp/crid/1361694367081585920","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Double knockout of OsWRKY36 and OsWRKY102 boosts lignification with altering culm morphology of rice"}]},{"@id":"https://cir.nii.ac.jp/crid/1390564227320029952","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Comparative co-expression network analysis extracts the <i>SlHSP70</i> gene affecting to shoot elongation of tomato"},{"@value":"Comparative co-expression network analysis extracts the SlHSP70 gene affecting to shoot elongation of tomato"}]}],"dataSourceIdentifier":[{"@type":"CROSSREF","@value":"10.1111/pbi.13000"},{"@type":"CROSSREF","@value":"10.1016/j.cpb.2020.100174_references_DOI_7AnDGWCuomfivNYN2qwh09oSM7i"},{"@type":"CROSSREF","@value":"10.1016/j.plantsci.2020.110466_references_DOI_7AnDGWCuomfivNYN2qwh09oSM7i"},{"@type":"CROSSREF","@value":"10.1111/nph.16411_references_DOI_7AnDGWCuomfivNYN2qwh09oSM7i"},{"@type":"CROSSREF","@value":"10.5511/plantbiotechnology.19.0603a_references_DOI_7AnDGWCuomfivNYN2qwh09oSM7i"}]}