title: A Predictive Coexpression Network Identifies Novel Genes Controlling the Seed-to-Seedling Phase Transition in Arabidopsis thaliana.
abstract: The transition from a quiescent dry seed to an actively growing photoautotrophic seedling is a complex and crucial trait for plant propagation. This study provides a detailed description of global gene expression in seven successive developmental stages of seedling establishment in Arabidopsis (Arabidopsis thaliana). Using the transcriptome signature from these developmental stages, we obtained a coexpression gene network that highlights interactions between known regulators of the seed-to-seedling transition and predicts the functions of uncharacterized genes in seedling establishment. The coexpressed gene data sets together with the transcriptional module indicate biological functions related to seedling establishment. Characterization of the homeodomain leucine zipper I transcription factor AtHB13, which is expressed during the seed-to-seedling transition, demonstrated that this gene regulates some of the network nodes and affects late seedling establishment. Knockout mutants for athb13 showed increased primary root length as compared with wild-type (Columbia-0) seedlings, suggesting that this transcription factor is a negative regulator of early root growth, possibly repressing cell division and/or cell elongation or the length of time that cells elongate. The signal transduction pathways present during the early phases of the seed-to-seedling transition anticipate the control of important events for a vigorous seedling, such as root growth. This study demonstrates that a gene coexpression network together with transcriptional modules can provide insights that are not derived from comparative transcript profiling alone.
authors.affiliation: Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (A.T.S., W.L., H.W.M.H.); andInstituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, 3000 Santa Fe, Argentina (P.A.R., R.L.C.) anderson.tadeu.silva@gmail.com henk.hilhorst@wur.nl.
authors.forename: Anderson Tadeu
authors.initials: AT
authors.lastname: Silva
authors.affiliation: Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (A.T.S., W.L., H.W.M.H.); andInstituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, 3000 Santa Fe, Argentina (P.A.R., R.L.C.).
authors.forename: Pamela A
authors.initials: PA
authors.lastname: Ribone
authors.affiliation: Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (A.T.S., W.L., H.W.M.H.); andInstituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, 3000 Santa Fe, Argentina (P.A.R., R.L.C.).
authors.forename: Raquel L
authors.identifier: 0000-0002-3264-0008
authors.initials: RL
authors.lastname: Chan
authors.affiliation: Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (A.T.S., W.L., H.W.M.H.); andInstituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, 3000 Santa Fe, Argentina (P.A.R., R.L.C.).
authors.forename: Wilco
authors.identifier: 0000-0002-0228-169X
authors.initials: W
authors.lastname: Ligterink
authors.affiliation: Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (A.T.S., W.L., H.W.M.H.); andInstituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, 3000 Santa Fe, Argentina (P.A.R., R.L.C.) anderson.tadeu.silva@gmail.com henk.hilhorst@wur.nl.
authors.forename: Henk W M
authors.identifier: 0000-0002-6743-583X
authors.initials: HW
authors.lastname: Hilhorst
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D018525:Germination / Q000235:genetics; D018517:Plant Roots / Q000235:genetics / Q000254:growth & development; D025341:Principal Component Analysis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D036226:Seedlings / Q000235:genetics*; D012639:Seeds / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D012333:RNA, Messenger