title: Identifying gene coexpression networks underlying the dynamic regulation of wood-forming tissues in Populus under diverse environmental conditions.
abstract: Trees modify wood formation through integration of environmental and developmental signals in complex but poorly defined transcriptional networks, allowing trees to produce woody tissues appropriate to diverse environmental conditions. In order to identify relationships among genes expressed during wood formation, we integrated data from new and publically available datasets in Populus. These datasets were generated from woody tissue and include transcriptome profiling, transcription factor binding, DNA accessibility and genome-wide association mapping experiments. Coexpression modules were calculated, each of which contains genes showing similar expression patterns across experimental conditions, genotypes and treatments. Conserved gene coexpression modules (four modules totaling 8398 genes) were identified that were highly preserved across diverse environmental conditions and genetic backgrounds. Functional annotations as well as correlations with specific experimental treatments associated individual conserved modules with distinct biological processes underlying wood formation, such as cell-wall biosynthesis, meristem development and epigenetic pathways. Module genes were also enriched for DNase I hypersensitivity footprints and binding from four transcription factors associated with wood formation. The conserved modules are excellent candidates for modeling core developmental pathways common to wood formation in diverse environments and genotypes, and serve as testbeds for hypothesis generation and testing for future studies.
authors.affiliation: USDA Forest Service, Pacific Southwest Research Station, Davis, CA, 95618, USA.|Department of Computer Science, University of California, Davis, CA, 95618, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Zinkgraf
authors.affiliation: USDA Forest Service, Pacific Southwest Research Station, Davis, CA, 95618, USA.
authors.forename: Lijun
authors.initials: L
authors.lastname: Liu
authors.affiliation: USDA Forest Service, Pacific Southwest Research Station, Davis, CA, 95618, USA.|Department of Plant Biology, University of California, Davis, CA, 95618, USA.
authors.forename: Andrew
authors.identifier: http://orcid.org/0000-0002-6686-5774
authors.initials: A
authors.lastname: Groover
authors.affiliation: Department of Computer Science, University of California, Davis, CA, 95618, USA.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Filkov
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D018744:DNA, Plant; D004777:Environment; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D055106:Genome-Wide Association Study; D032107:Populus / Q000235:genetics* / Q000254:growth & development; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014934:Wood / Q000235:genetics / Q000254:growth & development*
chemical_list: D018744:DNA, Plant; D014157:Transcription Factors
keywords: 
  Populus
  ; data integration; genomics; transcriptional networks; wood formation