title: Genetic architecture of wood properties based on association analysis and co-expression networks in white spruce.
abstract: Association studies are widely utilized to analyze complex traits but their ability to disclose genetic architectures is often limited by statistical constraints, and functional insights are usually minimal in nonmodel organisms like forest trees. We developed an approach to integrate association mapping results with co-expression networks. We tested single nucleotide polymorphisms (SNPs) in 2652 candidate genes for statistical associations with wood density, stiffness, microfibril angle and ring width in a population of 1694 white spruce trees (Picea glauca). Associations mapping identified 229-292 genes per wood trait using a statistical significance level of P < 0.05 to maximize discovery. Over-representation of genes associated for nearly all traits was found in a xylem preferential co-expression group developed in independent experiments. A xylem co-expression network was reconstructed with 180 wood associated genes and several known MYB and NAC regulators were identified as network hubs. The network revealed a link between the gene PgNAC8, wood stiffness and microfibril angle, as well as considerable within-season variation for both genetic control of wood traits and gene expression. Trait associations were distributed throughout the network suggesting complex interactions and pleiotropic effects. Our findings indicate that integration of association mapping and co-expression networks enhances our understanding of complex wood traits.
authors.affiliation: Forest Research Centre, and Institute for System and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.
authors.forename: Mebarek
authors.initials: M
authors.lastname: Lamara
authors.affiliation: Forest Research Centre, and Institute for System and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.
authors.forename: Elie
authors.initials: E
authors.lastname: Raherison
authors.affiliation: Forest Research Centre, and Institute for System and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.|Canadian Wood Fibre Centre, Canadian Forest Service, Natural Resources Canada, Québec, QC, G1V 4C7, Canada.
authors.forename: Patrick
authors.initials: P
authors.lastname: Lenz
authors.affiliation: Forest Research Centre, and Institute for System and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.|Canadian Wood Fibre Centre, Canadian Forest Service, Natural Resources Canada, Québec, QC, G1V 4C7, Canada.|Canada Research Chair in Forest and Environmental Genomics, Université Laval, Québec, QC, G1V 0A6, Canada.
authors.forename: Jean
authors.initials: J
authors.lastname: Beaulieu
authors.affiliation: Forest Research Centre, and Institute for System and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.|Canada Research Chair in Forest and Environmental Genomics, Université Laval, Québec, QC, G1V 0A6, Canada.
authors.forename: Jean
authors.initials: J
authors.lastname: Bousquet
authors.affiliation: Forest Research Centre, and Institute for System and Integrative Biology, Université Laval, Québec, QC, G1V 0A6, Canada.|Department of Plant Sciences, University of Oxford, Oxford, 0X1 3RB, UK.
authors.forename: John
authors.initials: J
authors.lastname: MacKay
mesh_terms: D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D056726:Genetic Association Studies; D058977:Molecular Sequence Annotation; D010641:Phenotype; D028222:Picea / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D000072417:Protein Domains; D019655:Quantitative Trait, Heritable; D014934:Wood / Q000235:genetics*; D052584:Xylem / Q000235:genetics
keywords: association genetics; co-expression network; quantitative genetics; white spruce (Picea glauca); wood traits