title: Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa.
abstract: In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa) from much of its range in western North America. Extensive data from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34 K Populus single nucleotide polymorphism (SNP) array) of all accessions were used for gene discovery in a genome-wide association study (GWAS). We performed GWAS with 40 biomass, ecophysiology and phenology traits and 29,355 filtered SNPs representing 3518 genes. The association analyses were carried out using a Unified Mixed Model accounting for population structure effects among accessions. We uncovered 410 significant SNPs using a Bonferroni-corrected threshold (P<1.7×10(-6)). Markers were found across 19 chromosomes, explained 1-13% of trait variation, and implicated 275 unique genes in trait associations. Phenology had the largest number of associated genes (240 genes), followed by biomass (53 genes) and ecophysiology traits (25 genes). The GWAS results propose numerous loci for further investigation. Many traits had significant associations with multiple genes, underscoring their genetic complexity. Genes were also identified with multiple trait associations within and/or across trait categories. In some cases, traits were genetically correlated while in others they were not.
authors.affiliation: Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Athena D
authors.initials: AD
authors.lastname: McKown
authors.affiliation: Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.|Department of Dendrology and Forest Tree Breeding, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, 165 21, Czech Republic.
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Klápště
authors.affiliation: Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Guy
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Armando
authors.initials: A
authors.lastname: Geraldes
authors.affiliation: Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.|Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Ilga
authors.initials: I
authors.lastname: Porth
authors.affiliation: Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada.
authors.forename: Jan
authors.initials: J
authors.lastname: Hannemann
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Michael
authors.initials: M
authors.lastname: Friedmann
authors.affiliation: BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Wellington
authors.initials: W
authors.lastname: Muchero
authors.affiliation: BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Gerald A
authors.initials: GA
authors.lastname: Tuskan
authors.affiliation: Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada.
authors.forename: Jürgen
authors.initials: J
authors.lastname: Ehlting
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Quentin C B
authors.initials: QCB
authors.lastname: Cronk
authors.affiliation: Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Yousry A
authors.initials: YA
authors.lastname: El-Kassaby
authors.affiliation: Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Shawn D
authors.initials: SD
authors.lastname: Mansfield
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
authors.forename: Carl J
authors.initials: CJ
authors.lastname: Douglas
mesh_terms: D018533:Biomass; D004463:Ecology; D005819:Genetic Markers; D005828:Genetics, Population; D055106:Genome-Wide Association Study; D009656:North America; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D032107:Populus / Q000235:genetics* / Q000502:physiology; D019655:Quantitative Trait, Heritable
chemical_list: D005819:Genetic Markers
keywords: Unified Mixed Model; biomass; ecophysiology; genome-wide association study (GWAS); phenology; pleiotropy; poplar; single nucleotide polymorphisms (SNP) array
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