title: Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms.
abstract: Establishing links between phenotypes and molecular variants is of central importance to accelerate genetic improvement of economically important plant species. Our work represents the first genome-wide association study to the inherently complex and currently poorly understood genetic architecture of industrially relevant wood traits. Here, we employed an Illumina Infinium 34K single nucleotide polymorphism (SNP) genotyping array that generated 29,233 high-quality SNPs in c. 3500 broad-based candidate genes within a population of 334 unrelated Populus trichocarpa individuals to establish genome-wide associations. The analysis revealed 141 significant SNPs (α ≤ 0.05) associated with 16 wood chemistry/ultrastructure traits, individually explaining 3-7% of the phenotypic variance. A large set of associations (41% of all hits) occurred in candidate genes preselected for their suggested a priori involvement with secondary growth. For example, an allelic variant in the FRA8 ortholog explained 21% of the total genetic variance in fiber length, when the trait's heritability estimate was considered. The remaining associations identified SNPs in genes not previously implicated in wood or secondary wall formation. Our findings provide unique insights into wood trait architecture and support efforts for population improvement based on desirable allelic variants.
authors.affiliation: Department of Wood Science, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.
authors.forename: Ilga
authors.initials: I
authors.lastname: Porth
authors.affiliation: Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.|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: Klapšte
authors.affiliation: Department of Wood Science, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.
authors.forename: Oleksandr
authors.initials: O
authors.lastname: Skyba
authors.affiliation: Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, Canada, V8W 3N5.
authors.forename: Jan
authors.initials: J
authors.lastname: Hannemann
authors.affiliation: Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.
authors.forename: Athena D
authors.initials: AD
authors.lastname: McKown
authors.affiliation: Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.
authors.forename: Robert D
authors.initials: RD
authors.lastname: Guy
authors.affiliation: Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA.
authors.forename: Stephen P
authors.initials: SP
authors.lastname: DiFazio
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: Priya
authors.initials: P
authors.lastname: Ranjan
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 Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Friedmann
authors.affiliation: Department of Biology and Centre for Forest Biology, University of Victoria, Victoria, BC, Canada, V8W 3N5.
authors.forename: Juergen
authors.initials: J
authors.lastname: Ehlting
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.
authors.forename: Quentin C B
authors.initials: QCB
authors.lastname: Cronk
authors.affiliation: Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.
authors.forename: Yousry A
authors.initials: YA
authors.lastname: El-Kassaby
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.
authors.forename: Carl J
authors.initials: CJ
authors.lastname: Douglas
authors.affiliation: Department of Wood Science, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4.
authors.forename: Shawn D
authors.initials: SD
authors.lastname: Mansfield
mesh_terms: D000483:Alleles; D002473:Cell Wall; D017343:Genes, Plant; D056726:Genetic Association Studies; D018745:Genome, Plant; D005838:Genotype; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D032107:Populus / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism / Q000648:ultrastructure; D014934:Wood / Q000254:growth & development / Q000378:metabolism / Q000648:ultrastructure
keywords: Populus; association genetics; cellulose; lignin; single nucleotide polymorphism (SNP); wood traits; wood ultrastructure
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