Genome‐wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa. Issue 2 (22nd April 2014)

• Record Type: Journal Article
• Authors: McKown, Athena D.; Klápště, Jaroslav; Guy, Robert D.; Geraldes, Armando; Porth, Ilga; Hannemann, Jan; Friedmann, Michael; Muchero, Wellington; Tuskan, Gerald A.; Ehlting, Jürgen; Cronk, Quentin C. B.; El‐Kassaby, Yousry A.; Mansfield, Shawn D.; Douglas, Carl J.
• Is Part Of: New phytologist. Volume 203:Issue 2(2014)
• Page Start: 535
• Page End: 553
• Publication Date: 2014-04-22
• Subjects: Botany -- Periodicals; 580
• DOI: 10.1111/nph.12815
• Languages: English
• ISSNs: 0028-646X

Abstract

<abstract abstract-type="main" id="nph12815-abs-0001"> <title>Summary</title> <p> <list id="nph12815-list-0001" list-type="bullet"> <list-item> <p>In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (<italic>Populus trichocarpa</italic>) 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 <italic>Populus</italic> single nucleotide polymorphism (SNP) array) of all accessions were used for gene discovery in a genome‐wide association study (GWAS).</p> </list-item> <list-item> <p>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.</p> </list-item> <list-item> <p>We uncovered 410 significant SNPs using a Bonferroni‐corrected threshold (<italic>P </italic>< 1.7 × 10<sup>−6</sup>). 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).</p> </list-item> <list-item> <p>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 <italic>within</italic> and/or <italic>across</italic> trait categories. In some cases, traits were genetically correlated while in others they were not.</p> </list-item> </list> </p> </abstract>