Genome‐wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa

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 &lt; 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.为揭示表型性状变异的遗传基础，本研究选取了来自北美西部大部分分布区域的448份无亲缘关系的野生毛果杨（Populus trichocarpa）种质资源。对所有种质开展了大规模性状表型鉴定（包含同质园试验内的空间与时间重复）与基因分型（采用34K毛果杨单核苷酸多态性（Single Nucleotide Polymorphism, SNP）芯片），上述数据被用于全基因组关联分析（Genome-Wide Association Study, GWAS）的基因挖掘。本研究针对40个生物量、生态生理学及物候学性状，以及代表3518个基因的29355个经过筛选的SNP开展GWAS。关联分析采用统一混合模型（Unified Mixed Model），以控制种质间的群体结构效应。通过邦费罗尼校正阈值（P < 1.7 × 10⁻⁶），本研究共检测到410个显著关联的SNP。这些标记分布于19条染色体上，可解释1%~13%的性状变异，共涉及275个参与性状关联的独特基因。其中，物候学性状关联的基因数量最多（240个），其次为生物量性状（53个）与生态生理学性状（25个）。本研究的GWAS结果为后续研究提供了大量候选基因座。诸多性状与多个基因存在显著关联，这凸显了其遗传复杂性。同时，本研究还鉴定出在单个性状类别内或跨性状类别间存在多性状关联的基因。部分性状间存在遗传相关性，而部分性状则无明显遗传关联。