Data from: Genomic and transcriptomic analyses reveal polygenic architecture for ecologically-important functional traits in aspen (Populus tremuloides Michx.)

Intraspecific genetic variation in foundation species such as aspen
(Populus tremuloides Michx.) shapes their impact on forest structure and
function. Identifying genes underlying ecologically important traits is
key to understanding that impact. Previous studies, using single-locus
genome-wide association (GWA) analyses to identify candidate genes, have
identified fewer genes than anticipated for highly heritable quantitative
traits. Mounting evidence suggests that polygenic control of quantitative
traits is largely responsible for this “missing heritability” phenomenon.
Our research characterized the genetic architecture of 30 ecologically
important traits using a common garden of aspen through genomic and
transcriptomic analyses. A multilocus association model revealed that most
traits displayed a highly polygenic architecture, with most variation
explained by loci with small effects (likely below the detection levels of
single-locus GWA methods). Consistent with a polygenic architecture, our
single-locus GWA analyses found only 38 significant SNPs in 22 genes
across 15 traits. Next, we used differential expression analysis on a
subset of aspen genets with divergent concentrations of salicinoid
phenolic glycosides (key defense traits). This complementary method to
traditional GWA discovered 1,243 differentially expressed genes for a
polygenic trait. Soft clustering analysis revealed three gene clusters
(241 candidate genes) involved in secondary metabolite biosynthesis and
regulation. Our work reveals that ecologically important traits governing
higher-order community- and ecosystem-level attributes of a foundation
forest tree species have complex underlying genetic structures and will
require methods beyond traditional GWA analyses to unravel.