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 35 ecologically important traits using a common garden of aspen through genomic and transcriptomic analyses. A multilocus association model revealed that most traits displayed a 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 results support the omnigenic model that complex traits are largely controlled by many small effect loci, most of which may not have obvious connections to the traits of interest. 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.

Background and Aims: At the population level, genetic diversity is a key determinant of a tree species’ capacity to cope with stress. However, little is known about the relative importance of the different components of genetic diversity for tree stress responses. We compared how two sources of genetic diversity, genotype and cytotype (i.e. differences in ploidy levels) influence growth, phytochemical, and physiological traits of Populus tremuloides in the presence and absence of environmental stress.Methods: In a series of field studies, we first assessed variation in traits across diploid and triploid aspen genotypes from Utah and Wisconsin under nonstressed conditions. In two follow-up experiments, we exposed diploid and triploid aspen genotypes from Wisconsin to individual and interactive drought stress and defoliation treatments and quantified trait variations under stress.Key Results: We found that 1) tree growth and associated traits did not differ significantly between ploidy levels under nonstressed conditions. Instead, variation in tree growth and most other traits was driven by genotypic and population differences. 2) Genotypic differences were critical for explaining variation of most of functional traits and their responses to stress. 3) Ploidy level played a subtle role in shaping traits and trait stress responses, as its influence was typically obscured by genotypic differences. 4) As an exception to the third conclusion, we showed that triploid trees expressed 17% higher foliar defense (tremulacin) levels, 11% higher photosynthesis levels, and 23% higher rubisco activity under well-watered conditions. Moreover, triploid trees displayed greater drought resilience than diploids as they produced 35% more new tissue than diploids when recovering from drought stress Conclusion: Although ploidy level can strongly influence the ecology of tree species, those effects may be relatively small in contrast to the effects of genotypic variation in highly diverse species.

Intraspecific genetic variation in foundation species such as trembling aspen shapes their impact on forest structure and function. Identifying genes and genomic regions underlying ecologically relevant traits is key to understanding that impact. Previous studies using genome-wide association (GWA) analyses to identify candidate genes have identified fewer genes than anticipated for highly heritable 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 40 functional traits using genomic and transcriptomic analyses in an association mapping population of aspen. A multi-marker association model revealed that most traits displayed a polygenic architecture, with most variation explained by loci with small effects (below the detection levels of single-marker GWA methods). Consistent with a polygenic architecture, our single-marker GWA analyses found only 35 significant SNPs in 22 genes across 15 trait/trait combinations. Next, we used differential expression analysis on a subset of aspen genets with divergent concentrations of salicinoid phenolic glycosides (key defense traits). This alternative method to traditional GWA discovered 1,243 differentially expressed genes for a polygenic trait. Soft clustering analysis revealed three gene clusters (246 candidate genes) involved in secondary metabolite biosynthesis and regulation. Our results support the omnigenic model that complex traits are largely controlled by many small effect loci, most of which may not have obvious connections to the traits of interest. Our work reveals that functional 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.