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.

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.

Despite the growing number of recent studies on genome-wide divergence during speciation, the genetic basis and mechanisms of genomic divergence are still incompletely understood. In most species, natural selection plays a key role in heterogeneous genomic divergence. Additionally, intrinsic barriers, such as chromosomal rearrangements or gene incompatibilities, can also cause genomic heterogeneity. Based on whole genome re-sequencing data from 27 Populus alba and 28 P. adenopoda individuals, we explored the reasons for heterogeneous genomic divergence of these two closely related species. The results showed that the two species diverged ~5-10 million years ago (Mya), when the Qinghai-Tibet Plateau reached a certain height and the inland climate of the Asian continent became arid, which is associated with the fact that the two species begin to diverge and eventually led to speciation. In highly differentiated regions, the absolute divergence (dxy) was significantly higher than genomic background, and relative and absolute divergence were highly correlated, which indicates that intrinsic barriers played an important role in maintaining genomic heterogeneous divergence. Additionally, θπ and shared polymorphisms decreased while fixed differences increased in highly differentiated regions, which are characteristics of natural selection. The above description indicates that the combination of intrinsic barriers and natural selection result in heterogeneous genomic divergence and reproductive isolation. We further found some genes that are related to reproduction may be involved in explaining the reproductive isolation of the two species.

Despite the growing number of recent studies on genome-wide divergence during speciation, the genetic basis and mechanisms of genomic divergence and speciation are still incompletely understood. In most species, natural selection plays a key role in genomic heterogeneous divergence. Additionally, barriers to gene flow, such as chromosomal rearrangements or gene incompatibilities, can also cause genome heterogeneity and speciation. Based on whole genome re-sequencing data from 27 Populus alba and 28 P. adenopoda individuals, we explored the reasons for the heterogeneous differentiation of genomes of these two closely related species. The results showed that the two species diverged ~5-10 million years ago (Mya), when the Qinghai-Tibet Plateau reached a certain height and the inland climate of the Asian continent became arid, which caused the two species begin to diverge and eventually led to speciation. In highly differentiated regions, neutrality tests (Tajima’s D and Fay & Wu’s H) of these regions revealed no difference while the absolute divergence (dxy) were significantly higher than genome background, which indicates that barriers to gene flow rather than natural selection played a major role in maintaining genomic heterogeneous divergence and reproductive isolation, which is the most important condition for speciation. We further found that some genes related to reproduction may be involved in explaining the reproductive isolation of the two species.