Natural plant populations often exhibit marked differences in gene expression patterns that can reflect heterogeneity in selective pressures. Analyzing gene expression as a quantitative trait provides a unique opportunity to evaluate the underlying genomic basis of a plethora of traits and their interactions in driving adaptive evolution. We investigated patterns and processes driving expression differentiation under conditions mimicking future climates by combining common garden experiments with transcriptome-wide datasets obtained from hybrid populations of Pinus strobiformis and P. flexilis. We found strong signals of genotype-environment interactions (GEI) at the individual transcript and the co-expression module levels suggesting a marked influence of drought related variables on adaptive evolution. Overall, survival was positively associated with P. flexilis ancestry, but it exhibited an environment-specific pattern. Co-expression modules exhibiting strong associations with survival and genomic ancestry were representative of similar functional categories across both gardens. Using network topology measures, putatively adaptive garden-specific expression traits were pleiotropic and belonged to modules exhibiting high population differentiation yet low preservation across gardens. Overall, our study suggests the presence of substantial genetic variation underlying univariate and multivariate traits in novel climates that may enable populations of long-lived forest trees to respond to rapid shifts in climatic conditions in early seedling stages when mortality tends to be the highest. Our finding of pleiotropic trait architectures underlying adaptive traits, however, implies rapid adaptive responses to changing selection pressures depend on whether trait covariances align with the direction of change in selection pressures.

We subjected southwestern white pine (Pinus strobiformis Engelm.) seeds to controlled warming treatments to study responses of seed and seedling demographics, and morphological and physiological traits following warming during embryogenesis, germination, and early seedling growth. Daytime air temperature surrounding cones in tree canopies was warmed by +2.1 ◦C during embryo development. Resulting seeds and seedlings were assigned to three thermal regimes in growth chambers, with each regime separated by 4 ◦C. The embryo-warming treatment reduced percent seedling emergence in all germination and growth environments and reduced mortality of seedlings grown in the warmest environment. Warm thermal regimes during early seedling growth increased seedling resistance to oxidative stress and seedling transpirational water use even after applying cooler temperatures and experimental drought. Experimental warming imposed during seed development affected seedling demographic processes, and warming imposed during germination and seedling growth affected stress resistance and water relations. This work illustrates that the study of numerous ecophysiological and functional trait responses to various types of stress across multiple plant developmental stages is essential for understanding the effects of climate warming on forest regeneration processes.