Evolutionary analyses of gene expression divergence inPanicum hallii: exploring constitutive and plastic responses using reciprocal transplants

Abstract

AbstractThe evolution of gene expression is thought to be an important mechanism of local adaptation and ecological speciation. Gene expression divergence occurs through the evolution of cis-polymorphisms and through more widespread effects driven by trans-regulatory factors. Lovell et al. (2018) studied expression divergence between two ecotypes ofPanicum halliiusing expression quantitative trait loci (eQTL) analyses and discovered a pre-dominance of cis and several trans-regulatory divergences. Here, we explore expression and sequence divergence in a large sample ofP. halliiaccessions encompassing the species range using a reciprocal transplantation experiment. We observed widespread genotype and transplant site drivers of expression divergence, with a limited number of genes exhibited genotype-by-site interactions. We used a modified Fst-Qstoutlier approach (QPCanalysis) to detect local adaptation. We identified 514 genes with constitutive expression divergence above and beyond the levels expected under neutral processes. However, no plastic expression responses met our multiple testing correction asQPCoutliers. ConstitutiveQPCoutlier genes were involved in a number of developmental processes and responses to abiotic environments. Leveraging the earlier eQTL results, we found a strong enrichment of expression divergence, including forQPCoutliers, in genes previously identified with cis and cis-drought interactions but found no patterns related to trans-factors. Population genetic analyses detected elevated sequence divergence (FST, DXY) of promoters and coding sequence of constitutive expression outliers, but little evidence for positive selection on these proteins. Our results are consistent with a hypothesis of cis-regulatory divergence as a primary driver of expression divergence inP. hallii.