Gene Expression Differentiation Is Consistent with Local Adaptation across an Elevational Gradient in Drummond’s Rockcress (Boechera stricta) 

J Hered. 2025 Oct 15:esaf081. doi: 10.1093/jhered/esaf081. Online ahead of print.

ABSTRACT

A central goal of evolutionary biology is to understand the mechanisms conferring adaptation. Gene expression is sensitive to environmental variability; thus, investigating gene expression differentiation among populations may reveal signatures of selection from predictable environmental conditions. Environmental pressures that covary with elevation gain (e.g., temperature) result in stark environmental differences along short distances. The phenological and life history traits of plants inhabiting elevational gradients might track these variables, providing an opportunity for testing hypotheses. Boechera stricta occupies a steep elevation gradient in the Rocky Mountains. Here, we grew F3 seeds from at least two genotypes each from five populations of B. stricta in a greenhouse. Analysis of leaf RNAseq data permitted tests of these hypotheses: 1) populations exhibit significant among population genetic variation in gene expression; 2) differentiation in gene expression (QST) exceeds neutral expectations (FST); and 3) the putative functions of differentially expressed genes are predicable based on a priori knowledge of environmental pressures that vary with elevation. Differentiation in gene expression (average QST = 0.53) significantly exceeded neutral differentiation (average FST = 0.17), implicating selection as a potential cause of genetically divergent patterns of gene expression. The putative functions of differentially expressed genes covarying with elevation were enriched for biological processes related to conditions that vary with elevation (circadian rhythm, response to light, chloroplast organization, and vegetative to reproductive meristem transitions). This study reveals considerable differentiation in gene expression, which may provide a mechanism for rapid adaptation to local environmental conditions in this and other species.

PMID:41092278 | DOI:10.1093/jhered/esaf081