Transcriptome and epigenome divergence can play an important role in adaptive evolution in nature. Recent advances in NGS techniques have revealed widespread differences in transcriptome and epigenome profiles among closely related species and populations, especially those adapting to ecologically diverse environments. In particular, chromatin accessibility, often associated with the specific functionalities of genomic regions involved in gene expression regulation, is modulated by genetic variation. These genetic variations can lead to differential gene expression levels, potentially contributing to phenotypic diversity. Despite their importance, we still know little about 1) the distribution of such genetic variations in the genome; 2) their roles in adaptive evolution; and 3) their regulatory impacts on gene expression that underlies the phenotypic diversification.
To address these questions, we performed an integrative QTL analysis of gene expression and chromatin accessibility in the pituitary of the three-spined stickleback (Gasterosteus aculeatus). The three-spined stickleback is an ancestral marine fish but has diversified into various phenotypically divergent freshwater populations. In addition, the pituitary gland which serves as a central regulator of physiological processes, plays a key role in the diversification of life history traits. Here, we analyzed the genetic variation (ddRADseq), gene expression (RNAseq), and chromatin accessibility (ATACseq) of the pituitary gland in F2 intercrosses between a marine and a freshwater stickleback population. Our analyses successfully identified thousands of regulatory expression quantitative trait loci (eQTL) and chromatin QTL (cQTL), highlighting the hotspots showing significant QTL enrichment. To improve the functional characterization of QTLs with higher precision, we further categorized them based on their proximity to target genes or open chromatin peaks. Local (cis)-QTLs are defined as those located within 1 megabase (Mb) upstream of their targets, whereas distal (trans) -QTLs lie beyond this range. Notably, subsequent genomic scans revealed a greater proportion of local eQTLs overlapping with highly differentiated genomic regions, suggesting divergent selection between marine and freshwater populations. By integrating previous single-cell multiome studies and current QTL mediation analyses, we propose a causal model for the distal genetic regulation of thyroid-stimulating hormone-β2 (TSHβ2) by the LIM Domain Transcription Factor LMO4b and chromatin intermediates. These findings provide a comprehensive understanding of the regulatory network of gene regulation and chromatin dynamics, and underscore its role in adaptive evolution.