Genomic landscape underlying pituitary epigenome divergence between stickleback ecotypes

The diversification of epigenetic regulation, including chromatin accessibility, is crucial for adaptation to diverse environments. Chromatin regulation in endocrine organs, such as the pituitary gland, plays a critical role in controlling various physiological processes underlying life-history traits, including growth, metabolism and reproduction. To understand the genetic architecture responsible for epigenomic divergence, we investigated chromatin accessibility in the pituitary gland using a parapatric pair of marine and stream ecotypes of the three-spined stickleback (Gasterosteus aculeatus). First, we characterized the distinct chromatin accessibility profiles of the ecotypes. Our chromatin quantitative trait loci (cQTL) mapping identified both cis- and trans-QTL across the genome. Further comparative analyses of effect size, direction of effect and functional enrichment suggest that cis- and trans-cQTLs may contribute differently to epigenomic divergence between ecotypes. These results suggest that epigenomic divergence could be a key regulatory mechanism underlying local adaptation and support the contribution of both cis- and trans-cQTL to the evolution of complex traits. This article is part of the theme issue 'Ecological epigenetics at the intersection of behaviour and life history variation in non-model animals'.