Among aquaculture sectors, salmonid farming stands out as one of the most significant contributors to global aquatic food production. Although Atlantic salmon (Salmo salar) dominates Chilean salmon production, rainbow trout (Oncorhynchus mykiss ) remains a key species within the industry, especially in freshwater-based systems. Valued for its robust adaptability, rapid growth, and high nutritional content, rainbow trout is cultivated under diverse environmental and operational conditions, ranging from small-scale farms to industrial production. Nevertheless, intensive farming environments frequently subject fish to various stressors that can impair immune defenses, suppress growth, and negatively impact overall health and welfare. These challenges ultimately threaten the sustainability of aquaculture operations. Cortisol, the primary glucocorticoid hormone in teleost fish, plays a central role in the physiological response to stress by modulating key processes such as metabolism, immune regulation, and energy allocation. Although the acute metabolic effects of cortisol have been extensively studied, its long-term influence on gene expression in the skeletal muscle of rainbow trout remains insufficiently explored. As the most abundant tissue in fish, skeletal muscle is fundamental to somatic growth and overall productivity, and its high sensitivity to hormonal and environmental cues makes it an ideal model for investigating the molecular mechanisms underlying chronic stress responses. In this study, we applied Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to evaluate changes in chromatin accessibility in the skeletal muscle of juvenile O. mykiss two weeks after exposure to exogenous cortisol. Fish were treated with cortisol dissolved in coconut oil and compared to a vehicle control group. Nuclear fractionation was performed, ATAC-seq libraries were constructed, and sequencing was carried out on the Illumina NovaSeq6000 platform (150 bp PE). Differentially accessible chromatin regions and enriched biological processes were identified, followed by candidate gene selection for RT-qPCR validation. These findings contribute to a better understanding of the epigenetic effects of long-term cortisol exposure in rainbow trout, providing tools for improving aquaculture management and fish resilience.
Funding: FONDECYT 1230794; FONDAP 1522A0004; FONDAP 1523A0007;