Epigenetic mechanisms and applications in aquaculture and fisheries, with perspectives on technology and analysis

Epigenetics has emerged as a promising field, providing the molecular framework that links an organism's genome to its environment. This review synthesizes recent advances in aquatic epigenomics, highlighting how a multi-layered network of core mechanisms, including DNA methylation, histone modifications, non-coding RNAs, and three-dimensional genome architecture, collectively shapes commercially valuable traits. These traits, which are fundamental to the productivity and resilience of aquatic species, encompass growth, development, reproduction, sex determination, metabolic efficiency, immune defense, and adaptation to environmental stressors. We explore the paradigm shift from passive genetic selection to proactive environmental programming, detailing applications in domestication, broodstock management, and disease resistance through strategies like epigenetic priming and microbial education. Furthermore, this review provides a critical overview of advanced technologies and bioinformatics pipelines that are democratizing the field, from enzymatic methylation sequencing and CUT&Tag to the development of non-invasive monitoring tools such as epigenetic clocks based on environmental DNA. Despite its immense promise, significant challenges remain, including elucidating the complex interplay between genetic and epigenetic variation, validating causal epi-markers, and understanding the mechanisms of stable transgenerational inheritance. Realizing the full potential of epigenetics through strategies such as epigenetic priming and microbiome-mediated programming will require sustained interdisciplinary efforts to integrate epigenomic insights into selective breeding and ecosystem-based management frameworks.