Epigenetic Regulation of Economically Important Traits in Farm Animals: From Fundamental Mechanisms to Breeding Strategies

The modern challenges faced by global animal husbandry necessitate a shift from classical breeding approaches, which rely solely on genotype, toward more integrative models that account for gene–environment interactions. Epigenetics—the study of heritable changes in gene expression that do not involve alterations in the DNA sequence—provides a powerful framework for understanding these interactions. This review systematizes current knowledge on the roles of major epigenetic mechanisms, including DNA methylation, histone modifications, and regulation by noncoding RNAs, in shaping economically important traits in farm animals. The impact of epigenetic regulation on meat and milk productivity, product quality, reproductive performance, and fertility is examined in detail. Particular attention is devoted to the epigenetic foundations of adaptation to such stress factors as housing conditions, temperature regimes, nutrition, and extreme environments, including high-altitude hypoxia. The phenomenon of transgenerational epigenetic inheritance—whereby environmentally induced epigenetic marks can be transmitted to subsequent generations—is analyzed as a promising avenue for the long-term improvement of livestock breeds. Moreover, modern technological approaches to epigenomic research, from whole-genome bisulfite sequencing (WGBS) to single-cell chromatin accessibility assays (scATAC-seq), and their applications in animal science are discussed. Finally, the review highlights prospects and opportunities for the implementation of epigenomic selection and epigenome-editing technologies (CRISPR/dCas9) as next-generation tools for targeted enhancement of productivity, health, and resilience in farm animals.