Epigenomics of Livestock Animals: From Epigenetic Reprogramming in Clones to Environmentally Induced Epigenetic Variation and Its Breeding Implications

Abstract

Epigenetics - heritable changes in gene expression that occur without alteration of the underlying DNA sequence - has emerged as a critically important dimension of livestock biology with far- reaching implications for reproductive biotechnology, genetic improvement, developmental programming, and the emerging field of epigenomic breeding. In livestock, epigenetic phenomena underlie the fundamental challenge of somatic cell nuclear transfer (SCNT), where incomplete reprogramming of donor cell epigenomes remains the primary cause of the low efficiency and high developmental failure rates that have constrained practical cloning applications for three decades. The same epigenetic machinery - DNA methylation, histone modification, chromatin remodelling, and non- coding RNA regulation - mediates the developmental programming effects of maternal nutrition, thermal stress, social environment, and management practices on offspring phenotype, with consequences that may persist across multiple generations through the germline. This review comprehensively examines the epigenetic marks and enzymatic machinery relevant to livestock species, the mechanisms and limitations of epigenetic reprogramming during SCNT and iPSC generation, the growing evidence for environmentally- induced epigenetic variation and its potential contribution to phenotypic plasticity and non- Mendelian inheritance in cattle, pigs, sheep, and poultry, and the current state of epigenome- wide association studies (EWAS) and their integration with genomic selection models. The FAANG initiative's systematic functional epigenetic annotation of livestock genomes is highlighted as an essential resource for functional interpretation of QTL and GWAS signals. Finally, the review examines the prospects for epigenetic editing - targeted modification of specific epigenetic marks using dCas9- based epi- tools - as a next- generation precision tool for livestock biotechnology.