Beyond genomics to epigenomics: emerging frontiers of DNA methylation in livestock

DNA methylation influences gene regulation and economically important traits in livestock, yet many reviews remain descriptive and biased toward short-read analyses. This review characterized various biological functions of DNA methylation in cellular development, reprogramming, transgenerational inheritance, and economic traits by reshaping gene and chromatin patterns and genomic imprinting in livestock. DNA methylation detection technologies are further appraised, and the advantages of native long-read sequencing with PacBio HiFi and Oxford Nanopore highlighted. Meanwhile, the fact that epigenome editing showed significant potential in precision breeding without changing genomic sequences is presented. Finally, artificial intelligence is described as an enabler of modified base calling, multi-omics integration, and interpretable decision support for livestock research. This review summarizes advances in DNA methylation in livestock and discusses future directions.