Abstract
Genome-wide studies provide considerable insights into the genetic background of animals; however, the inheritance of several heritable factors cannot be elucidated. Epigenetics explains these heritabilities, including those of genes influenced by environmental factors. Knowledge of the mechanisms underlying epigenetics enables understanding the processes of gene regulation through interactions with the environment. Recently developed next-generation sequencing (NGS) technologies help understand the interactional changes in epigenetic mechanisms. There are large sets of NGS data available; however, the integrative data analysis approaches still have limitations with regard to reliably interpreting the epigenetic changes. This review focuses on the epigenetic mechanisms and profiling methods and multi-omics integration methods that can provide comprehensive biological insights in animal genetic studies.
Highlights
Genome-wide studies have provided considerable insights into the genetic basis of inheritance; they could only partially explain the heritability of complex traits [1]
Epigenetic information is encoded in the gene sequence and is regulated through DNA methylation, histone modification, and RNA interference (RNAi) [3]
We introduce the Multi-omics integration (MOI) analysis method using omics data at different molecular levels that can be applied to epigenetic research (Table 3)
Summary
Genome-wide studies have provided considerable insights into the genetic basis of inheritance; they could only partially explain the heritability of complex traits [1]. Complex traits in livestock can be attributed to genetic factors; the final phenotypic outcome is highly dependent on the farm environment, ecotypes, and individual genetic backgrounds. This missing heritability in complex traits can be attributed to the contribution of epigenetic variability, arising from the interactions with environmental factors. Epigenetic information is encoded in the gene sequence and is regulated through DNA methylation, histone modification, and RNA interference (RNAi) [3]. DNA methylation, histone modifications, and RNAi regulate gene expression through interactions with the genetic and environmental factors, in turn influencing the phenotype, resulting in variations in various biological mechanisms. Identifying and understanding the mechanisms of epigenetics is important in a variety of traits, such as disease and pro-
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