Epigenetic marks: regulators of livestock phenotypes and conceivable sources of missing variation in livestock improvement programs

Abstract

Improvement in animal productivity has been achieved over the years through careful breeding and selection programs. Today, variations in the genome are gaining increasing importance in livestock improvement strategies. Genomic information alone, however, explains only a part of the phenotypic variance in traits. It is likely that a portion of the unaccounted variance is embedded in the epigenome. The epigenome encompasses epigenetic marks such as DNA methylation, histone tail modifications, chromatin remodeling, and other molecules that can transmit epigenetic information such as non-coding RNA species. Epigenetic factors respond to external or internal environmental cues such as nutrition, pathogens, and climate, and have the ability to change gene expression leading to emergence of specific phenotypes. Accumulating evidence shows that epigenetic marks influence gene expression and phenotypic outcome in livestock species. This review examines available evidence of the influence of epigenetic marks on livestock (cattle, sheep, goat, and pig) traits and discusses the potential for consideration of epigenetic markers in livestock improvement programs. However, epigenetic research activities on farm animal species are currently limited partly due to lack of recognition, funding and a global network of researchers. Therefore, considerable less attention has been given to epigenetic research in livestock species in comparison to extensive work in humans and model organisms. Elucidating therefore the epigenetic determinants of animal diseases and complex traits may represent one of the principal challenges to use epigenetic markers for further improvement of animal productivity.

Keywords: cattle; epigenetics; genetic improvement; goat; livestock; pig; sheep.

FIGURE 1

Epigenetic marks respond to internal and environmental cues (A) resulting in various effects on chromatic conformation and gene expression. (B) Compact chromatin: tends to contain silent genes, modified DNA and histones. A number of nuclear factors such as DNA methyltransferases (DNMTs), methyl-CpG binding domain proteins (MBDs), histone methyltransferases (HMT, K9, H3), histonedeactylases (HDACs), and DNA methylation are involved in silencing gene expression. In the compact state, genes are inaccessible to transcription factors and non-coding RNAs (ncRNAs). (C) Relaxed chromatin: has dispersed appearance and is gene rich. Transcriptionally active genes are rich in unmethylated DNA. Histones are generally hyperacetylated. Histone methyltransferases (HMT, K4, H3) and acetyltransferaces (HATs) are associated with unmethylated promoters and transcriptional activity. Genes are accessible to transcription factors and ncRNAs. (D) Diverse phenotypes may result.

FIGURE 2

Increasing evidence shows that the phenotype results from interaction of the genotype, epigenotype and environmental forces. Establishment of the epigenotype can be perturbed during the zygotic stage (maternal environment) and during growth and development by several forces. The effect of such forces on epigenetic marks and influence on the phenotype needs to be recognized and determined before application in improvement breeding/management.