Abstract
Genetic and epigenetic factors contribute towards phenotypic variation in complex traits. Epigenetic modifications can affect transcription and translation and have been shown to influence variation in economically important phenotypes in agricultural species. The onset of pangenomics in livestock species is disconnected from pan-epigenomics and hence lacks a fully comprehensive view of diversity in livestock species. To establish a pan-epigenome for cattle and sheep we are comprehensively characterizing epigenomic conservation and diversity through examination of 5-methylcytosine, 5-hydroxymethylcytosine, histone marks H3K4me3, H3K27ac, H3K4me1 and H3K27me3, open chromatin, chromatin accessibility and n6-methyladenosine in the liver, muscle and prefrontal cortex of Brahman, Angus and Holstein cattle as well as Suffolk, Rambouillet and Katahdin sheep. Finally, comparative epigenomics is being used to identify orthologous regions of the sheep and bovine epigenomes that harbor conserved epigenetic modifications and variants. The establishment of a cattle and sheep pan-epigenome will increase our understanding of how different genomes, epigenomes, and gene products from diverse breeds of cattle and sheep affect a variety of important biological phenotypes, supporting more accurate prediction of traits and improving breeding strategies.