Whole Genome Bisulfite Sequencing of Three Tissues Related to the Bovine Reference Genome

Phenotypic variation in economically important complex traits in cattle is regulated by genetics and environment, the latter by means of epigenetic mechanisms. Knowledge of the epigenetic contribution to phenotypic variation will require the bovine epigenetic landscape to be explored, which will rely upon high resolution sequencing data. Here, we used whole genome bisulfite sequencing (WGBS) to gain a single base pair resolution characterization of the methylome of liver, mammary gland and longissimi dorsi tissues from L1 Dominette 01449. An average of 350 million sequence read pairs were generated from each tissue, of which over 80% mapped to the reference genome. Initially, data were assessed to determine the correlation of cytosines detected throughout the genome with cytosine density of the genome. Next, methylated and non-methylated CGs, as well as methylated CHG (H= A, C or T) and CHH were measured and annotated. Subsequently, uneven distribution patterns of methylation throughout the genome were investigated. Finally, methylation patterns were compared among tissues and the effect of differentially methylated cytosines on gene expression was examined. This in-depth characterization of the methylome provides an epigenetic reference which can be used to elucidate the epigenetic contribution to variation in economically important traits and diseases.