Feed Efficiency in Cattle: An Epigenetic Perspective

Advances in next-generation sequencing (NGS) technology now allow an unprecedented ability to investigate the epigenome and provide an opportunity to more thoroughly explore the relationship between genetic and epigenetic variation and downstream phenotypic consequences.  This study was designed to characterize differential methylation in the livers, small intestines and longissimus dorsci muscles of animals that are phenotypically extreme for residual feed intake (RFI).  MIRA-Seq was performed using the Illumina HiSeq 2000 to generate tissue-specific methylation profiles for these tissues in eight cattle (4 high RFI and 4 low RFI).  NextGENe (SoftGenetics, State College, PA) software  was employed for quality trimming and aligning the sequence reads to the UMD3.1 reference genome, generating counts of matched reads and peak identification. Differential methylation is currently being investigated within each tissue type between animals differing for feed efficiency.  Finally, the methylation data will be integrated with gene expression data also generated by NGS using RNA-seq to elucidate the extent to which DNA methylation affects gene expression and potentially phenotypic variation in the feed efficiency of cattle.