To What Extent Does DNA Methylation Affect Phenotypic Variation in Cattle?

Methylation is an epigenetic modification of DNA that regulates gene transcription and may influence variation in economically important phenotypes in agricultural species.  Here we integrate RNA-Seq and methyl binding domain sequencing (MBD-Seq) data to determine the extent to which DNA methylation may affect phenotypic variation in economically important traits of cattle.  MBD-Seq is a technique that involves the sample enrichment of methylated genomic regions followed by their next-generation sequencing.  This study utilized Illumina next generation sequencing technology to perform RNA-Seq and MBD-Seq.  Subsequently, differential methylation and differential gene expression were characterized in the livers, small intestines and longissimus dorsci muscles of 8 animals that are phenotypically extreme for residual feed intake (4 high and 4 low RFI). NextGENe software (SoftGenetics, State College, PA) was employed for quality trimming and aligning the sequence reads to the UMD3.1 reference genome, generating counts of matched reads and peak identification.  Currently, methylation and gene expression data are being integrated to identify the extent to which DNA methylation affects gene expression and phenotypic variation in the feed efficiency of cattle.