Genome Wide DNA Methylation and Transcription Analysis in a Sheep Muscle Hypertrophy Model

Advances made in DNA sequencing technologies over recent years have resulted in genome wide selection for production traits becoming a reality.  Soon all sequence variations in closed breeding schemes will be known. What is not currently known is how to rank these variations, especially those that involve changes in gene expression. One of the key determinants in the control of gene expression in mammals is DNA methylation – a mechanism known to play a central role in regulating many aspects of growth and development. High-throughput sequencing is a vital tool in the analysis of DNA methylation, and reduced representation bisulfite sequencing (RRBS) has proven to be effective in understanding DNA methylation landscapes in humans and mice.  Here we describe development of RRBS in sheep. The Carwell phenotype, used as a proof of principle, is a desirable inherited muscular hypertrophy for which, in spite of considerable resequencing efforts, the causative mutation has not been identified. Muscle DNA was used for RRBS and epigenomic pipeline development to generate single nucleotide resolution analysis of DNA methylation in sheep.  Analysis of 1% of the genome resulted in precise and accurate analysis of >20% of all CpG sites. Methylation levels across the genomic region responsible for the Carwell phenotype were analysed to determine if DNA methylation patterns correlated muscular hypertrophy. Methylome results were combined with mRNAseq and miRNAseq to interrogate the underlying cause of the phenotype. These epigenomic technologies will facilitate identification of superior individuals in animal production systems to enhance productivity in the future.