156 Genome-wide DNA Methylation Profile of Mammary Gland Tissues from Holstein Cattle Producing Various Milk Protein Yields

Abstract Milk protein content is attracting considerable attention due to increasing demand for high-quality products. Epigenetic marks including DNA methylation have demonstrated considerable potential to contribute to the achievement of increased gain in bovine milk traits. To investigate potential roles of DNA methylation in regulating milk protein productivity, whole genome bisulfite sequencing was used to profile the global DNA methylation of mammary gland (MG) tissues from Canadian Holstein cows producing milk with high protein (HMP) (>4.0%, n = 5) or low protein (LMP) (< 3.0%, n = 7) contents. Bioinformatics processing using standard tools and construction of the methylation landscape of MG was based on methylation sites with ≥10× coverage. A total of 2420 differentially methylated CpG (DMC) sites, including 1842 with higher and 578 with lower methylation levels (FDR< 0.1) were identified when HMP group was compared with LMP group. DMCs were most abundant on chromosomes 2 (n=347) and 27 (N=535), respectively. The most DMCs were annotated to mRNAs, followed by lncRNAs, pseudogenes and rRNAs. Eight genes harbored five or more DMCs each, including LOC112443250 (5S ribosomal RNA) and LOC112443149 (liprin-alpha-1-like, LIP1) (harbored 20 hypermethylated and 1 hypomethylated sites, each), followed by miR-2287-1 (12 hypomethylated sites), etc. LIP1, a liprin family member interacts with LAR family members to play important roles in MG development. MiR-2287-1 and other family members are frequently identified in MG tissues and milk and are associated with many livestock diseases. Interestingly, among the DMCs that overlap with QTLs related to milk production were clusters on chromosomes 27 (N=534) and 14 (N=91) that associated with milk protein yield. In conclusion, DNA methylation showed potential involvement in the genetic variation underlying milk protein content and MG biological processes. More analysis with a higher sample size is however necessary to adequately quantify the involvement of DNA methylation in the regulation of milk protein content and mammary gland development.