[Comparative analysis on content and distribution of CpG sites in milk production traits and mastitis-related genes in dairy cattle].

DNA methylation is a major part of epigenetics. DNA methylation on the CpG sites in gene promoter and the first exon often represses gene expression, but demethylation activates gene expression. Previous research has shown that a negative correlation was found between mastitis index (somatic cell count, SCC) and milk production traits in Holsteins. The content and distribution of CpG dinucleotide sites in different regions of the candidate genes related to milk production traits and mastitis were studied in the present study. The regions contained promoter (2000 bp upstream of transcriptional start site), exon 1, and 2000 bp downstream of transcriptional end site. The CpG number of promoter and exon 1 in the mastitis-related genes was significantly less than that of the milk production-associated genes. However, the CpG number of 2000 bp downstream of the genes for the two traits was not significantly different. Two new index quantified CpG characterizations were proposed. One is the CpG distance, which can measure the distribution of CpG. The other is the conditional probability p(G|C), which is used to quantify the probability of CpG in a nucleotide sequence along with C. The two indexes of promoter and exon 1 in the two types of genes and their statistic analysis were carried out. This study sets the basis for DNA methylation regulation of milk production traits- and mastitis-related genes.