| Betaine has the effect of methyl donor,which can affect the methylation modification and promote the fat metabolism.In the production practice,the content of intramuscular fat in pigs was significantly increased after feeding betaine,suggesting that DNA methylation is an important factor in the regulation of fat metabolism.Therefore,it is of great significance to carry out the research on the production and breeding of livestock and poultry.Based on the comparison of carcass traits and meat quality,we used Duroc and Luchuan pig breeds as typical lean and obese animal models.The new generation of high-throughput RRBS was used to study the DNA methylation level and function in the promoter and CpG island(CGIs)of the two adipose tissue.We obtained 98720992 and 97254298 Clean Reads in the Duroc and Luchuan sample,accounting for 99.4%and 99.56%of Reads,respectively.We found that methylation of CG type is the main methylation C sites(mC)in two samples by methylation analysis and the mC of the different distribution types are different;The chromosomes of 10,17 and 18 were selected from the two samples,and their promoter,CGI and the overlap methylation patterns were shown,the differences in the methylation distribution types in the different chromosomes of one sample and the same chromosome in different samples are shown;The differentially methylated regions(DMRs)in the genome of two pig breeds was successfully identified by enrichment analysis,and its annotation of the gene body is mainly distributed in the gene intron region;the methylation level of different samples in DMRs was plotted and the results showed that the methylation level of lean pigs(Duroc)was higher;A total of 792 differentially methylated genes(DMG)were screened out,Gene ontogeny and KEGG pathway analyses indicated that these were mainly involved in intracellular part,binding,biological regulation,endocytosis,MAPK signaling pathway and calcium signaling pathway,these pathways are associated with fat metabolism.Combining the results of DNA methylation sequencing with those of transcriptome sequencing,we obtained that Duroc has a higher methylation level in the promoter region of the differentially expressed genes;By analyzing the relationship between methylation and expression,methylation gene has the lower expression in Duroc.Moreover,the DNA methylation level of the different distribution types in the two samples was different with the change of functional element length through analysis of the relationship between methylation level and functional element length.Integrated the data of DNA methylation sequencing with those of the whole genome resequencing,it showed that Duroc has higher methylation level than Luchuan and the SNP has obvious effect on Duroc methylation,which also provides envidence to support for higher DNA methylation of Duroc in DMRs.This study explored the pattern of DNA methylation,the relationship DNA methylation levels and gene expression regulation,and factors affecting DNA methylation levels.It is of great significance for the development of livestock and poultry breeding industry to provide a theoretical basis for the high quality and high efficiency of pork production by linking the epigenetic inheritance of DNA and fat metabolism. |
