Study On Genome-wide Methylation Differential Analysis And Candidate Genes In Pig IMF

IMF is economically important in swine breeding, so it has important practical significance to explore the mechanism of this process. We cloned the full-length NUDT3 cDNA sequences by using RACE for its important role in IMF. The whole sequence was 8628 base pairs long and encodes a protein of 172 amino acids. Expression patterns of NUDT3 in various tissues showed the highest expression in longissimus dorsi.We used F2 pigs with the extreme high or low IMF of the Yorkshire×Min zhu resource population built by our laboratory to do this research to analysis the methylation degree of important candidate genes of IMF deposition, such as, NUDT3, AOC3, PPARG1, SOD3 and NTN1. Longissimus dorsi were collected to detect the methylation profiling of CGI by using BSP, intending to explore the connection between DNA methylation level and IMF. The results showed no significant methylation level differences in all five candidates between the IMF extreme high and low groups, suggesting that the phenotypic differences in this population might not be controlled by the degree of DNA methylation level. More researches were needed to find out the IMF molecular mechanism of these candidate genes.Further more, the study used F2 pigs with the extreme high or low IMF of the same resource population as research object. WGBS was used to construct the methylation pattern atlas of longissimus dorsi, and to explore the regulatory mechanism that how the methylation level impact IMF. The profiling accuracy of the atlas reached single nucleotide standard. The result showed that more than 96% methylation occurred in CpG regions, the degree of methylation in the region on each chromosome maintained around 60%, which was generally inversely proportional to the length of the chromosome. The highest methylation level in gene function area appeared in the whole intron region and upstream of the promoter region, which might indicate the position of methylation regulation function; CpG, CHG sites did not obtain methylation sequence environment preferences, but CHH upstream adjacent site got a higher probability of TN, which could be used to predict where may get methylation. According to the DMR methylation analysis, DMR length mainly between 300 to 400 bp, the low group got more DMRs in the length extremum area, but less in the average area than the high group, indicating that abnormal methylation degree might cause the decreasing of IMF. In addition, GO enrichment analysis showed that the number of DMR-related genes(p < 0.05) in GO database was more than ten thousand, related to cellular component, biological process and molecular function, and especially related with cell development, protein binding, signal conditioning and the composition of cytoskeleton, which provided good materials for exploring the methylation mechanism in IMF. By the DMR comparison between the high-low group and intergroup, a total of 11 significantly differentially methylated region were found. The functions of the 7 genes which were located on the areas above such as ACTG1,UBB,NMD3,SUPV3L1,TUBA1 A,TUBA1B and JUN still needs further study.