Comparative Analysis of the N6-Methyladenosine of Skeletal Muscle in Jinhua and Landrace Pigs

Methylation of the N6 position of adenosine (m⁶A) is the most prevalent internal mRNA modification in eukaryotes; it is a reversible modification, and it plays important roles in cell differentiation and tissue development. Jinhua, a Chinese pig breed, contains considerably higher levels of intramuscular fat (IMF) than does Landrace, a Danish pig breed. However, how m⁶A methylation dictates the difference in IMF of skeletal muscle between lean and obese pigs remains unclear. In this study, the longissimus dorsi muscles of Jinhua and Landrace pigs (n = 4) at 180 days were used to: (i) investigate the difference in m⁶A/A ratio between Jinhua and Landrace pigs; (ii) analyze the differences in the expression of m⁶A modification-related proteins between Jinhua and Landrace pigs; and finally (iii) perform a comparative analysis of whole N6-transcriptome methylation between Jinhua and Landrace pigs. The results showed that: (i) the ratio of m⁶A/A was significantly lower in Jinhua pigs than in Landrace pigs (p < 0.05); (ii) the expression of m⁶A “readers” (YTHDF1, YTHDF2) was significantly lower in Jinhua pigs than in Landrace pigs (p < 0.01), whereas that of the “eraser” FTO was significantly higher in Jinhua pigs than in Landrace pigs (p < 0.05); and (iii) the differentially methylated genes (DMGs) were significantly associated with lipid metabolism, oxidative stress, and muscle development; among the identified DMGs, 53 genes were associated with obesity. The expression of the genes UCP2, FAM134B and MTCH2 was probably associated with the m⁶A methylation levels of their mRNAs; these genes were associated with oxidation–reduction and fatty acid metabolism. RNA methylation potentially influences the propensity for obesity by affecting gene expression in skeletal muscle. The findings of this study provide valuable information on epitranscriptome that will be useful for pig breeding and nutrition research.