Construction of a competitive endogenous RNA regulatory network for intramuscular fat content in Laiwu pig based on whole transcriptome analysis

Abstract Intramuscular fat (IMF) content is an important factor for meat quality evaluation, which varies between species, and mainly involves the number and size of intramuscular adipocytes. However, the potential mechanism has not been well elucidated. In this study, the whole transcriptomic data of longissimus dorsi muscle from Laiwu pigs (LW, fatty type) and Duroc×Landrace×Yorkshire pigs (DLY, lean type) were collected and an in‐depth analysis was conducted. Through differentially expressed analysis between species, 1899 mRNAs, 10 microRNAs (miRNAs), and 247 circular RNAs were identified. An integrated analysis of differentially expressed mRNAs and miRNAs generated two network modules that potentially regulate IMF formation in LW pigs, one consisted of 13 mRNAs (such as ESR1 and COQ3 ) and one miRNA gene (ssc‐miR‐874), and another included 31 mRNAs (such as SCML4 and PDE7B ) and three miRNAs (ssc‐miR‐125a, ssc‐miR‐1343, and ssc‐miR‐204). In addition, a competitive endogenous RNA network including 13 circular RNAs, three miRNAs, and 31 genes was also delineated, which is probably involved in differential regulatory patterns of IMF deposition between LW and DLY pigs. The function of the SCML4 gene was verified with the 3T3‐L1 cell line in vitro, and, when SCML4 was decreased, the expression of key proteins associated with fat formation (PPARγ and FABP4) was significantly inhibited. In summary, the study provided the novel insight of a competitive endogenous RNA regulatory network for IMF content in pig, and our results indicated that SCML4 is likely to be a regulatory gene promoting IMF formation.