Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes

Abstract

Intramuscular fat (IMF) content is vital for pork quality, serving an important role in economic performance in pig industry. Non-coding RNAs, with mRNAs, are involved in IMF deposition; however, their functions and regulatory mechanisms in porcine IMF remain elusive. This study assessed the whole transcriptome expression profiles of the Longissimus dorsi muscle of pigs with high (H) and low (L) IMF content to identify genes implicated in porcine IMF adipogenesis and their regulatory functions. Hundreds of differentially expressed RNAs were found to be involved in fatty acid metabolic processes, lipid metabolism, and fat cell differentiation. Furthermore, combing co-differential expression analyses, we constructed competing endogenous RNAs (ceRNA) regulatory networks, showing crosstalk among 30 lncRNAs and 61 mRNAs through 20 miRNAs, five circRNAs and 11 mRNAs through four miRNAs, and potential IMF deposition-related ceRNA subnetworks. Functional lncRNAs and circRNAs (such as MSTRG.12440.1, ENSSSCT00000066779, novel_circ_011355, novel_circ_011355) were found to act as ceRNAs of important lipid metabolism-related mRNAs (LEP, IP6K1, FFAR4, CEBPA, etc.) by sponging functional miRNAs (such as ssc-miR-196a, ssc-miR-200b, ssc-miR10391, miR486-y). These findings provide potential regulators and molecular regulatory networks that can be utilized for research on IMF traits in pigs, which would aid in marker-assisted selection to improve pork quality.

Impacts of Dietary Standardized Ileal Digestible Lysine to Net Energy Ratio on Lipid Metabolism in Finishing Pigs Fed High-Wheat Diets

“…In the present study, lowering the dietary SID Lys:NE ratio did not show adverse effects on dressing percentage, average fat thickness, or LEA. The marbling score, which has been proven to directly reflect IMF content [ 17 ], increased in the LR group. The finding offered compelling evidence supporting the notion that a reduction in the dietary SID Lys:NE ratio facilitated IMF deposition, as indicated by the increase in serum TG concentration.…”

Identification of Differentially Expressed miRNAs in Porcine Adipose Tissues and Evaluation of Their Effects on Feed Efficiency

“…miR-196a is a key regulator of fat deposition [ 89 , 90 ], and our data showed that miR-196a is up-regulated in the adipose tissue of high-FE pigs, in contrast to that of low-FE pigs. In pigs, miR-196a has been reported to be associated with preadipocyte differentiation and adipogenesis [ 91 , 92 ]. Overexpression of miR-196a can increase lipid accumulation and promote preadipocyte differentiation [ 93 ].…”

Whole-Transcriptome Analysis Sheds Light on the Biological Contexts of Intramuscular Fat Deposition in Ningxiang Pigs

“…Previous studies have compared the genetic profiles of Laiwu pigs with different IMF levels, and the results indicated that the different IMF levels between individual pigs may be due to DE lncRNAs and mRNAs associated with lipid droplets and fat deposition [11]. By comparing the whole transcriptome expression profiles of the longest dorsal muscles of pigs with high and low IMF contents in Yorkshire pigs, the results have shown that IMF fat formation in Yorkshire pigs is regulated by the ceRNA network formed by functional lncRNAs and circRNAs [12]. The Ningxiang pig is one of China's most outstanding native pig breeds, renowned for its high and evenly distributed intermuscular fat content, tender meat, and slender muscle fibers [13].…”