Intramuscular fat (IMF) is a significant marker for pork quality. The Anqing Six‐end‐white pig has the characteristics of high meat quality and IMF content. Owing to the influence of European commercial pigs and a late start in resource conservation, the IMF content within local populations varies between individuals. This study analyzed the longissimus dorsi transcriptome of purebred Anqing Six‐end‐white pigs with varying IMF content to recognize differentially expressed genes. We identified 1528 differentially expressed genes between the pigs with high (H) and low (L) IMF content. Based on these data, 1775 Gene Ontology terms were significantly enriched, including lipid metabolism, modification and storage, and regulation of lipid biosynthesis. Pathway analysis revealed 79 significantly enriched pathways, including the Peroxisome proliferator‐activated receptor and mitogen‐activated protein kinase signaling pathways. Moreover, gene set enrichment analysis indicated that the L group had increased the expression of genes related to ribosome function. Additionally, the protein–protein interaction network analyses revealed that VEGFA, KDR, LEP, IRS1, IGF1R, FLT1 and FLT4 were promising candidate genes associated with the IMF content. Our study identified the candidate genes and pathways involved in IMF deposition and lipid metabolism and provides data for developing local pig germplasm resources.

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.