Abstract

Intramuscular Fat (IMF) content is an important trait closely related to meat quality, which is highly variable among pig breeds from diverse genetic backgrounds. This study identifies and compares the differential expression of functional genes associated with muscle growth and fat deposition. High-throughput sequencing has become a powerful technique for analyzing the whole transcription profiles of organisms. We adopted RNA sequencing to detect transcriptome in the longissimus dorsi muscle of Wujin pigs (a Chinese indigenous breed) and Landrace pigs (a western lean-type breed) with different IMF content. For the Wujin and Landrace pig libraries, over 6.6 and 7.2 million clean reads were generated by transcriptome sequencing, respectively. A total of 682 Differentially Expressed Genes (DEGs) were identified in our study (|log2FC| > 1, p < 0.05), with 296 up-regulated and 386 down-regulated genes in Wujin pigs compared with Landrace pigs. The Gene Ontology analysis revealed that DEGs were significantly associated with processes such as cholesterol import, chylomicron remnant clearance, and cholesterol efflux. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that DEGs were significantly enriched in pathways related to the biosynthesis of unsaturated fatty acids, ErbB (Erythroblastic Oncogene B) signaling pathway, metabolic pathways, and oxidative phosphorylation. The key genes, namely PDP1 (Pyruvate Dehydrogenase Phosphatase Catalytic Subunit 1), EGR1 (Early Growth Response 1), IL6R (Interleukin 6 Receptor), and ATF3 (Activating Transcription Factor 3) exhibit correlations with muscle growth, while TMEM182 (Transmembrane Protein 182), AGL (Amylo-Alpha-1, 6-Glucosidase, 4-Alpha-Glucanotransferase), and ADCY9 (Adenylate Cyclase 9) exhibit correlations with lipid deposition. The Protein-Protein Interaction (PPI) network with 418 nodes and 863 edges was constructed and 4 modules were extracted from the entire network. In summary, this study identified candidate genes and putative signaling pathways and provided useful information to further investigation of the mechanism of muscle growth and lipid deposition in pigs.

Keywords:Pigs; Longissimus muscle; Transcriptomics; Lipid deposition; Candidate gene

Abbreviations: IMF: Intramuscular Fat; DEGs: Differentially Expressed Genes; KEGG: Kyoto Encyclopedia of Genes and Genomes; ErbB: Erythroblastic Oncogene B; PDP1: Pyruvate Dehydrogenase Phosphatase Catalytic Subunit 1; EGR1: Early Growth Response 1; IL6R: Interleukin 6 Receptor; ATF3: Activating Transcription Factor 3; TMEM182: Transmembrane Protein 182; AGL: Amylo-Alpha-1, 6-Glucosidase, 4-Alpha-Glucanotransferase; ADCY9: Adenylate Cyclase 9; PPI: Protein-Protein Interaction; SFA: Saturated Fatty Acid; MUFA: Monounsaturated Fatty Acid; PUFA: Polyunsaturated Fatty Acid; GC: Gas Chromatography; GO: Gene Ontolog; STRING: Search Tool for the Retrieval of Interacting Genes; MCODE: Molecular Complex Detection; FC: Fold Change; SEM: Standard Errors of the Means; NDUFV1: NADH Ubiquinone Oxidoreductase Core Subunit V1; NDUFB9: NADH Ubiquinone Oxidoreductase Subunit B9; UQCRC1: Ubiquinol-Cytochrome C Reductase Core Protein 1; NDUFA10: NADH Ubiquinone Oxidoreductase Subunit A10; NDUFS2: NADH Ubiquinone Oxidoreductase Core Subunit S2; ATP5MC1: ATP Synthase Membrane Subunit C Locus 1; NDUFS6: NADH Ubiquinone Oxidoreductase Subunit S6; COX4I1: Cytochrome C Oxidase Subunit 4I1; TUFM: Tu Translation Elongation Factor, Mitochondrial; NDUFB8: NADH Ubiquinone Oxidoreductase Subunit B8