Meat quality is a complex trait that exhibits significant variation across pig breeds, and the regulatory mechanisms governing pork meat quality are not fully elucidated. We compared the transcriptomics and metabolomics of the longissimus dorsi (LD) muscle between the Songliao Black Pig (SBP) and Large White × Landrace Pig (LWLDP) to investigate breed-specific differences in meat quality and underlying regulatory pathways. The results showed that SBP meat had a higher marbling score and backfat thickness, a richer color, a lower shear force, and reduced drip loss. Fatty acid (FA) analysis identified 15 significant FAs in the LWLDP, with docosahexaenoic acid (DHA) in the SBP, while amino acid (AA) analysis revealed no breed-based differences. Transcriptome analysis identified 134 upregulated and 362 downregulated genes in the SBP. Protein–protein interaction (PPI) network analysis found 25 key genes, which are associated with muscle development, fat deposition, and overall meat quality, while genes in the insulin signaling pathway, such as PPP1R3B, PPARGC1A, SOCS1, EIF4E, PRKAR2A, PRKAG2, and FASN, play a crucial role in balancing fat metabolism and catabolism. Metabolomic analysis identified 89 upregulated and 10 downregulated metabolites in the SBP, primarily involved in fructose and mannose metabolism, amino acid biosynthesis, nucleotide sugar metabolism, and glucagon signaling pathways. Gene–metabolite association analysis found that the PPP1R3B gene had a strong association with Thr-Leu, Maltol, D-myo-Inositol-4-phosphate, and Fructose-6-phosphate, while MYOG correlated with Mannose-6-phosphate, Fructose-1-phosphate, Mannose-1-phosphate, and Glucose-6-phosphate. In contrast, NR4A3 and PPARGC1A showed a strong negative correlation with most upregulated metabolites. In conclusion, this study identified functional genes, elucidated the mechanisms associated with meat quality traits, and identified gene–metabolite associations involved in energy metabolism, muscle development, and fat deposition, providing valuable insights into the molecular mechanisms that regulate meat quality between pig breeds.

Gut microbiota ferment non-digestible substances to produce metabolites that accumulate in muscle and influence host metabolism. However, the regulatory mechanisms connecting gut microbiota, metabolites, and fat deposition across pig breeds remain unclear. This study explores the gut–muscle axis regulating fat deposition and meat quality in Chinese Songliao Black Pig (SBP) and Large White × Landrace Pigs (LWLDP). Digesta samples from the ileum, cecum, and rectum of both breeds were analyzed using 16 S rRNA sequencing for microbiome profiling and ultra-high-performance liquid chromatography (UHPLC) for metabolomics. Multi-omics data, including microbiota and metabolite profiles were integrated with our previously published data of transcriptomics and metabolomics insights into fat deposition in the longissimus dorsi (LD) muscle using the MixOmics DIABLO method. Microbiome analysis revealed that Fibrobacter, Unidentified_Peptostreptococcaceae, Sutterella, and Unidentifed_Rickettsiales were enriched in SBP, while Ruminococcus, Corynebacterium, and Streptococcaceae in LWLDP. Metabolomic analysis indicated that SBP was enriched in fatty acid biosynthesis pathways, including linoleic acid, α-linolenic acid, and arachidonic acid, whereas LWLDP was associated with insulin signaling, starch and sucrose metabolism. Integrated analysis identified Peptostreptococcaceae and Rickettsiales in SBP, along with metabolites phosphatidylcholine (PC(22:4)), N-acylethanolamine (NAE(20:4)), and lysophosphatidylcholine (LysoPC(24:1)) were correlated with key genes (EIF4E, MSTN, PPARGC1A, NR4A3, and SOCS1) regulating fat deposition. In LWLDP, Corynebacterium and Streptococcaceae were linked to the PPP1R3B gene, which is involved in glycogen metabolism, as well as metabolites 2-methyl-3-hydroxybutyric acid and 5-keto-gluconic acid, suggesting a shift toward glycolysis over lipolysis. This study concluded that cecum-associated microbes in LWLDP may enhance carbohydrate metabolism, leading to reduced fat deposition, whereas rectum-associated microbes in SBP contribute to docosahexaenoic acid (DHA) biosynthesis, thereby improving meat quality. These findings highlight gut microbiota-derived metabolites as potential biomarkers for optimizing meat production and livestock breeding strategies.

With the ongoing upgrade in consumption patterns, the pork market is shifting from a focus on quantity to an emphasis on quality, demanding higher intramuscular fat content alongside maintained growth rates. Crossbreeding between the Chinese lean-type Songliao black pig and the high-quality local breed Leixiang pig allows rapid integration of parental superior traits, resulting in hybrid vigor that effectively improves pork quality, growth performance, and economic benefits. We conducted transcriptomic and 4D microDIA proteomic sequencing analyses on the longissimus dorsi muscle tissue from hybrid offspring of purebred Songliao black pigs and Songliao × Leixiang black pigs. Extensive phenotypic analyses were performed on Songliao black pigs and Songlei black pigs using multiple trait indicators. Six pigs were selected and categorized into relatively high and low intramuscular fat groups. Integrated analysis of transcriptomic and proteomic data identified candidate genes within significantly annotated lipid-related pathways via KEGG, including ACSL1 , ACSL6 , SREBF1 , PLIN2 , CEPT1 , CPT1B , CPT1C , and ACSF3 . Among these, CPT1B was significantly associated with fatty acid metabolism pathways. By analyzing all significantly differential genes and proteins, six candidate genes were identified as key determinants of genetic variation in lipid deposition: UCP3 , CPT1B , LSMEM1 , NEXN , PPP1R14C , and LOC100624149 . This preliminary exploratory multi-omics study provides a valuable resource for probing intramuscular fat deposition, aiming to support pork-trait improvement in breeding and to establish a fresh theoretical basis for clarifying the molecular mechanisms of meat-quality heterosis in Songlei black pigs.

Background The rising demand for high-quality pork among consumers has driven interest in genetic improvement strategies. Crossbreeding is well known to influence carcass performance and meat quality; however, the molecular mechanisms underlying these effects are still poorly understood. In this study, the F1 generation of the Songlei Crossbred Pig (SL) was developed through crossing the Songliao Black Pig (male) (SS) and the Leixiang Pig (female) (LL). We integrated the transcriptomes and metabolomes of the longissimus dorsi (LD) muscle of SS and SL under identical conditions to identify key mechanisms regulating the quality of crossbred meat. Results Compared with those of SS, the slaughter weight, carcass weight, and dressing percentage of SL were significantly lower, but the backfat thickness was greater; however, meat quality traits, including intramuscular fat (IMF), colour, and pH 24h , were significantly greater, and the pressure loss and shear force were lower in SL. Transcriptome and metabolome analyses revealed a total of 616 differentially expressed genes (DEGs) and 681 significantly differentially expressed metabolites (DEMs) in the LD muscles of SS and SL. Protein-protein interaction (PPI) network analysis revealed key FASN, ADIPOQ, IGF1R and SREBF1 genes that regulate fat metabolism. Furthermore, multiomics joint analysis identified 99 common KEGG pathways, among which the first four pathways were related to fat metabolism, including the AMPK signalling pathway, PPAR signalling pathway, and the regulation of lipolysis in adipocytes and insulin resistance. Gene and metabolite association analysis revealed that the expression of alphadimorphecolic acid metabolites was strongly correlated with that of the adipose metabolism-related genes IRS1 and ANGPTL4. Conclusions The meat quality of SL was better than that of their male parents, but not the carcass traits were not. Additionally, several critical genes and pathways related to lipid metabolism were identified. These findings provide new insights into how meat quality can be improved by hybridization.

Heterosis or hybrid vigor is a well-recognized biological phenomenon, where crossbred progeny exhibit superior growth performance, stress tolerance, and productivity compared to their purebred parents. However, the molecular mechanisms underlying heterosis for meat quality traits in pigs remain poorly understood. In this study, we compared the longissimus dorsi muscle transcriptomes of Songliao Black Pig (SBP), Large White × Landrace pig (LWLDP), and their crossbred progeny (BXW) to uncover genetic mechanisms contributing to hybrid vigor in meat quality. Results identified 4290 differentially expressed genes (DEGs) in SBP vs. BXW and 3820 in LWLDP vs. BXW. Among these, 1358 genes displayed overdominant expression in BXW, indicating potential heterotic activation. Functional enrichment analysis identified key pathways involved in lipid metabolism, energy homeostasis, and muscle growth, including mTOR, AMPK, insulin, PI3K-Akt, MAPK, and calcium signaling. Over dominantly expressed genes such as FASN, CPT1A, PPARG, ACACA, PPARA, SREBF1, FABP4, DGAT1, PPARGC1A, LIPC, ACSL5, PLCG2, and members of the COX family were closely associated with intramuscular fat deposition, oxidative metabolism, and tenderness. Phenotypically, BXW exhibited improved meat color, moderate fat deposition, and lower shear force compared with parental breeds, clearly aligning with transcriptomic findings. These transcriptomic findings offer valuable insights into precision breeding strategies targeting superior meat quality through genomic selection and crossbreeding programs.

The study analyzed ten reproductive traits in three major commercial breeds—Yorkshire, Landrace, and Duroc—raised under uniform management. Genetic parameters were estimated using a repeatability animal model in ASReml, genome-wide association studies (GWAS) were performed with 46,358 post-QC SNPs using GCTA, and genomic prediction was evaluated with GBLUP. Heritability estimates were low to moderate, with gestation length (GL) highest (0.33–0.41). GWAS identified significant loci across breeds: in Yorkshire, 37 genome-wide significant SNPs across 17 SSCs for seven traits; in Landrace, 16 SNPs for TNB and one for NBW; and in Duroc, 31 SNPs across 12 SSCs (predominantly for TNB). Among these SNPs, CNC10042060, CNC10160995, and CNCB10003799 were consistently associated with TNB in both Yorkshire and Duroc pigs. Additionally, five SNPs, CNC10012965, CNC10042060, CNC10120451, CNCB10003799, and CNCB10007759, showed significant associations with NBW in Yorkshire and Landrace pigs. Candidate genes mapped within ±1 Mb of significant SNPs were enriched for biologically plausible pathways. Genomic prediction accuracies ranged from low to high depending on trait and breed, such as reaching 0.68 for GL in 39 Yorkshire and 0.59 in Landrace. These results delineate shared and breed-specific genetic architectures, provide actionable markers and candidate genes, and can accelerate genetic gains in commercial breeding programs.