Transcriptome and Metabolome Insights into Key Genes Regulating Fat Deposition and Meat Quality in Pig Breeds
Suthar Teerath Kumar,
Yunlong Zheng,
Jing Xu,
Ziyi Zhao,
Qi Zhang,
Yunpeng Zhang,
Min Li,
Hong Zou,
Riaz Muhammad Azeem,
Wu-Sheng Sun,
Yuan Zhao,
Shu-Min Zhang
Affiliations
Suthar Teerath Kumar
Key Laboratory of Animal Production, Product Quality and Security, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
Yunlong Zheng
Key Laboratory of Animal Production, Product Quality and Security, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
Jing Xu
Key Laboratory of Animal Production, Product Quality and Security, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
Ziyi Zhao
Key Laboratory of Animal Production, Product Quality and Security, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
Qi Zhang
Institute of Animal and Veterinary Sciences, Jilin Academy of Agricultural Sciences, Changchun 130033, China
Yunpeng Zhang
Key Laboratory of Animal Production, Product Quality and Security, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
Min Li
Key Laboratory of Animal Production, Product Quality and Security, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
Hong Zou
Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, China
Riaz Muhammad Azeem
Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Provincial Key Laboratory of Animal Microbiological Vaccine (Durg) for Major Animal Diseases, Ministry of Education, Collage of Veterinary Medicine, Jilin Agricultural University, Changchun 130118, China
Wu-Sheng Sun
Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Engineering Research Center of Microecological Vaccines (Drugs) for Major Animal Diseases, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, 2888 Xincheng Street, Changchun 130118, China
Yuan Zhao
Key Laboratory of Animal Production, Product Quality and Security, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
Shu-Min Zhang
Key Laboratory of Animal Production, Product Quality and Security, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
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.
