Deep Proteomic Analysis Reveals Intermuscular Variation Associated with Chicken Meat Quality

To elucidate the molecular mechanisms underlying chicken meat quality, this study first evaluated variation in chicken meat quality with respect to age, breed, sex, and muscle location. High-throughput quantitative proteomic analysis was then performed on the pectoralis major muscle (PEM) and medial gastrocnemius muscle (MGM), a leg muscle subpopulation previously shown to be enriched in slow-twitch oxidative fibers. Marked differences were observed between the PEM and leg muscle in pH, meat color, tenderness, water-holding capacity (WHC), amino acid composition, intramuscular fat composition, and intramuscular fat content. A total of 4413 proteins were identified in PEM and MGM (n = 3 biological replicates per muscle type), of which 516 were differentially abundant. Functional enrichment analyses of protein domains, GO terms, and KEGG pathways for the differentially abundant proteins indicated that the intermuscular proteomic differences were mainly associated with carbohydrate metabolism, purine metabolism, calcium signaling, and proteostasis. Protein–protein interaction (PPI) analysis further revealed that the differential expression of node proteins, including GAPDH, TPI1, PGM1, LDHA, ENO3, FHL1, NT5E, RYR2, and MRPS6, may be associated with intermuscular meat quality variation in the early postmortem period. These findings revealed molecular disparities between chicken skeletal muscles with distinct phenotypes and may facilitate postmortem quality control in the poultry meat industry.