Identification of Biomarkers for Meat Quality in Sichuan Goats Through 4D Label-Free Quantitative Proteomics

The Nanjiang Yellow Goat (NJYG), Jintang Black Goat (JTBG), and Jianzhou Da’er Goat (JZDEG) are representative local goat breeds for meat production in Sichuan Province, China. This study conducted a comprehensive evaluation of the meat quality of the longissimus dorsi muscle of three goat breeds. Variations in meat quality were observed in terms of meat pH, color, ash and fat content, water activity, and muscle fiber structure. Quantitative proteomics analysis was employed to identify biomarkers for goat meat quality, revealing hundreds of differentially expressed proteins among three goat breeds. KEGG enrichment analysis revealed enriched pathways including oxidative phosphorylation, thermogenesis, citrate cycle (TCA cycle), fatty acid degradation and metabolism, as well as valine, leucine, and isoleucine degradation. Moreover, weighted protein co-expression network analysis and protein–protein interaction analysis uncovered valuable biomarkers, including GSTM3, NDUFS, OGDH, ACO2, HADH, ACAT1, ACADS, ACAA2, HSPG2, ITGA7, PARVB, ALDH9A1, ADH5, and LOC102190016, for assessing goat meat quality. This investigation highlighted the disparities in meat quality among local goat breeds in Sichuan, China, and provided insights into underlying biological pathways and valuable biomarkers for goat meat quality.