Integrated transcriptomic and metabolomic analyses identify molecular signatures associated with meat quality...

Meat quality varies among goat breeds, but the molecular features associated with this variation remain incompletely characterized. This study compared the longissimus dorsi muscle of Yunling (YL) and Nubian (NB) goats using phenotypic, transcriptomic, and metabolomic analyses. YL goats exhibited lower shear force than NB goats (38.86 vs. 53.88 N) and higher pH at 45 min postmortem (pH_45min), whereas ultimate pH (pH_24h) did not differ significantly between breeds. These results indicate that the two breeds differed in early postmortem pH status despite having comparable ultimate pH. Transcriptomic analysis identified 241 differentially expressed genes (160 upregulated and 81 downregulated in YL goats), with enrichment in HIF-1 signaling pathway and Pyruvate metabolism. Metabolomic analysis identified 59 differentially abundant metabolites (29 increased and 30 decreased in YL goats), with glycerophospholipids representing the predominant class. Weighted gene co-expression network analysis (WGCNA) identified 19 gene modules and 13 metabolite modules, among which several modules were significantly associated with shear force and pH_45min. Integration of differential analysis with trait-associated modules prioritized candidate molecular features associated with breed-related variation in these traits. The pH_45min-associated profile included HIF-1- and carbohydrate metabolism-related genes such as PFKFB3 and HMOX1, whereas the shear force-associated profile included mitochondrial-, energy metabolism-, and iron-related genes such as NDUFA5, ND6, and TFRC. At the metabolite level, trait-associated candidate metabolites were dominated by phospholipid species, with enrichment in several lipid-related pathways. Gene-metabolite correlation analysis further revealed covariation between selected candidate genes and phospholipid-related metabolites. Collectively, these findings provide a descriptive multi-omics characterization of breed-related meat-quality differences and identify candidate molecular features associated with variation in shear force and pH_45min. These candidates and their biological relevance require validation in larger independent populations and through targeted functional analyses.