Transcriptomic and metabolomic profiling of the Longissimus thoracis muscle insights into variations in meat quality between Hainan Black and Nubian Black goats

The increasing emphasis on meat quality within tropical goat breeding initiatives has led to the recognition of its defining attributes as intricate outcomes of breed-specific interactions. This investigation aimed to identify specific genes, metabolites, and signaling pathways correlated with meat quality traits in two tropical goat breeds, namely Nubian Black (NB) and Hainan Black (HN). To delve into the factors influencing goat meat quality, extensive transcriptomic and metabolomic analyses were carried out on Longissimus thoracis muscle tissue. Moreover, we conducted a meticulous comparative evaluation of muscle fiber structure, chemical composition, and pivotal meat quality traits between NB and HN breeds. The findings revealed that HN goats had markedly lower slaughter weight, hot and cold carcass weights, collagen content, Warner-Bratzler shear force, muscle fiber diameter, area, perimeter, perimysium thickness, and proportion of Type IIB fibers relative to NB goats (all P < 0.05). In contrast, crude fat content, intramuscular fat, muscle fiber density, and the proportion of type I and IIA fibers were higher in HN goats than in NB goats (all P < 0.05). Additionally, NB goats displayed elevated serum catalase activity ( P < 0.05). Transcriptomic analysis identified over two thousand differentially expressed genes (DEGs) between HN and NB goats. Functional enrichment analysis indicated that these DEGs were predominantly engaged in various biological processes, including lipid metabolism regulation, thermogenesis, and muscular system development. Metabolomic profiling revealed 185 significantly altered metabolites (SCMs). Pathway enrichment analysis highlighted significant associations between these SCMs and crucial metabolic pathways, such as fatty acid biosynthesis; aspartate, glutamate, and alanine metabolism; and linoleic acid metabolism. An integrated transcriptomic and metabolomic analysis pinpointed 17 key genes enriched within four overlapping KEGG pathways. Overall, the integration of traditional meat quality phenotyping with multi-omics investigations elucidated novel molecular mechanisms underlying the breed-specific variations in meat quality in tropical goats. • Hainan Black goats show higher intramuscular fat and favorable muscle fiber composition (type I/IIA fibers) than Nubian Black goats. • Multi-omics reveal 17 key genes (e.g., MEF2C, RYR1) and 110 metabolites (e.g., IMP, taurine) driving breed-specific lipid metabolism and muscle traits. • Four KEGG pathways (e.g., glutamatergic synapse, taurine metabolism) link gene-metabolite networks to tenderness and flavor formation. • The findings provide actionable markers for optimizing tropical goat meat quality in breeding programs.