Integrative QTL and Transcriptomic Analyses Identify Candidate Genes Associated with Muscle Crude Fat Content and Fatty Acid Composition in Trachinotus ovatus

Muscle crude fat content and fatty acid composition are important flesh-quality traits in golden pompano (Trachinotus ovatus), yet their genetic and molecular bases remain poorly understood. Here, quantitative trait locus (QTL) mapping, fatty acid profiling, and transcriptome analysis were integrated to identify genomic regions and candidate genes associated with muscle lipid traits. Crude fat content was measured in 143 individuals from a single F1 full-sib family and showed substantial variation (CV = 43.13%). Multiple-QTL model (MQM) mapping identified nine linkage-group-wise significant QTLs across eight linkage groups, explaining 10.1–13.9% of phenotypic variance. Thirty-one candidate genes were identified within QTL-supported regions, including lipid metabolism-related genes gpat4, dgat2, acaca, chrebp, mogat2, dgat1, atgl, scd2, abcg5, and abcg8. Fatty acid profiling of 24 individuals detected 23 fatty acids, 22 of which were positively correlated with crude fat content, with C18:1n9c showing the strongest correlation (Spearman’s ρ = 0.71, FDR < 0.01). Liver transcriptome analysis of three high-fat and three low-fat individuals identified 1311 differentially expressed genes (DEGs). Integration of QTL and transcriptomic data identified seven DEGs within QTL-supported regions, with acaca and dgat1 emerging as key overlapping candidates. Both genes were upregulated in the high-crude-fat group. ACACA mediates a key step in de novo fatty acid synthesis, whereas DGAT1 catalyzes the final step of triacylglycerol synthesis, suggesting important roles in lipid synthesis and storage. These findings identify genomic regions and candidate genes associated with muscle crude fat content and fatty acid composition, providing a basis for functional validation and marker-assisted improvement of flesh lipid quality in golden pompano.