Metabolite-based genome-wide association analysis reveals genetic loci and candidate genes affecting breast muscle metabolites in Sansui ducks

Duck meat is highly appreciated for its unique flavor and rich nutritional value, and metabolites have become important phenotypic indicators of meat quality. The Sansui duck, a celebrated local breed from Guizhou, is known for its tender, savory meat, yet its metabolomic composition and underlying genetic basis remain unexplored. In our study, non-targeted LC-MS/MS metabolomics of 305 Sansui duck breast muscles detected 4,729 metabolic features (459 annotated) and identified 136 sex-differential metabolites enriched in fatty acid and amino acid metabolism pathways. Metabolite-based genome-wide association studies (mGWAS) further identified 355 significant LD-independent SNPs and 267 potential candidate genes associated with 103 metabolites. The signal peaks for amino acid metabolites were mainly concentrated on chromosomes 1, 5, and 20. A QTL on chromosome 2 (63.90-64.10 Mb), containing candidate genes ZNF407, CNDP1, and CNDP2, was identified for three methylglyoxal derivatives, with the lead SNP (chr2: 63928783) accounting for about 18.3 % of their variance. Additional QTLs on chromosomes 5, 20, 1, and 24 were associated with Carnosine, N-Acetylhistidine, Acetylcholine, N-Acetyl-L-aspartic acid, 11b-PGF2a, and 12(S)-HpETE. These intervals harbor BBOX1 and ACACA, two key rate-limiting enzymes in fatty acid metabolism. Our results revealed the genetic basis of breast muscle metabolites in Sansui ducks and identified associated genetic loci and candidate genes. These findings deepen our understanding of muscle metabolism and provide valuable insights for improving meat quality and nutritional breeding.