Genetic loci and key candidate genes associated with fatty acid composition in the breast muscle of Sansui ducks identified through GWAS

Abstract Background The composition of fatty acids, particularly the content of unsaturated fatty acids (UFA), is closely related to meat quality and flavor in ducks. Result In this study, 38 fatty acids were detected in the breast muscle of Sansui ducks, yielding 50 distinct fatty acid composition traits. The results showed that the predominant fatty acids were C18:1n-9, C16:0, C18:2n-6, C18:0, and C20:4n-6. Moreover, the breast muscle of Sansui duck was rich in UFA, accounting for 64.01% of the total fatty acids. Genome-wide association analysis (GWAS) identified 158 single nucleotide polymorphisms (SNPs) significantly associated with fatty acid composition traits, which were annotated to 70 protein-coding genes, including LDLRAD3 , ACVR1 , FGF6 , and CASQ2 . Additionally, linkage disequilibrium (LD) analysis revealed a candidate region (10,533,318 − 10,546,189 bp) on chromosome 14, where NSG2 was identified as a key candidate gene influencing C17:1 content. Functional enrichment analysis suggested that pathways such as Adherens junctions and MAPK signaling may play significant roles in fatty acid biosynthesis. Conclusion These findings reveal the genetic structure of fatty acids composition in the breast muscle of Sansui duck, providing strong evidence for understanding the genetic regulatory mechanisms of fatty acid composition.