Fatty acid composition and genetic associations in breast muscle of Kaijiang Sheldrake ducks

1. Fatty acid (FA) composition determines the nutritional value of duck meat. Systematic characterisation of FA profiles in indigenous breeds, such as the certified Kaijiang Sheldrake, is essential for genetic improvement of meat quality.2. This study used gas chromatography–mass spectrometry (GC–MS) to comprehensively analyse the fatty acid composition in the breast muscle of 60 Kaijiang Sheldrake ducks and explored their potential genetic basis using genome-wide association analysis (GWAS).3. The GC–MS detected 51 FA, with saturated FA (SFA) accounting for the largest proportion (49.45%). Palmitic acid (C16:0, 27.96%), stearic acid (C18:0, 19.95%) and linoleic acid (C18:2n-6, 13.74%) were the most abundant. ω-3 and ω-6 polyunsaturated FA (PUFA) showed strong intra-series correlations. Several individual FA showed significant associations with phenotypic traits, including positive correlations with breast muscle weight and percentage (p < 0.05), whereas short-chain SFAs (C6:0, C13:0) and specific PUFA (C20:3n-3, C20:5n-3) were negatively associated with post-mortem pH (0 h). In contrast, no significant associations were detected between aggregated ω-3 and ω-6 indices and most slaughter or meat quality traits. GWAS further suggested potential associations for both saturated and unsaturated FA, identifying candidate genes, such as RASGEF1A, BPHL, FAF1, SPAG16, FGF12, GPC1 and HK2 located near associated loci, with enrichment in metabolic pathways including carbohydrate metabolism and glycolysis.4. Overall, this study systematically evaluated slaughter performance, meat quality traits and the fatty acid composition of breast muscle in Kaijiang Sheldrake, providing comprehensive data to support the utilisation and precision breeding of local duck genetic resources.