Integration of whole genome resequencing and transcriptomics reveals key candidate genes and pathway for fatty acid and amino acid compositions among duck breeds

The differences fatty acids and amino acids composition may be key factors influencing flavor variation among duck breeds. This study systematically analyzed the fatty acids and amino acids compositions in the pectoral muscle of 49 days old Cherry valley ducks (CV), Jinling white ducks (JL), and Liancheng white ducks (LC). Fatty acid analysis identified 27 fatty acids that exhibited significant differences across breeds (P < 0.05). The CV group had the highest total saturated fatty acid (SFAs) content, while total monounsaturated fatty acid (MUFAs) content ranked in the order of LC > JL > CV (P < 0.05). The total polyunsaturated fatty acids (PUFAs) content was significantly higher in both the JL and LC groups than in the CV group (P < 0.05), while the LC group showed a higher content than the JL group, though the difference was not significant. Amino acid analysis identified 20 amino acids that showed significant differences among breeds (P < 0.05). Furthermore, the total essential amino acids (EAAs) and non-essential amino acids (NEAAs) content ranked in the order of LC > JL > CV (P < 0.05). Whole-genome resequencing identified 2734 selected genes. The joint pathway analysis revealed co-enrichment of 9 fatty acids and 110 selected genes across 25 KEGG pathways, as well as 20 amino acids and 266 selected genes co-enriched in 78 KEGG pathways. RNA sequencing revealed 2539 differentially expressed genes (DEGs) between JL and CV, 6574 DEGs between JL and LC, and 7072 DEGs between LC and CV. Venn analysis showed that 9 and 24 of these DEGs overlapped with selected genes associated with fatty acid and amino acid variation, respectively. Further analysis revealed that the DEGs MGLL, NDUFV1, NDUFS4, and GNG10 may cooperatively regulate retrograde endocannabinoid signaling, thereby jointly influencing the deposition levels of arachidonic acid, γ-Aminobutyric-Acid, and l-glutamate in duck pectoral muscle. These findings provide a theoretical basis for the genetic improvement of meat quality traits.