Background: Sebum deposition is a vital trait influencing meat quality and production efficiency in Pekin ducks. Providing insights into the genetic basis of fat deposition could help improve breeding strategies aimed at producing high-quality meat ducks. This study aimed to identify the genetic mechanisms and lipid metabolism pathways regulating subcutaneous and intramuscular fat deposition in two Pekin duck strains: Nankou No. 1 and Jingdian. Methods: A total of 72 male ducks, Nankou No. 1 (n = 36) and Jingdian (n = 36), were raised under controlled conditions for 42 days. On days 28, 35, and 42, ducks from each group were selected and slaughtered, and their subcutaneous and liver tissues were collected to analyze lipid enzyme activities. On day 42, additional ducks from each strain were slaughtered and evaluated for carcass performance, as well as intramuscular and sebum yield. Genome-wide association analysis (GWAS) was conducted in the Nankou No. 1 strain. Conclusion: Our results showed statistically significant differences in intramuscular and subcutaneous fat yield between the two strains, with Nankou No. 1 exhibiting a higher yield than Jingdian (p < 0.05). The GWAS results identified 96 significant single nucleotide polymorphisms (SNPs), associated with sebum deposition. Functional annotation identified ALDH7A1 as a key candidate gene involved in lipid metabolism and fat storage regulation in Pekin ducks, Nankou No. 1 strain. Enzyme activity assays in liver and subcutaneous tissues revealed breed-specific differences in lipid metabolism, aligning with genetic findings. The activities of the lipid enzymes changed over time, suggesting changes in the developmental stages. The results on fat yield and enzymatic activities further align with molecular findings from the GWAS, which identified variations in lipid metabolism pathways. These results highlight genetic markers and biochemical pathways related to fat deposition in Pekin ducks, offering new insights for selective breeding programs aimed at optimizing fat content in meat production. Further research is needed to clarify the specific role of ALDH7A1 in lipid metabolism and its potential to enhance fat deposition traits in poultry.
