Duck meat presents a wealth of high-quality amino acids, proteins, and unsaturated fatty acids, along with other essential nutritional elements. The metabolites present in duck meat, such as amino acids, peptides, vitamins, and inosinic acid, play a vital role in creating a robust and distinctive meaty flavor through diverse processing methods. This unique flavor profile is a result of the intricate interplay of metabolites and flavor compounds in duck meat. To uncover the genetic underpinnings of these crucial metabolites and flavor compounds, a comprehensive genome-wide association analysis is conducted. The ultimate objective is to pinpoint the key genes that influence the development of essential metabolites and flavor compounds in duck meat.

This study is centered on a gradient lineage population resulting from the crossbreeding of Beijing ducks and Liancheng white ducks. The ducks were uniformly raised until six weeks of age, and specimens were collected from seven distinct lineage gradients, totaling 423 individuals. The metabolites in the breast muscles were analyzed using liquid chromatography-mass spectrometry (LC-MS), while flavor compounds were assessed with gas chromatography-high resolution mass spectrometry combined with the solid-phase microextraction technique (SPME-GC-MS). The results revealed the detection of 4133 metabolites in the breast muscles, including 2481 hydrophilic substances, 950 lipids, and 702 flavor compounds. Integrating data from whole-genome resequencing, a metabolite-genome-wide association analysis (mGWAS) was conducted, unveiling significant signals for 673 metabolites, covering 427 hydrophilic substances, 75 lipids, and 171 flavor compounds. In the fine-mapping of these GWAS signals, it was discovered that the  TMEM189  gene regulates the content of plasmalogen crucial for the human nervous system. Additionally, the  GADL1  and  CARNMT2  genes jointly regulate the levels of carnosine and anserine, vital for human antioxidation, anti-aging, anti-fatigue, and muscle buffering enhancement. Furthermore, the  AOX1  gene influences the content of 2-pyrrolidone, a flavor compound with a cotton candy or maple syrup taste after heating. The  ACBD5  gene controls the variation in the content of decanal, an important flavor compound with sweet and floral notes after immediate heating, attributed to differences in the precursor substance glycerophospholipid. In conclusion, 48 candidate genes were identified that significantly impact essential nutritional metabolites and flavor compounds in duck meat, holding crucial implications for breeding new high-quality meat ducks and enhancing the overall quality of duck meat.