Domestic ducks are raised for meat, eggs and feather down, and almost all varieties are descended from the Mallard (Anas platyrhynchos). Here, we report chromosome-level high-quality genome assemblies for meat and laying duck breeds, and the Mallard. Our new genomic databases contain annotations for thousands of new protein-coding genes and recover a major percentage of the presumed “missing genes” in birds. We obtain the entire genomic sequences for the C-type lectin (CTL) family members that regulate eggshell biomineralization. Our population and comparative genomics analyses provide more than 36 million sequence variants between duck populations. Furthermore, a mutant cell line allows confirmation of the predicted anti-adipogenic function of NR2F2 in the duck, and uncovered mutations specific to Pekin duck that potentially affect adipose deposition. Our study provides insights into avian evolution and the genetics of oviparity, and will be a rich resource for the future genetic improvement of commercial traits in the duck.

According to market demand, meat duck breeding mainly includes 2 breeding directions: lean Pekin duck (LPD) and fat Pekin duck (FPD). The aim of the present study was to compare carcass and meat quality traits between 2 strains, and to provide basic data for guidelines of processing and meat quality improvement. Methods A total of 62 female Pekin ducks (32 LPDs and 30 FPDs) at the age of 42 days were slaughtered. The live body weight and carcass traits were measured and calculated. Physical properties of breast muscle were determined by texture analyzer and muscle fibers were measured by paraffin sections. The content of inosine monophosphate (IMP), intramuscular fat (IMF) and fatty acids composition were measured by high-performance liquid chromatography, Soxhlet extraction method and automated gas chromatography respectively. Results The results showed that the bodyweight of LPDs was higher than that of FPDs. FPDs were significantly higher than LPDs in subcutaneous fat thickness, subcutaneous fat weight, subcutaneous fat percentage, abdominal fat percentage and abdominal fat shear force (P < 0.01). LPDs were significantly higher than FPDs in breast muscle thickness, breast muscle weight, breast muscle rate and breast muscle shear force (P < 0.01). The muscle fiber average area and fiber diameter of LPDs were significantly higher than those of FPDs (P < 0.01). The muscle fiber density of LPDs was significantly lower than that of FPDs (P < 0.01). The intramuscular fat of LPDs in the breast muscle was significantly higher than that in the FPDs A c c e p t e d A r t i c l e (P < 0.01). There was no significant difference between the 2 strains in inosine monophosphate content (P＞0.05). The polyunsaturated fatty acid content of LPDs was significantly higher than that of FPDs (P < 0.01), and FPDs had higher saturated fatty acid and monounsaturated fatty acid levels (P < 0.05). Conclusion Long-term breeding work resulted in vast differences between the two strains Pekin ducks. This study provides a reference for differences between LPD and FPD that manifest as a result of long-term selection.

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