Genome-wide analysis reveals signatures of artificial selection in Pekin ducks across decades of breeding

Decades of artificial selection have left distinct genomic signatures in Pekin duck. Here, we used whole-genome resequencing data from six Pekin duck populations, including two conservation populations and four breeding populations, to explore the genomic footprints left by decades of artificial selection in Pekin ducks. Through allele frequency analyses, we identified specific selective regions among the breeding populations. Compared with the conservation populations, the strongest selection signals in Maple Leaf ducks were found in genomic regions encompassing FAM184B and LAP3, with two missense mutations in FAM184B showing marked allele frequency differences between Maple Leaf and conservation populations, while in Cherry Valley ducks, the top signals were located within or near XRCC3, MNAT1, and SLC34A2. In comparisons between the Nankou Pekin duck breeding populations and the conservation population, NUDT6 and INPP4A were identified as the candidate genes under selection in PK4 and PK3, respectively. Analysis of the shared selective regions revealed 214 candidate genes, which were mainly enriched in pathways related to lipid metabolism and organ development. These results suggest that different breeding programs have imposed distinct selection pressures on the Pekin duck genome. Overall, this study provides valuable insights for the conservation and genetic improvement of Pekin ducks.