A total of 34 key candidate genes were identified as gonadal development- or infertility-related genes according to our clustering analyses, functional enrichment analyses, and the published literature (Figure 5), of which 22 sex-biased DEGs (female-biased or male-biased), namely, Dmrt1, Amh, Sox9, Tex14, Trim71, Slc26a8, Spam1, Tdrp, Tsga10, Boc, Cxcl14, Hsd17b3, Hsd17b1, Cyp19a1, Cyp17a1, Hhipl2, Uts2r, Cdon, Axin2, Nxph1, Brinp2, and Brinp3 were identified as sex-related genes in Mule ducks, Jinding ducks, and Muscovy ducks. This evidence concerns the gene SOX9 and Infertility.