Positive selection of skeleton genes during domestication indicates the potential genetic mechanism for loss of flight in ducks

Abstract Background Domestication alters lots of phenotypic, neurologic and physiologic traits between domestic animals and their wild ancestors. Domestic ducks were originated from mallards (Anas platyrhynchos) and some documents also showed that spot-billed ducks (Anas zonorhyncha) could also genetically contribute a small part to the domestication. Compared with the two ancestral species, domestic ducks generally present changes in body size and bone morphology, which is supposed to lead to loss of fight in domestic ducks. In the present study, we performed both genomic and transcriptomic analysis to identify candidate genes in order to elucidate the genetic mechanism underlying the phenotypic variation. Results Our results showed that genes associated with the skeleton systems were positively selected during domestication by Fst analysis between the wild and domestic ducks. We also found that many differentially expressed genes (DEGs) in the breast muscle between the wild and domestic ducks were enriched in the pathway for ossification. Among the genes, FGF14 and EIF2AK3 were also under strong selection by the genomic data, and they were both reported to be associated with limb morphology, bone development and flightlessness in some bird species. Conclusions Our study showed that the skeleton related genes were positively selected in the process of domestication, which could also cause the loss of flight in domestic ducks.