Domestication including captivity and artificial selection has brought great morphological changes in ducks. Meanwhile, breeding also introduced large number of variants into domesticated duck genome. In our study, the wild and domesticated ducks could be distinguished by first principal component (Fig. 1a), and it showed that long-term artificial selection brought tremendous variation of duck genomes. In previous study, the differences mainly reflected in agronomic traits, such as egg production, growth rate and fat deposition [8, 22]. The domestic ducks were clustered into two groups by second principal component, corresponding to its biological origin place. Our results suggested that genetic distances in Chinese indigenous duck are related to geographical distances, and indigenous ducks in southern China may originate from a common ancestor.
In our study, the Fst algorithm was employed to identify the diverged genomic regions or genes between the wild and domesticated ducks. In total, 542 genes were identified and 1 GO item contains 14 genes was found related to bone development. Furthermore, the differentially expressed genes (DEGs) in breast muscle also showed that changes of bone development related genes played a key role in the differences between the wild and domestic ducks. Many studies suggested that loss of flight in birds was always accompanied with limb modification and skeletal changes [18, 19, 32].
Beyond that, we noticed EIF2AK3 gene on chromosome 4 also under selection, and we found EIF2AK3 gene is associated with body size, abnormal skeleton morphology and abnormal hind limb morphology in mouse [33–35]. Morphological changes could contribute to loss of flight in birds. Compared to their flightless relatives, flight birds always have a lighter mass, higher wing area and longer bone length [18, 32, 36]. This change is consistent with the breeding goal of domesticated ducks as body weight is a major breeding goal in ducks. For example, as one of most famous meat-type ducks in the world, the Peking ducks was bred to growth rate and fat deposition, and its body weight can up to 3.1 kg at 35 day old while the adult mallard is only 1.1 to 1.2 kg [37–40]. Breeding greatly increased the body weight of ducks, and long-term captivity weakened the importance of wings, which is accompany with the physiologic change. The change may include in flight muscle atrophy, bone strength, relative size of wings (limbs). Therefore, EIF2AK3 gene could be involved in the body weight and limb development and partially lead to flightlessness in ducks.
Considering that slide window algorithm might produce both false positive and false negative results, we also calculated Fst and pi values for each SNP. By this method, 22 SNPs and 11 genes were identified to be diverged. It is noteworthy that one SNP is in a TMTM family gene and 2 SNPs are in FGF14 gene. FGF14 is fibroblast growth factor 14, and the protein encoded by FGF14 is a member of the fibroblast growth factor (FGF) family. FGF family gene has been widely reported associated with flight in animals. Weatherbee et al. found FGF8 gene displayed unique expression in forelimb and hindlimb at embryonic stage, BMP and FGF signaling had a role in the inhibition of interdigital apoptosis [41]. Tokita et al. found FGF10 signaling was involved in wing membrane development and patterning of the wing muscles [42]. Interestingly, previous studies found that FGF10 emanated from the prospective limb mesoderm in birds to serve as an endogenous initiator for limb bud formation, which is associated with the loss of flight in emu (Dromaius novaehollandiae) [43, 44]. In drosophila, components of FGF signaling are expressed in myoblasts, a series of experiments show that FGF is a key factor of the development of flight muscle in drosophila [45, 46]. Therefore, FGF14 very likely plays an important role in loss of flight in domesticated ducks.
We also detected the expression level for the diverged genes in liver, breast, and brain. We found that the expression levels of FGF14, FGF6 and TMEM132B in wild ducks were all higher than those in domesticated ducks. This unusual expression difference furtherly supports our hypothesis. We also checked the RNA-seq data for expression levels of the genes including DYRK1A, IFT122, CUX1 and ACOT7, which have previously been identified to be associated with flight in other birds [18, 32, 47, 48]. We did not find expression differences of the genes between the wild and domesticated ducks in our samples (data not shown here). One of explanations is that the genetic mechanisms of loss of flight is different in different species, and it also could be attribute to gene expression spatio-temporal, and many morphology related genes only expressed at embryonic stage.
In our study, by comparing the two ancestral duck species to the domesticated ducks by both genomic and transcriptomic data, we found morphologic genes, especially bone developmental genes, were both positively selected and expressively enriched during domestication, which on one hand satisfied human requirements for food and husbandry, one the other hand led to loss of flight in domestication ducks.