Abstract
BackgroundDomestication alters several phenotypic, neurological, and physiological traits in domestic animals compared to those in their wild ancestors. Domestic ducks originated from mallards, and some studies have shown that spot-billed ducks may have also made minor genetic contributions to domestication. Compared with the two ancestral species, domestic ducks generally differ in body size and bone morphology. In this study, we performed both genomic and transcriptomic analyses to identify candidate genes for elucidating the genetic mechanisms underlying phenotypic variation.MethodsIn this study, the duck genome data from eight domestic breeds and two wild species were collected to study the genetic changes during domestication. And the transcriptome data of different tissues from wild ducks and seven domestic ducks were used to reveal the expression difference between wild and domestic ducks.ResultsUsing fixation index (Fst) algorithm and transcriptome data, we found that the genes related to skeletal development had high Fst values in wild and domestic breeds, and the differentially expressed genes were mainly enriched in the ossification pathway. Our data strongly suggest that the skeletal systems of domestic ducks were changed to adapt to artificial selection for larger sizes. In addition, by combining the genome and transcriptome data, we found that some Fst candidate genes exhibited different expression patterns, and these genes were found to be involved in digestive, immune, and metabolic functions.ConclusionsA wide range of phenotypic differences exists between domestic and wild ducks. Through both genome and transcriptome analyses, we found that genes related to the skeletal system in domestic ducks were strongly selected. Our findings provide new insight into duck domestication and selection effects during the domestication.
Highlights
Domestication alters several phenotypic, neurological, and physiological traits in domestic animals compared to those in their wild ancestors
The results showed that the wild and domesticated ducks were classified by a line in which component 1 equals 0, whereas component 1 of wild ducks was less than 0 (Fig. 1A)
All individuals were clustered into three groups, with the wild species MD and spot-billed ducks (SB) separated from Pekin duck (PK), Cherry Valley duck (CV), and Maple Leaf duck (ML) ducks, which were clustered into one group, and the remaining ducks clustered together in another group
Summary
Domestication alters several phenotypic, neurological, and physiological traits in domestic animals compared to those in their wild ancestors. Various features distinguish domestic animals from their wild ancestors, and it is well-documented that the genetic architecture underlying variations in phenotypic traits (such as morphology in chickens [1, 2], pigs [3,4,5], and pigeons [6, 7]; Zhu et al BMC Ecol Evo (2021) 21:165 feather color [8, 9]; neurological aspects such as tameness in companion animals [10,11,12]; and physiological aspects such as starch digestibility in dogs [13] and reproduction in chickens [14, 15]) are altered dramatically in domestic animals compared to those in their wild ancestors. The domestication process has greatly changed the body shape, including the size, elevation, and fat content These phenotypic differences indicate that large changes have occurred in the genome, and is important for animal genetics to identify the genes selected during the domestication process
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