Comparative population genomics offers an opportunity to discover the signatures of artificial selection during animal domestication, however, their function cannot be directly revealed. We discover the selection signatures using genome-wide comparisons among 40 mallards, 36 indigenous-breed ducks, and 30 Pekin ducks. Then, the phenotypes are fine-mapped based on resequencing of 1026 ducks from an F2 segregating population generated by wild × domestic crosses. Interestingly, the two key economic traits of Pekin duck are associated with two selective sweeps with fixed mutations. A novel intronic insertion most possibly leads to a splicing change in MITF accounted for white duck down feathers. And a putative long-distance regulatory mutation causes continuous expression of the IGF2BP1 gene after birth which increases body size by 15% and feed efficiency by 6%. This study provides new insights into genotype–phenotype associations in animal research and constitutes a promising resource on economically important genes in fowl.

BackgroundThe genetic basis of animal domestication remains poorly understood, and systems with substantial phenotypic differences between wild and domestic populations are useful for elucidating the genetic basis of adaptation to new environments as well as the genetic basis of rapid phenotypic change. Here, we sequenced the whole genome of 78 individual ducks, from two wild and seven domesticated populations, with an average sequencing depth of 6.42X per individual.ResultsOur population and demographic analyses indicate a complex history of domestication, with early selection for separate meat and egg lineages. Genomic comparison of wild to domesticated populations suggests that genes that affect brain and neuronal development have undergone strong positive selection during domestication. Our FST analysis also indicates that the duck white plumage is the result of selection at the melanogenesis-associated transcription factor locus.ConclusionsOur results advance the understanding of animal domestication and selection for complex phenotypic traits.

Two experiments were conducted to study the effects of stocking density on growth performance, carcass yield, and foot pad lesions of White Pekin ducks from hatch to 14 d of age (experiment 1) and from 14 to 42 d of age (experiment 2), respectively. All ducks were reared in raised plastic wire-floor pens with a pen size of 30 m(2), and males and females were mixed at a ratio of 1:1 in each pen of both experiments. In experiment 1, a total of 10,200 ducks that were 1 d old were allotted to 20 pens according to the stocking densities of 13, 15, 17, 19, and 21 birds/m(2) (or 8.4, 9.7, 10.9, 11.9, and 13.0 kg of actually achieved BW/m(2)), respectively, with 4 replicates per treatment. In experiment 2, a total of 3,150 ducks that were 14 d old were allotted to 15 pens according to the stocking densities of 5, 6, 7, 8, and 9 birds/m(2) (or 17.0, 20.3, 23.6, 26.9, and 29.9 kg of actually achieved BW/m(2)), respectively, with 3 replicates per treatment. The stocking density had significant effects on final BW and weight gain of starter and growing ducks (P < 0.05), but not on feed/gain and mortality in both periods (P > 0.05). The final BW and weight gain of starter and growing ducks all decreased with increasing density (P < 0.05). Final BW and weight gain of starter ducks were reduced significantly as stocking density increased from 17 to 21 birds/m(2) (P < 0.05). In addition, final BW and weight gain of growing ducks decreased significantly when stocking density was 9 birds/m(2) (P < 0.05). On the other hand, increasing stocking density did not markedly influence the carcass, breast meat, leg meat, abdominal fat, and foot pad lesions of growing ducks (P > 0.05).

A dose-response experiment with 6 dietary energy levels (2,600, 2,700, 2,800, 2,900, 3,000, 3,100 kcal of AME /kg) was conducted to study the effects of dietary energy on growth performance and carcass quality of White Pekin ducks from 2 to 6 wk of age. Six hundred 14-d-old White Pekin ducks were randomly divided to 6 dietary treatments, each containing 5 replicate pens with 10 males and 10 females per pen, and these birds were raised until 6 wk of age. At 42 d of age, weight gain, feed intake, and feed:gain of ducks from each pen were measured, and 2 ducks (1 male and 1 female) selected randomly from each pen were slaughtered to evaluate the yields of abdominal fat, breast meat (including pectoralis major and pectoralis minor), and leg meat (including thigh and drumstick). As dietary energy increased from 2,600 to 3,100 kcal of AME/kg, the weight gain of ducks increased significantly, and the feed intake and feed:gain decreased significantly. According to the broken-line regression analysis, the AME requirements of White Pekin ducks from 2 to 6 wk of age for optimal weight gain and feed:gain were 3,008 and 3,030 kcal/kg, respectively, when dietary protein was 18%. On the other hand, high dietary energy did not affect breast and leg meat (P > 0.05), but abdominal fat increased (P < 0.05) when dietary AME was above 2,700 kcal/kg.