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.

Uncovering genetic variation through resequencing is limited by the fact that only sequences with similarity to the reference genome are examined. Reference genomes are often incomplete and cannot represent the full range of genetic diversity as a result of geographical divergence and independent demographic events. To more comprehensively characterize genetic variation of pigs (Sus scrofa), we generated de novo assemblies of nine geographically and phenotypically representative pigs from Eurasia. By comparing them to the reference pig assembly, we uncovered a substantial number of novel SNPs and structural variants, as well as 137.02-Mb sequences harboring 1737 protein-coding genes that were absent in the reference assembly, revealing variants left by selection. Our results illustrate the power of whole-genome de novo sequencing relative to resequencing and provide valuable genetic resources that enable effective use of pigs in both agricultural production and biomedical research.

BackgroundGenesis of novel gene regulatory modules is largely responsible for morphological and functional evolution. De novo generation of novel cis-regulatory elements (CREs) is much rarer than genomic events that alter existing CREs such as transposition, promoter switching or co-option. Only one case of de novo generation has been reported to date, in fish and without involvement of phenotype alteration. Yet, this event likely occurs in other animals and helps drive genetic/phenotypic variation.ResultsUsing a porcine model of spontaneous hearing loss not previously characterized we performed gene mapping and mutation screening to determine the genetic foundation of the phenotype. We identified a mutation in the non-regulatory region of the melanocyte-specific promoter of microphthalmia-associated transcription factor (MITF) gene that generated a novel silencer. The consequent elimination of expression of the MITF-M isoform led to early degeneration of the intermediate cells of the cochlear stria vascularis and profound hearing loss, as well as depigmentation, all of which resemble the typical phenotype of Waardenburg syndrome in humans. The mutation exclusively affected MITF-M and no other isoforms. The essential function of Mitf-m in hearing development was further validated using a knock-out mouse model.ConclusionsElimination of the MITF-M isoform alone is sufficient to cause deafness and depigmentation. To our knowledge, this study provides the first evidence of a de novo CRE in mammals that produces a systemic functional effect.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-016-0273-2) contains supplementary material, which is available to authorized users.

BackgroundMaternal riboflavin deficiency (RD) induces embryonic death in poultry. The underlying mechanisms, however, remain to be established and an overview of molecular alterations at the protein level is still lacking. We investigated embryonic hepatic proteome changes induced by maternal RD to explain embryonic death.MethodsA total of 80 45-week-old breeding female ducks were divided into two groups of 40 birds each, and all birds were raised individually for 8 weeks. All the female ducks received either a RD or a riboflavin adequate (control, CON) diet, which supplemented the basal diet with 0 or 10 mg riboflavin /kg of diet respectively.ResultsThe riboflavin concentrations of maternal plasma and egg yolk, as well as egg hatchability declined markedly in the RD group compared to those in the CON group after 2 weeks, and declined further over time. The hepatic proteome of E13 viable embryos from 8-week fertile eggs showed that 223 proteins were upregulated and 366 proteins were downregulated (> 1.5-fold change) in the RD group compared to those in the CON group. Pathway analysis showed that differentially expressed proteins were mainly enriched in the fatty acid beta-oxidation, electron transport chain (ETC), and tricarboxylic acid (TCA) cycle. Specifically, all the proteins involved in the fatty acid beta-oxidation and ETC, as well as six out of seven proteins involved in the TCA cycle, were diminished in the RD group, indicating that these processes could be impaired by RD.ConclusionMaternal RD leads to embryonic death of offspring and is associated with impaired energy generation processes, indicated by a number of downregulated proteins involved in the fatty acid beta-oxidation, ETC, and TCA cycle in the hepatic of duck embryos. These findings contribute to our understanding of the mechanisms of liver metabolic disorders due to maternal RD.Electronic supplementary materialThe online version of this article (10.1186/s12986-019-0345-8) contains supplementary material, which is available to authorized users.

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Avian egg coloration is shaped by natural selection, but its genetic basis remains unclear. Here, we used genome‐wide association analysis and identity by descent to finely map green egg colour to a 179‐kb region of Chr4 based on the resequencing of 352 ducks (Anas platyrhynchos) from a segregating population resulting from the mating of Pekin ducks (white‐shelled eggs) and mallards (green‐shelled eggs). We further narrowed the candidate region to a 30‐kb interval by comparing genome divergence in seven indigenous duck populations. Among the genes located in the finely mapped region, only one transcript of the ABCG2 gene (XM_013093252.2) exhibited higher uterine expression in green‐shelled individuals than in white‐shelled individuals, as supported by transcriptome data from four populations. ABCG2 has been reported to encode a protein that functions as a membrane transporter for biliverdin. Sanger sequencing of the whole 30‐kb candidate region (Chr4: 47.41–47.44 Mb) and a plasmid reporter assay helped to identify a single nucleotide polymorphism (Chr4: 47,418,074 G>A) located in a conserved predicted promoter region whose variation may alter ABCG2 transcription activity. We provide a useful molecular marker for duck breeding and contribute data to the research on ecological evolution based on egg colour patterns among birds.

An experiment was conducted to investigate the effects of dietary pantothenic acid levels on growth performance, carcass traits, pantothenic acid status, and antioxidant status of male white Pekin ducks from 15 to 42 D of age and to evaluate the requirement of this vitamin for growing ducks. Different levels pantothenic acid (0, 2, 4, 6, 8, and 10 mg/kg) were supplemented to a corn-soy isolate protein basal diet to produce 6 dietary treatments with different analyzed total pantothenic acid levels (4.52, 6.44, 8.37, 9.88, 12.32, and 14.61 mg/kg). A total of 240 15-day-old male white Pekin ducks were allotted to 6 dietary treatments with 8 replicate pens of 5 birds per pen. At 42 D of age, growth performance, carcass traits, tissue pantothenic acid concentrations, and antioxidant status of white Pekin ducks were examined. Significant effects of dietary pantothenic acid on BW, average daily weight gain ( ADG ), plasma, and liver pantothenic acid concentrations were observed ( P < 0.05) but not carcass traits. The growing ducks fed the basal diet without pantothenic acid supplementation had the lowest BW, ADG, plasma, and liver pantothenic acid content among all ducks ( P < 0.05). In addition, the ducks fed the basal diet without pantothenic acid supplementation showed the lowest antioxidant capacity indicated by greatest plasma malondialdehyde content and lowest liver total antioxidant capacity ( P < 0.05). And, these criteria responded linearly as dietary pantothenic acid levels increased ( P < 0.05). These results indicated that dietary pantothenic acid supplementation improved growth performance and antioxidant status of the growing ducks. In accordance with the broken-line model, the pantothenic acid requirements (based on dietary total pantothenic acid) of male white Pekin ducks from 15 to 42 D of age for BW, ADG, and plasma and liver pantothenic acid contents were 10.18, 10.27, 12.06, and 10.79 mg/kg, respectively.

ObjectiveThis study was conducted to estimate the genetic parameters and breeding values of breast meat related traits of Pekin ducks. Selection response was also determined by using ultrasound breast muscle thickness (BMT) measurements in combination with bosom breadth (BB) and keel length (KL) values.MethodsThe traits analyzed were breast meat weight (BMW), body weight (BW), breast meat percentage (BMP) and the three parameters of breast meat (BB, KL, and BMT). These measurements were derived from studying 15,781 Pekin ducks selected from 10 generations based on breast meat weight. Genetic parameters and breeding value were estimated for the analysis of the breeding process.ResultsEstimated heritability of BMW and BMP were moderate (0.23 and 0.16, respectively), and heritability of BW was high (0.48). Other traits such as BB, KL, and BMT indicated moderate heritability ranging between 0.11 and 0.28. Significant phenotypic correlations of BMW with BW and BMP were discovered (p<0.05), and genetic correlations of BMW with BW and BMP were positive and high (0.83 and 0.66, respectively). It was noted that BMW had positive correlations with all the other traits. Generational average estimated breeding values of all traits increased substantially over the course of selection, which demonstrated that the ducks responded efficiently to increased breast meat yield after 10 generations of breeding.ConclusionThe results indicated that duck BMW had the potential to be increased through genetic selection with positive effects on BW and BMP. The ultrasound BMT, in combination with the measurement of BB and KL, is shown to be essential and effective in the process of high breast meat yield duck breeding.