Genome-wide association study of the level of blood components in Pekin ducks

Blood components are considered to reflect nutrient metabolism and immune activity in both humans and animals. In this study, we measured 12 blood components in Pekin ducks and performed genome-wide association analysis to identify the QTLs (quantitative trait locus) using a genotyping-by-sequencing strategy. A total of 54 QTLs were identified for blood components. One genome-wide significant QTL for alkaline phosphatase was identified within the intron-region of the OTOG gene (P = 1.31E-07). Moreover, 21 genome-wide significant SNPs for the level of serum cholinesterase were identified on six different scaffolds. In addition, for serum calcium, one genome-wide significant QTL was identified in the upstream region of gene RAB11B. These results provide new markers for functional studies in Pekin ducks, and several candidate genes were identified, which may provide additional insights into specific mechanisms for blood metabolism in ducks and their potential application for duck breeding programs.     

Hybridization between white-headed ducks and introduced ruddy ducks in Spain

The ruddy duck, Oxyura jamaicensis, was introduced to Great Britain in the mid-20th century and has recently spread to other Western European countries. In Spain, ruddy ducks hybridize with the globally endangered white-headed duck, Oxyura leucocephala. We assessed the effects of hybridization on the Spanish white-headed ducks, which constitute 25% of the global population of this species, using a panel of eight nuclear intron markers, 10 microsatellite loci, and mtDNA control region sequences. These data allowed parental individuals, F(1) hybrids, and the progeny of backcrossing to be reliably distinguished. We show that hybrids between the two species are fertile and produce viable offspring in backcrosses with both parental species. To date, however, we found no extensive introgression of ruddy duck genes into the Spanish white-headed duck population, probably due to the early implementation of an effective ruddy duck and hybrid control programme. We also show that genetic diversity in the expanding European ruddy duck population, which was founded by just seven individuals, exceeds that of the native Spanish white-headed duck population, which recently recovered from a severe bottleneck. Unless effective control of ruddy ducks is continued, genetic introgression will compromise the unique behavioural and ecological adaptations of white-headed ducks and consequently their survival as a genetically and evolutionary distinct species.     

AFLP analysis of genetic diversity and relationship among some Chinese domestic ducks and wild ducks

The amplified fragment length polymorphic (AFLP) technique was used to analyze the genome DNA polymorphism among 8 breeds of domestic ducks and 2 species of wild ducks. Nine of the 17 selected primers pairs gave reproducible polymorphic DNA amplification bands. The amplified bands ranged from 44 to 83 per primer pair. Of the 513 AFLP markers obtained, 498 were polymorphic. The proportion of polymorphic loci was 97.1%. The genetic distance (D) and similarity coefficients (GS) were calculated based on the polymorphic data. Between domestic ducks D ranged from 0.331 to 0.589, while between domestic ducks and the wild ducks, it ranged from 0.298 to 0.520 (vs. Anas Platyrhynchos) and from 0.316 to 0.522 (vs. A. Poecilorhyncha), respectively. The variance analysis showed no significant difference between the two groups of data, which indicated that both mallard and spot-billed ducks made contributions to domestic duck evolution. A dendrogram was constructed according to the D value. __________ Translated from Journal of Xiamen University (Natural Science), 2005, 44(5): 729–733 [译自: 厦门大学学报 (自然科学版), 2005, 44(5): 729–733]     

Resource limitation of diving ducks at Myvatn: Food limits production

We monitored numbers and production of diving ducks on Lake Myvatn and its outlet river, the Laxá, over a period of 25 years, 1975–1999. Aquatic insects, a major food source, were monitored for 23 years, 1977–1999, using window traps. In this paper, we focus on the relationship between the demography of five species of diving ducks and the abundance of aquatic insect species, mainly Chironomidae and Simuliidae. Production of ducks was estimated when most young were 2–4 weeks old, either as young per female (Aythya marila and Aythya fuligula) or as total young found (Melanitta nigra, Bucephala islandica, Histrionicus histrionicus). Variation between years in production of young ducks was strongly correlated with variation in the abundance of aquatic insects. Procladius islandicus and Psectrocladius barbimanus, both of which are univoltine with peak emergence in late July (when many young ducks hatch), as well as the bivoltine Orthocladius consobrinus, showed particularly high correlations with duckling numbers. In one year, 1992, catastrophic weather depressed production. Food appeared to determine production, primarily through its availability to the young. Changes in spring density of breeding ducks of all five species were negatively associated with density in the year before. Resources, estimated as food availability or reproductive success in the year before, were positively correlated with change in breeding numbers in A. marila, A. fuligula and B. islandica. Production three years earlier had a weak but significant effect on change in numbers of M. nigra.     

Assessing changes in genomic divergence following a century of human‐mediated secondary contact among wild and captive‐bred ducks

Along with manipulating habitat, the direct release of domesticated individuals into the wild is a practice used worldwide to augment wildlife populations. We test between possible outcomes of human‐mediated secondary contact using genomic techniques at both historical and contemporary timescales for two iconic duck species. First, we sequence several thousand ddRAD‐seq loci for contemporary mallards (Anas platyrhynchos) throughout North America and two domestic mallard types (i.e., known game‐farm mallards and feral Khaki Campbell's). We show that North American mallards may well be becoming a hybrid swarm due to interbreeding with domesticated game‐farm mallards released for hunting. Next, to attain a historical perspective, we applied a bait‐capture array targeting thousands of loci in century‐old (1842–1915) and contemporary (2009–2010) mallard and American black duck (Anas rubripes) specimens. We conclude that American black ducks and mallards have always been closely related, with a divergence time of ~600,000 years before present, and likely evolved through prolonged isolation followed by limited bouts of gene flow (i.e., secondary contact). They continue to maintain genetic separation, a finding that overturns decades of prior research and speculation suggesting the genetic extinction of the American black duck due to contemporary interbreeding with mallards. Thus, despite having high rates of hybridization, actual gene flow is limited between mallards and American black ducks. Conversely, our historical and contemporary data confirm that the intensive stocking of game‐farm mallards during the last ~100 years has fundamentally changed the genetic integrity of North America's wild mallard population, especially in the east. It thus becomes of great interest to ask whether the iconic North American mallard is declining in the wild due to introgression of maladaptive traits from domesticated forms. Moreover, we hypothesize that differential gene flow from domestic game‐farm mallards into the wild mallard population may explain the overall temporal increase in differentiation between wild black ducks and mallards, as well as the uncoupling of genetic diversity and effective population size estimates across time in our results. Finally, our findings highlight how genomic methods can recover complex population histories by capturing DNA preserved in traditional museum specimens.     

Factors affecting nest choice by Pekin ducks

To encourage nest use in breeder poultry flocks, it is important that nest boxes are attractive. Few studies have evaluated factors affecting nest attractiveness to ducks. We assessed the effects of nest box experience (Experiments 1 and 2) and features of nests, including degree of enclosure (Experiments 1 and 2) and the presence of an egg (Experiment 3), on nest site selection by sexually mature Pekin ducks. The hens were tested individually in pens containing different nest box choices. Nest preferences were determined based on the locations of 14 successively laid eggs. Ducks in Experiment 1 were provided with nest box access prior to the onset of lay (20 weeks of age, EXP group, N = 12) or at the time of preference testing (35 weeks of age, DELAYED-EXP group, N = 12). Delaying nest box access by 15 weeks did not significantly affect the proportion of eggs laid in nest boxes rather than on the floor (P = 0.40). Regardless of experience ducks laid more than 66% of their eggs in nest boxes offering a higher degree of enclosure. Ducks in Experiment 2 were reared with either open-top (OP, N = 12) or closed-top (CL, N = 12) boxes. Regardless of rearing condition, ducks preferred boxes with the highest level of enclosure offered. Ducks laid twice the expected proportion (25%) of eggs in CL boxes with curtains (P = 0.0004). CL boxes without curtains were used as predicted by chance, 25% (P = 0.746), while OP boxes with (P = 0.009) and without (P = 0.015) curtains each contained only half the expected number of eggs. Ducks in Experiment 3 were provided with two nest boxes, one of which contained the egg laid the previous day. Each day, the newly laid egg was marked and either placed back in the nest box where it was found (HANDLED, N = 12) or moved into the adjacent nest box (MOVED, N = 12). Ducks in HANDLED and MOVED laid 97.6% and 79.8%, respectively, of their eggs in boxes containing the previous day's egg. While ducks in HANDLED were consistent in their choice throughout the test, those in MOVED developed the preference over time (P = 0.039), suggesting that the preference for laying in a nest containing an egg may be influenced by experience. These results indicate that nest box enclosure and the presence of an egg are important in determining the nesting choices of Pekin ducks. Incorporating these features into nest boxes may be useful for increasing consistency of nest use in breeder duck flocks.     

Interspecific interactions and co-existence in dabbling ducks: observations and an experiment

We studied the possible role of resource limitation and interspecific competition in assemblages of dabbling ducks on breeding lakes in Finland and Sweden with observational and experimental data. After initial vegetation mapping and yearly censuses of ducks in 1985–1990, we collected observational data in 1991–1994 from 28 lakes with natural populations of mallard Anas platyrhynchos and teal A. crecca. Mallard and teal co-occur over vast areas in the Holarctic and they are the only breeding dabbling ducks on many oligotrophic lakes. Both species are migratory in our study regions, teal arriving later in spring than mallards. Log-linear model analysis of observational presence/absence data revealed a positive, not a negative, association between the species. This association was independent of habitat diversity as well as of lake size. Mallard-teal interaction was also studied in a cross-over introduction experiment in 32 other lakes in two years. Wing-clipped mallards were introduced to breeding lakes before the arrival of teal to induce resource limitation and interspecific competition, hypothesized to reduce lake use by teal. The density of mallard pairs on experimental lakes was 2.9–8.0 times higher than on controls, but there was no negative response by teal to the treatment. This is the first combined observational-experimental demonstration of lack of interspecific competition in waterfowl. Our results indicate that heterospecific attraction may affect species co-existence in dabbling ducks. Received: 28 October 1996 / Accepted: 13 January 1997     

Mallard–Black Duck Hybridization and Population Genetic Structure in North Carolina

North Carolina, USA, represents the southern extent of the American black duck's (Anas rubripes) breeding range. Mallards (A. platyrhynchos) are present on the breeding grounds of the American black duck and hybridization is observed between these species; therefore, we assessed the genetic integrity, hybridization rates, and population structure of this local breeding population. We extracted genomic and mitochondrial DNA from chorioallantoic membranes and contour feathers from monitored black duck nests. We then prepared the extracted DNA for analysis using high-throughput DNA sequencing methods (ddRAD-seq). First, we assessed nuclear and mitochondrial population structure, genetic diversity, and differentiation across samples from North Carolina, and compared them against 199 genetically vetted mallards, black ducks, and mallard × black duck hybrids that served as genetic references. Next, we tested for parentage and sibling relationship and overall relatedness of black ducks in North Carolina. We recovered strong population structure and high co-ancestry across genetic markers due to interrelatedness among sampled nests in North Carolina and concluded that black ducks have been locally breeding in this area for a prolonged period of time. Despite a high level of interrelatedness among our samples, nucleotide diversity was similar to the reference continental black duck population, suggesting little effect of genetic drift, including inbreeding. Additionally, we conclude that molecular diversity of black ducks in North Carolina is maintained at reference population levels through the influx of genetic material from unrelated, migrating male black ducks. Finally, we report a hybridization level of 47.5%, covering 3 filial generations. Of identified hybrids, 54.7% and 53% were the direct result of interbreeding between black ducks and captive-reared or wild mallards, respectively. We conclude that because of high rates of interspecific hybridization and successive backcrossing events, introgression from wild and feral mallards is occurring into this population of breeding black ducks and requires careful consideration in future management efforts. © 2021 The Wildlife Society.     

AFLP analysis of genetic diversity and relationship among some Chinese domestic ducks and wild ducks

The amplified fragment length polymorphic(AFLP)technique was used to analyze the genome DNA polymorphism among 8 breeds of domestic ducks and 2 species of wild ducks.Nine of the 17 selected primers pairs gave reproducible polymorphic DNA amplification bands.The amplified bands ranged from 44 to 83 per primer pair.Of the 513 AFLP markers obtained.498 were polymorphic.The proportion of polymorphic loci was 97.1%.The genetic distance(D)and similarity coefficients(GS)were calculated based on the polymorphic data.Between domestic ducks D ranged from 0.331 to 0.589,while between domestic ducks and the wild ducks,it ranged from 0.298 to 0.520(vs.Anas Platyrhynchos)and from 0.316 to 0.522(vs.A.Poecilorhyncha),respectively.The variance analysis showed no significant difference between the two groups of data,which indicated that both mallard and spot-billed ducks made contributions to domestic duck evolution.A dendrogram was constructed according to the D value.     

Genetic structure of Eurasian and North American mallard ducks based on mtDNA data

To elucidate the origin and genetic structure of the domesticated duck in Eurasia and North America, we sequenced 114 duck D-loop sequences and retrieved 489 D-loop sequences from GenBank. In total, 603 ducks including 50 duck breeds/populations from eight countries (China, France, Russia, India, Kazakhstan, Mongolia, Thailand and USA) were used in this study. One hundred and thirty-four haplotypes and 81 variable sites were detected. H49 was the predominant haplotype, which was considered to be the same dominant haplotype found in the previous studies, and was found in 309 birds. The smallest values for both genetic differentiation index (F(ST), 0.04156) and the number of the net nucleotide substitutions between two populations (D(A), 0.00018) were observed between Eurasian domestic ducks and Eurasian mallards. No geography, breed or population clusters were observed in the Eurasian domestic ducks and mallards. Five haplotypes were shared by USA mallards and Eurasian domestic duck/Eurasian mallards. Only one haplotype (H49) was shared by Eurasian domestic ducks and China spot-billed ducks. By combining phylogenetic analyses, haplotype network profile, genetic distances and shared haplotypes, we can draw two major conclusions: (i) Eurasian and North American mallards show a clear geographic distribution pattern; (ii) Eurasian domestic ducks are derived from the Eurasian mallards, not from the spot-billed ducks.     

Genome-wide association study reveals novel loci associated with fat-deposition and meat-quality traits in Pekin ducks

Meat-quality traits play an essential role in meat poultry production. To determine the genetic mechanisms of meat quality in Pekin ducks, we performed a large-scale GWAS to identify quantitative trait loci affecting meat quality in Pekin ducks. We measured 10 traits in 542 Pekin ducks and genotyped each duck using genotyping-by-sequencing. The genetic parameters (genomic heritability, genetic correlation) for 10 meat-quality related traits were evaluated. Based on the large genotype–phenotype dataset, we performed GWASs for all of these traits. A total of 33 significant QTL (P < 3.03 × 10⁻⁵) across 13 chromosomes were identified by loci-based analysis. Some newly identified candidate genes were discovered for fat-deposition and meat-quality traits, including PAG1 for body weight and eviscerated weight, INTU and NUP35 for abdominal fat weight and ratio, NUP3 and ARHGDIB for skin fat weight and ratio, GOLGA5 for breast muscle toughness and breast tenderness, and CTDSPL and PKP1 for breast muscle thickness. The current study is the first systematic report regarding duck meat quality.     

Exogenous leptin promotes the recovery of regressed ovary in fasted ducks

The present study was undertaken to examine the effect of administered recombinant mouse leptin on the recovery of regressed ovary in fasted ducks. Twenty-eight ducks were divided into five groups: fed ad libitum (control; n = 5), fasted control (FC; n = 5), fasted + low dose of leptin (F + L; n = 5), fasted + medium dose of leptin (F + M; n = 5) and fasted + high dose of leptin (F + H; n = 3). All four fasted groups were fasted for 2 days and then ad libitum and the ducks were treated with leptin at doses of 0 (control and FC), 50 (F + L), 250 (F + M) and 1000 (F + H) μg/kg body weight/day on day 3–5. Results showed that a moderate dose of leptin (250 μg/kg body weight/day) injected during the re-feeding period: (i) promoted the recovery of the regressed ovary as evidenced by an increase in ovary weight and recovery of yellow hierarchical follicles; (ii) elevated the plasma 17β-estradiol (E₂) level; (iii) increased the mRNA levels of ovary follicle-stimulating hormone receptor (FSHR), luteinizing hormone receptor (LHR) and estrogen receptor-β (ER-β). Furthermore, the results also showed that a high dose of leptin (1000 μg/kg body weight/day) may have a negative effect on the recovery of the regressed ovary. In conclusion, this study indicates that, in ducks, leptin may be involved in the recovery of the regressed ovary caused by 2 days of fasting. This effect may be related to increased plasma E₂ levels and stimulation of the mRNA levels of ovarian FSHR, LHR and especially ER-β.     

Comparative transcriptome analysis reveals PERP upregulated during Salmonella Enteritidis challenge in laying ducks

Salmonella Enteritidis (SE) can be transmitted to eggs through cecum or the ovary from infected layers and causes food poisoning in humans. The mechanism of cecal transmission has been extensively studied. However, the mechanism and route of transovarian transmission of SE remain unclear. In this study, the ducks were orally inoculated with SE, and the ovarian follicles and stroma were collected to detect SE infection. The immune responses were triggered and the innate and adaptive immune genes (TLR4, NOD1, AvβD7, and IL-1β) were upregulated significantly during the SE challenge. Moreover, the ovary tissues (small follicle and stroma) of susceptible and resistant–laying ducks were performed by RNA sequencing. We obtained and identified 23 differentially expressed genes (DEGs) between susceptible and resistant–laying ducks in both small follicle and stroma tissues ( p < 0.05). The DEGs were predominately identified in the p53 signaling pathway. The expression of key genes (p53, MDM2, PERP, caspase-3, and Bcl-2) involved in the signaling pathway was significantly higher in granulosa cells (dGCs) from SE-infected ducks than those from uninfected ducks. Moreover, the overexpression of PERP resulted in further induction of p53, MDM2, caspase-3, and Bcl-2 during SE infection in dGCs. Whereas, an opposite trend was observed with the knockdown of PERP. Besides, it is further revealed that the PERP could enhance cell apoptosis, SE adhesion, and SE invasion in SE-infected dGCs overexpression. Altogether, our results demonstrate the duck PERP involved in the ovarian local immune niche through p53 signaling pathway in dGCs challenged with SE.     

Pike predation affects breeding success and habitat selection of ducks

1. Fish and ducks often belong to the same local food web, and several studies indicate that there is a general negative effect of fish on breeding ducks. This pattern has so far been addressed mainly within the framework of competition for common invertebrate prey, while predation by large fish as a force behind settlement and abundance patterns in ducks remains largely unknown. This is the first study to address the effect of fish predation on breeding ducks, isolated from that of competition, and the first experiment to explore the ability of ducks to identify and avoid lakes with high risk of fish predation. 2. We used a before–after control–impact design and 11 naturally fishless lakes. Waterfowl on the lakes were surveyed during the breeding season of 2005. Large adult pike (Esox lucius) were added to two lakes in early spring 2008, and waterfowl surveys were repeated on all 11 lakes. 3. Pike introduction did not affect the number of pairs on lakes during the nesting season in any of three focal duck species (mallard Anas platyrhynchos, teal Anas crecca, and goldeneye Bucephala clangula). During the brood‐rearing season, however, there was a decrease in duck days in teal and goldeneye in lakes with pike, with similar trends observed in mallard. The number of goldeneye ducklings was also significantly lower in lakes with pike. We were unable to determine whether the response was attributable to direct pike predation or to broods leaving experimental lakes, but in either case, our study demonstrates high fitness costs for ducks breeding on lakes with pike. 4. The apparent inability of nesting ducks to detect pike and the clear fitness implications may influence the annual recruitment of ducks on a larger scale as pike are both common and widespread. Vegetation complexity and food abundance are likely to be of overriding importance when breeding ducks are choosing a nesting site. As pike have a strong influence on breeding birds, relying on vegetation and cues of food abundance, while ignoring indicators of predation risk from fish, could lead to lakes with pike acting as an ecological trap.