Whole genome resequencing reveals genomic regions related to red plumage in ducks.

Plumage color is a characteristic trait of ducks that originates as a result of natural and artificial selection. As a conspicuous phenotypic feature, it is a breed characteristic. Previous studies have identified some genes associated with the formation of black and white plumage in ducks. However, studies on the genetic basis underlying the red plumage phenotype in ducks are limited. Here, genome-wide association analysis (GWAS) and selection signal detection (Fst, θπ ratio, and cross-population composite likelihood ratio [XP-CLR]) were conducted to identify candidate regions and genes underlying duck plumage color phenotype. Selection signal detection revealed 29 overlapping genes (including ENPP1 and ULK1) significantly associated with red plumage color in Ji'an Red ducks. ENSAPLG00000012679, ESRRG, and SPATA5 were identified as candidate genes associated with red plumage using GWAS. Selection signal detection revealed that 19 overlapping genes (including GMDS, PDIA6, and ODC1) significantly correlated with light brown plumage in Brown Tsaiya ducks. GWAS to narrow down the significant regions further revealed nine candidate genes (AKT1, ATP6V1C2, GMDS, LRP4, MAML3, PDIA6, PLD5, TMEM63B, and TSPAN8). Notably, in Brown Tsaiya ducks, GMDS, ODC1, and PDIA6 exhibit significantly differentiated allele frequencies among other feather-colored ducks, while in Ji'an Red ducks, ENSAPLG00000012679 has different allele frequency distributions compared with that in other feather-colored ducks. This study offers new insights into the variation and selection of the red plumage phenotype using GWAS and selective signals.

A novel candidate gene CLN8 regulates fat deposition in avian.

BACKGROUND: The fat deposition has a crucial role in animal meat flavor, and fat deposition-related traits are vital for breeding in the commercial duck industry. Avian fat-related traits are typical complex phenotypes, which need a large amount of data to analyze the genetic loci. RESULTS: In this study, we performed a new phenotypic analysis of fat traits and genotyped whole-genome variations for 1,246 ducks, and combed with previous GWAS data to reach 1,880 ducks for following analysis. The carcass composition traits, subcutaneous fat weight (SFW), subcutaneous fat percentage (SFP), abdominal fat weight (AFW), abdominal fat percentage (AFP) and the body weight of day 42 (BW42) for each duck were collected. We identified a set of new loci that affect the traits related to fat deposition in avian. Among these loci, ceroid-lipofuscinosis, neuronal 8 (CLN8) is a novel candidate gene controlling fat deposition. We investigated its novel function and regulation in avian adipogenesis. Five significant SNPs (the most significant SNP, P-value = 21.37E-12) and a single haplotype were detected in the upstream of CLN8 for subcutaneous fat percentage. Subsequently, luciferase assay demonstrated that 5 linked SNPs in the upstream of the CLN8 gene significantly decreased the transcriptional activity of CLN8. Further, ATAC-seq analysis showed that transcription factor binding sites were identified in a region close to the haplotype. A set of luciferase reporter gene vectors that contained different deletion fragments of the CLN8 promoter were constructed, and the core promoter area of CLN8 was finally identified in the -1,884/-1,207 bp region of the 5' flanking sequences, which contains adipogenesis-related transcription factors binding sites. Moreover, the over-expression of CLN8 can remarkably facilitate adipocyte differentiation in ICPs. Consistent with these, the global transcriptome profiling and functional analysis of the over-expressed CLN8 in the cell line further revealed that the lipid biosynthetic process during the adipogenesis was significantly enriched. CONCLUSIONS: Our results demonstrated that CLN8 is a positive regulator of avian adipocyte differentiation. These findings identify a novel function of CLN8 in adipocyte differentiation, which provides important clues for the further study of the mechanism of avian fat deposition.

A fluorescent probe for alkylating agents and its quantification of triflate as a genotoxic impurity.

The responses of a reaction-based fluorescent probe BI-Py towards alkyl halide, epoxide, carbonate, sulfate, sulphonate and triflate were evaluated and the probe achieved selective detection of ethyl triflate in acetonitrile with a LOD of 1.08 µM. BI-Py exhibited great potential for detecting triflate as a genotoxic impurity in drug substances.

Visual inspection of acidic pH and bisulfite in white wine using a colorimetric and fluorescent probe.

The acidic pH and total amount of SO2 are both important quality control indexes of wine, but conventional detection techniques depend heavily on specialized instrument and professional staff, thus are not available to general customers. In this paper, a hemicyanine-based colorimetric and fluorescent probe Hcy-Py was designed and synthesized. It responded to bisulfite selectively with a LOD of 0.68 µM and responded to proton with a pKa of 3.78. Upon the treatment of solutions with different pH values and concentrations of bisulfite, the probe-loaded paper strips displayed distinct color changes under both natural light and UV lamp. When a real white wine sample was subjected to the paper strip experiment, pH as well as bisulfite concentration could be determined by naked-eye quickly and conveniently, thus a visual detection of acidic pH and bisulfite in white wine without involving any sophisticated instrument or professional skill was successfully demonstrated.

Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication.

Domestic ducks are raised for meat, eggs and feather down, and almost all varieties are descended from the Mallard (Anas platyrhynchos). Here, we report chromosome-level high-quality genome assemblies for meat and laying duck breeds, and the Mallard. Our new genomic databases contain annotations for thousands of new protein-coding genes and recover a major percentage of the presumed "missing genes" in birds. We obtain the entire genomic sequences for the C-type lectin (CTL) family members that regulate eggshell biomineralization. Our population and comparative genomics analyses provide more than 36 million sequence variants between duck populations. Furthermore, a mutant cell line allows confirmation of the predicted anti-adipogenic function of NR2F2 in the duck, and uncovered mutations specific to Pekin duck that potentially affect adipose deposition. Our study provides insights into avian evolution and the genetics of oviparity, and will be a rich resource for the future genetic improvement of commercial traits in the duck.

Genome-wide association study reveals novel loci associated with feeding behavior in Pekin ducks.

BACKGROUND: Feeding behavior traits are an essential part of livestock production. However, the genetic base of feeding behavior traits remains unclear in Pekin ducks. This study aimed to determine novel loci related to feeding behavior in Pekin ducks. RESULTS: In this study, the feeding information of 540 Pekin ducks was recorded, and individual genotype was evaluated using genotyping-by-sequencing methods. Genome-wide association analysis (GWAS) was conducted for feeding behavior traits. Overall, thirty significant (P-value < 4.74E-06) SNPs for feeding behavior traits were discovered, and four of them reached the genome-wide significance level (P-value < 2.37E-07). One genome-wide significance locus associated with daily meal times was located in a 122.25 Mb region on chromosome 2, which was within the intron of gene ubiquitin-conjugating enzyme E2 E2 (UBE2E2), and could explain 2.64% of the phenotypic variation. This locus was also significantly associated with meal feed intake, and explained 2.72% of this phenotypic variation. CONCLUSIONS: This study is the first GWAS for feeding behavior traits in ducks. Our results provide a list of candidate genes associated with feeding behavior, and also help to better understand the genetic mechanisms of feeding behavior patterns in ducks.

Comparison of carcass and meat quality traits between lean and fat Pekin ducks.

OBJECTIVE: According to market demand, meat duck breeding mainly includes 2 breeding directions: lean Pekin duck (LPD) and fat Pekin duck (FPD). The aim of the present study was to compare carcass and meat quality traits between 2 strains, and to provide basic data for guidelines of processing and meat quality improvement. METHODS: A total of 62 female Pekin ducks (32 LPDs and 30 FPDs) were slaughtered at the age of 42 days. The live body weight and carcass traits were measured and calculated. Physical properties of breast muscle were determined by texture analyzer and muscle fibers were measured by paraffin sections. The content of inosine monophosphate (IMP), intramuscular fat (IMF) and fatty acids composition were measured by high-performance liquid chromatography, Soxhlet extraction method and automated gas chromatography respectively. RESULTS: The results showed that the bodyweight of LPDs was higher than that of FPDs. FPDs were significantly higher than LPDs in subcutaneous fat thickness, subcutaneous fat weight, subcutaneous fat percentage, abdominal fat percentage and abdominal fat shear force (p<0.01). LPDs were significantly higher than FPDs in breast muscle thickness, breast muscle weight, breast muscle rate and breast muscle shear force (p<0.01). The muscle fiber average area and fiber diameter of LPDs were significantly higher than those of FPDs (p<0.01). The muscle fiber density of LPDs was significantly lower than that of FPDs (p<0.01). The IMF of LPDs in the breast muscle was significantly higher than that in the FPDs (p<0.01). There was no significant difference between the 2 strains in IMP content (p>0.05). The polyunsaturated fatty acid content of LPDs was significantly higher than that of FPDs (p<0.01), and FPDs had higher saturated fatty acid and monounsaturated fatty acid levels (p<0.05). CONCLUSION: Long-term breeding work resulted in vast differences between the two strains Pekin ducks. This study provides a reference for differences between LPD and FPD that manifest as a result of long-term selection.

Genome-wide association study of bone quality and feed efficiency-related traits in Pekin ducks.

Feeding and bone traits are vital for breeding and reproduction in the commercial duck industry. In this study, we performed a genome-wide association study for feeding and bone traits in a population of 540 lean-type Pekin ducks, followed by genotyping-by-sequencing procedures. The genetic parameters of feeding and bone traits were also estimated using genomic information. In total, seventy-eight significant SNPs were determined, and eleven of them reached the genome-wide significant level for 7 traits except for body weight at 42-day old. A peak of genome-wide significant SNPs was detected on chromosome 2 for feed conversion ratio (P-value = 7.46E-11), and the top SNP (P-value = 2.23E-08) for bone-breaking strength was also obtained in the upstream of gene RAPGEF5. This study provided a list of novel markers and candidate genes associated with feeding and bone traits in Pekin ducks, which could contribute to the genetic selection in duck breeding.

Selection response and genetic parameter estimation of feeding behavior traits in Pekin ducks.

Body weight-related traits and feeding behavior traits are important in poultry breeding and production. To investigate the heritability of feeding behavior and their genetic correlation with body weight-related traits in Pekin ducks, 5,594 Pekin ducks were selected. The information about body weight-related traits and feeding behavior from 3 to 6 wk of age were recorded by automatic electronic feeders. The heritability estimates for body weight, residual feed intake, and feeding behavior traits are relatively high (ranging from 0.29 to 0.65). We observed that total feed intake, meal feed intake, body weight at the age of 3 wk, and daily body weight gain had strong positive genetic correlations with body weight at the age of 6 wk. Moreover, body weight at the age of 3 wk also showed a positive genetic correlation with the feed conversion ratio (0.33). Total feeding time, daily feed intake, and feeding rate had significant positive phenotypic correlations with feed efficiency. However, the average interval between meals, the number of daily visits, and the number of meals all had a low genetic or phenotypic relationship with body weight and feed efficiency. In conclusion, our study revealed that body weight, residual feed intake, and feeding behavior traits were all highly heritable traits, and the selection for certain feeding behaviors could improve feed efficiency in Pekin ducks. This study is the first report about genetic parameter estimates about feeding behaviors in ducks based on large datasets and provides solid data for genetic study in ducks.

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.

Genome-Wide Association Study of Growth and Feeding Traits in Pekin Ducks.

Growth rate and feeding efficiency are the most important economic traits for meat animals. Pekin duck is one of the major global breeds of meat-type duck. This study aims to identify QTL for duck growth and feeding efficiency traits in order to assist artificial selection. In this study, the growth and feeding related phenotypes of 639 Pekin ducks were recorded, and each individual genotype was evaluated using a genotyping-by-sequencing (GBS) protocol. The genetic parameters for growth and feeding efficiency related traits were estimated. Genome-wide association analysis (GWAS) was then performed for these traits. In total, 15 non-overlapping QTLs for the measured traits and 12 significant SNPs for feed efficiency traits were discovered using a mixed linear model. The most significant loci of feed intake (FI) is located in a 182Mb region on Chr1, which is downstream of gene RNF17, and can explain 2.3% of the phenotypic variation. This locus is also significantly associated with residual feed intake (RFI), and can explain 3% of this phenotypic variation. Among 12 SNPs associated with the feed conversion ratio (FCR), the most significant SNP (P-value = 1.65E-06), which was located in the region between the 3rd and 4th exon of the SORCS1 gene on Chr6, explained 3% of the phenotypic variance. Using gene-set analysis, a total of two significant genes were detected be associated with RFI on Chr1. This study is the first GWAS for growth and feeding efficiency related traits in ducks. Our results provide a list of candidate genes for marker assisted selection for growth and feeding efficiency, and also help to better understand the genetic mechanisms of feed efficiency and growth in ducks.

Analysis of fishy taint in duck eggs reveals the causative constituent of the fishy odor and factors affecting the perception ability of this odor.

Fresh duck eggs normally have an unpleasant fishy odor when compared with eggs from other poultry. However, the cause of this unpleasant smell remains unknown. Besides, we have limited knowledge regarding the perception ability of this odor. Therefore, we aimed to identify the causative substances responsible for the fishy odor in duck eggs, and further evaluate the factors affecting the perception ability of this odor. We detected and quantified the volatile substances in the yolks of Jingjiang duck and Beijing duck eggs using headspace gas chromatography, and evaluated the fishy odor rating scores. We performed association studies on the relationship between the relative content of volatile substances and fishy odor rating scores. The fishy odor of egg yolks from different species/breeds was also characterized. Furthermore, we assessed the species/breeds of poultry eggs and the effects of gender and region of the evaluators on the fishy odor rating score by using an ordinal logistic regression model. Results showed that trimethylamine (TMA) is responsible for the fishy odor of duck eggs, which was confirmed with subsequent verification (P < 0.001). The fishy odor of duck eggs was stronger than that of chicken eggs; the fishy odor of Jingjiang duck eggs was the strongest. Results also indicated that the fishy odor perception ability was affected by the gender and region of the evaluators (P < 0.001). Overall, these data clarified that TMA imparted the fishy odor to duck eggs; factors such as gender and region may affect the fishy odor perception ability.

Genome-wide association study reveals novel loci associated with body size and carcass yields in Pekin ducks.

BACKGROUND: Pekin duck products have become popular in Asia over recent decades and account for an increasing market share. However, the genetic mechanisms affecting carcass growth in Pekin ducks remain unknown. This study aimed to identify quantitative trait loci affecting body size and carcass yields in Pekin ducks. RESULTS: We measured 18 carcass traits in 639 Pekin ducks and performed genotyping using genotyping-by-sequencing (GBS). Loci-based association analysis detected 37 significant loci for the 17 traits. Thirty-seven identified candidate genes were involved in many biological processes. One single nucleotide polymorphism (SNP) (Chr1_140105435 A > T) located in the intron of the ATPase phospholipid transporting 11A gene (ATP11A) attained genome-wide significance associated with five weight traits. Eight SNPs were significantly associated with three body size traits, including the candidate gene plexin domain containing 2 (PLXDC2) associated with breast width and tensin 3 (TNS3) associated with fossil bone length. Only two SNPs were significantly associated with foot weight and four SNPs were significantly associated with heart weight. In the gene-based analysis, three genes (LOC101791418, TUBGCP3 (encoding tubulin gamma complex-associated protein 3), and ATP11A) were associated with four traits (42-day body weight, eviscerated weight, half-eviscerated weight, and leg muscle weight percentage). However, no loci were significantly associated with leg muscle weight in this study. CONCLUSIONS: The novel results of this study improve our understanding of the genetic mechanisms regulating body growth in ducks and thus provide a genetic basis for breeding programs aimed at maximizing the economic potential of Pekin ducks.

In vivo prediction of the carcass fatness using live body measurements in Pekin ducks.

The purpose of this study was to evaluate the correlation between live body measurements and several fat traits in Pekin ducks, and ultimately to formulate multiple regression equations for the in vivo estimation of the carcass fatness of Pekin ducks. Several traits were measured in a total of 208 Pekin ducks aged 6 wk (107 males and 101 females). All ducks were weighed and measured for a set of body measurements including live body weight, body slope length, breast muscle thickness, skin fat thickness, chest width, keel length, and neck length. The breast muscle thickness and skin fat thickness was measured using B-scan sonography. Carcass information, including eviscerated weight, subcutaneous fat with skin weight, and abdominal fat weight, was collected after slaughter. Our results revealed that sex effects on most traits were significant (P < 0.05), and that the weight of subcutaneous fat with skin was significantly correlated with live body weight (r = 0.57 to 0.71, P < 0.01). Four additional traits of males were closely correlated with the weight of subcutaneous fat with skin, namely breast muscle thickness (r = 0.20, P < 0.01), skin fat thickness (r = 0.43, P < 0.01), chest width (r = 0.24, P < 0.01), and neck length (r = 0.20, P < 0.05). The abdominal fat weight, percentage of fat, and percentage of subcutaneous fat with skin of ducks were significantly correlated with live body weight (r = 0.38 to 0.43, P < 0.01), and skin fat thickness (r = 0.38 to 0.49, P < 0.01). These traits provided the basis for constructing regression equations to predict weight (or percentage) of subcutaneous fat and abdominal fat with high values of coefficients of multiple correlation (R) between the dependent variable and the independent variables. Two equations were verified to be applicable in other duck groups, with high accuracy, as more than 80% of estimated values were within the margin of error (<10%), compared with the actual values.

Whole-genome resequencing reveals signatures of selection and timing of duck domestication.

Background: The 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. Results: Our 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. Conclusions: Our results advance the understanding of animal domestication and selection for complex phenotypic traits.

Systematic analysis of feeding behaviors and their effects on feed efficiency in Pekin ducks.

BACKGROUND: Feeding behavior study is important for animal husbandry and production. However, few studies were conducted on the feeding behavior and their relationship with feeding efficiency in Pekin ducks. In order to investigate the feeding behavior and their relationship with feed efficiency and other economic traits in Pekin ducks, we selected 358 male Pekin ducks and recorded feeding information between 3 to 6 wk of age using automatic electronic feeders, and compared the feeding behavior under different residual feed intake (RFI) levels. RESULTS: We observed that total feed time, daily feed intake and feed intake per meal had strong positive correlations with feed efficiency traits; moreover, strong correlation between feed intake per meal and body weight was found (R=0.32, 0.36). Daily feeding rate meal and meal duration had weak correlations with feed efficiency (R=0.14~0.15). The phenotypic correlation of between-meal pauses, with feed efficiency was not observed. When daily changes were analyzed, high RFI ducks had the highest feed consumption over all times, and obvious differences in daily visits were found among different RFI level animals during the middle period; these differences were magnified with age, but there was no difference in daily meal number. Moreover, our data indicate that high RFI birds mainly take their meals at the edge of the population enclosure, where they are more susceptible to environmental interference. CONCLUSIONS: Overall, this study suggests that the general feeding behaviors can be accurately measured using automatic electronic feeders and certain feeding behaviors in Pekin ducks are associated with improved feed efficiency.

De novo transcriptome assembly and identification of genes associated with feed conversion ratio and breast muscle yield in domestic ducks.

Breast muscle yield and feed conversion efficiency are the major breeding aims in duck breeding. Understanding the role of specific transcripts in the muscle and small intestine might lead to the elucidation of interrelated biological processes. In this study, we obtained jejunum and breast muscle samples from two strains of Peking ducks that were sorted by feed conversion ratio (FCR) and breast muscle percentage into two-tailed populations. Ten RNA-Seq libraries were developed from the pooled samples and sequenced using the Hiseq2000 platform. We created a reference duck transcript database using de novo assembly methods, which included 16 663 irredundant contigs with an N50 length of 1530 bp. This new duck reference cDNA dataset significantly improved the mapping rate for RNA-Seq data, from 50% to 70%. Mapping and annotation were followed by Gene Ontology analysis, which showed that numerous genes were differentially expressed between the low and high FCR groups. The differentially expressed genes in the jejunum were enriched in biological processes related to immune response and immune response activation, whereas those in the breast muscle were significantly enriched in biological processes related to muscle cell differentiation and organ development. We identified new candidate genes, that is, PCK1, for improving the FCR and breast muscle yield of ducks and obtained much better reference duck transcripts. This study suggested that de novo assembly is essential when applying transcriptome analysis to a species with an incomplete genome.

Origin and domestication history of Peking ducks deltermined through microsatellite and mitochondrial marker analysis.

In order to elucidate the domestication history of Peking ducks, 190 blood samples from six Chinese indigenous duck breeds were collected with 186 individuals genotyped by 15 microsatellite markers. Both the F(ST) and Nei's standard genetic distances (D(s)) from the microsatellite data indicated high genetic differentiation between Peking duck and other Chinese indigenous breeds. The haplotype network with mtDNA data showed that most of the Peking duck haplotypes were distinctly different from those of other domestic breeds. Although the H01 haplotype was shared by all domesticated duck breeds, Peking ducks displayed 12 specific domestic duck haplotypes, including four similar haplotypes H02, H04, H08 and H22, that formed a single haplogroup (A). Both H02 and H22 haplotypes were also shared by mallard and Peking ducks, indicating that Peking ducks originated from wild mallard ducks.