Unique feather color characteristics and transcriptome analysis of hair follicles in Liancheng White ducks.

Avian feather color is a fascinating trait, and the genetic mechanism of duck plumage formation is still in the preliminary stage. In this study, feather color of Liancheng White ducks was analyzed by determination of melanin content and RNA-seq analysis. In this research, 9 ducks from Mallards (n = 3), Liancheng White (n = 3) and Pekin ducks (n = 3) were used by high performance liquid chromatography (HPLC) and Masson-Fontana staining to reveal the difference of feather melanin content. RNA-seq from 11 hair follicle tissues (1- and 8-wk-old) of Liancheng White ducks (n = 5) and Pekin ducks (n = 7) was used to analyze the candidate genes for the feather melanin synthesis, and Immunofluorescence experiment was used to show the protein expression in 6 black- and white-feathered ducks. Pectorale, skin, liver, fat, brain, heart, kidney, lung, spleen of an 8-wk-old black-feathered Mallard were collected for candidate gene expression. The results showed that the contents of feathers, beak, web melanin in Liancheng White ducks were higher than in Pekin ducks (p < 0.05). Melanin within hair follicles was located in the barb ridge and hair matrix of black feather duck, also we found that TYRP1, TYR, SOX10 genes were differentially expressed between Liancheng White and Pekin ducks (p < 0.05), and these genes were mainly expressed showed in duck skin tissues. This study revealed the unique feather color phenotype of Liancheng White duck shedding light on the transcriptome that underlies it.

Cis-eQTLs in seven duck tissues identify novel candidate genes for growth and carcass traits.

BACKGROUND: Expression quantitative trait loci (eQTL) studies aim to understand the influence of genetic variants on gene expression. The colocalization of eQTL mapping and GWAS strategy could help identify essential candidate genes and causal DNA variants vital to complex traits in human and many farm animals. However, eQTL mapping has not been conducted in ducks. It is desirable to know whether eQTLs within GWAS signals contributed to duck economic traits. RESULTS: In this study, we conducted an eQTL analysis using publicly available RNA sequencing data from 820 samples, focusing on liver, muscle, blood, adipose, ovary, spleen, and lung tissues. We identified 113,374 cis-eQTLs for 12,266 genes, a substantial fraction 39.1% of which were discovered in at least two tissues. The cis-eQTLs of blood were less conserved across tissues, while cis-eQTLs from any tissue exhibit a strong sharing pattern to liver tissue. Colocalization between cis-eQTLs and genome-wide association studies (GWAS) of 50 traits uncovered new associations between gene expression and potential loci influencing growth and carcass traits. SRSF4, GSS, and IGF2BP1 in liver, NDUFC2 in muscle, ELF3 in adipose, and RUNDC1 in blood could serve as the candidate genes for duck growth and carcass traits. CONCLUSIONS: Our findings highlight substantial differences in genetic regulation of gene expression across duck primary tissues, shedding light on potential mechanisms through which candidate genes may impact growth and carcass traits. Furthermore, this availability of eQTL data offers a valuable resource for deciphering further genetic association signals that may arise from ongoing extensive endeavors aimed at enhancing duck production traits.

Embryonic growth and effect of embryonic age on quantitative and functional characteristics of duck primary hepatocytes.

Primary hepatocytes (PH) have been widely used in metabolic and disease-resistance mechanism research. However, hepatocyte isolation (HI) remains challenging in ducks. This study aimed to explore embryonic growth and the effect of embryonic age (EA) on the quantitative and functional characteristics of PH in ducks. For embryonic growth, the size and weight of the embryo and liver were determined from 6 to 28 EA (E6-E28, similar below). As EA increased, the corresponding size and weight grew significantly. Specifically, embryonic length varied from 12.5 mm to 133.0 mm, and liver width varied from 2.0 mm to 26.2 mm. Embryonic weight ranged from 0.259 g to 53.58 g, and liver weight ranged from 0.007 g to 1.765 g. Liver index initially decreased and then increased with a ratio ranging from 1.06 to 3.29%. For quantitative and functional characteristics, they were determined from E6 to E22, as there were no obvious liver features before E6 and few cells obtained after E22. The number of cells isolated in liver increased from E6 to E16 and then sharply decreased from E16 to E22. The viability remained relatively stable from E6 to E10 and then decreased from E12 to E22. The comprehensive intensity of hepatic glycogen was stronger at E8 and E14. Albumin expression increased markedly from E6 to E18 by qPCR, and the overall albumin expression was stronger at E8 and E14 by immunofluorescence assay. Hepatocyte purity exceeded 90% except for E20 and E22. During culture, cell clusters appeared after 24-h culture, which were identified as nonhepatocytes. The growth curve showed an initial increase in cell quantity followed by a decrease, another increase, and then remaining stable. In conclusion, EA had a significant effect on the quantitative and functional characteristics of PH, and the suitable EA for HI were E8 and E14. Considering better operability and quantity, E14 was the optimal EA, laying a solid foundation for further hepatocyte purification, nutrient metabolism, and disease-resistance mechanism explorations in ducks.

Genetic parameters and genomic prediction of growth and breast morphological traits in a crossbreed duck population.

Genomic selection (GS) has great potential to increase genetic gain in poultry breeding. However, the performance of genomic prediction in duck growth and breast morphological (BM) traits remains largely unknown. The objective of this study was to evaluate the benefits of genomic prediction for duck growth and BM traits using methods such as GBLUP, single-step GBLUP, Bayesian models, and different marker densities. This study collected phenotypic data for 14 growth and BM traits in a crossbreed population of 1893 Pekin duck × mallard, which included 941 genotyped ducks. The estimation of genetic parameters indicated high heritabilities for body weight (0.54-0.72), whereas moderate-to-high heritabilities for average daily gain (0.21-0.57) traits. The heritabilities of BM traits ranged from low to moderate (0.18-0.39). The prediction ability of GS on growth and BM traits increased by 7.6% on average compared to the pedigree-based BLUP method. The single-step GBLUP outperformed GBLUP in most traits with an average of 0.3% higher reliability in our study. Most of the Bayesian models had better performance on predictive reliability, except for BayesR. BayesN emerged as the top-performing model for genomic prediction of both growth and BM traits, exhibiting an average increase in reliability of 3.0% compared to GBLUP. The permutation studies revealed that 50 K markers had achieved ideal prediction reliability, while 3 K markers still achieved 90.8% predictive capability would further reduce the cost for duck growth and BM traits. This study provides promising evidence for the application of GS in improving duck growth and BM traits. Our findings offer some useful strategies for optimizing the predictive ability of GS in growth and BM traits and provide theoretical foundations for designing a low-density panel in ducks.

Whole-transcriptome sequencing revealed the role of noncoding RNAs in susceptibility and resistance of Pekin ducks to DHAV-3.

As the most prevalent pathogen of duck viral hepatitis (DVH), duck hepatitis A virus genotype 3 (DHAV-3) has caused huge economic losses to the duck industry in China. Herein, we obtained whole-transcriptome sequencing data of susceptible (S) and resistant (R) Pekin duckling samples at 0 h, 12 h, and 24 h after DHAV-3 infection. We found that DHAV-3 infection induces 5,396 differentially expressed genes (DEGs), 85 differentially expressed miRNAs (DEMs), and 727 differentially expressed lncRNAs (DELs) at 24 hpi in S vs. R ducks, those upregulated genes were enriched in inflammation and cell communications pathways and downregulated genes were related to metabolic processes. Upregulated genes showed high connectivity with the miR-33, miR-193, and miR-11591, and downregulated genes were mainly regulated by miR-2954, miR-125, and miR-146b. With the construction of lncRNA-miRNA-mRNA axis, we further identified a few aberrantly expressed lncRNAs (e.g., MSTRG.36194.1, MSTRG.50601.1, MSTRG.34328.7, and MSTRG.29445.1) that regulate expression of hub genes (e.g., THBD, CLIC2, IL8, ACOX2, GPHN, SMLR1, and HAO1) by sponging those highly connected miRNAs. Altogether, our findings defined a dual role of ncRNAs in immune and metabolic regulation during DHAV-3 infection, suggesting potential new targets for treating DHAV-3 infected ducks.

Effects of age on differential resistance to duck hepatitis A virus genotype 3 in Pekin ducks by 16 S and transcriptomics.

Duck hepatitis A virus genotype 3 (DHAV-3) is the major cause of viral hepatitis in ducks in Asia. Previous studies have shown that ducklings younger than 21 days are more susceptible to DHAV-3. To elucidate the mechanism by which age affects the differential susceptibility of Pekin ducks to DHAV-3, intestinal (n = 520), liver (n = 40) and blood (n = 260) samples were collected from control and DHAV-3-infected ducks at 7, 10, 14, and 21 days of age. Comparisons of plasma markers, mortality rates, and intestinal histopathological data showed that the resistance of Pekin ducks to DHAV-3 varied with age. 16 S sequencing revealed that the ileal microbial composition was influenced by age, and this correlation was greater than that recorded for caecal microbes. Candidatus Arthromitus, Bacteroides, Corynebacterium, Enterococcus, Romboutsia, and Streptococcus were the differntially abundant microbes in the ileum at the genus level after DHAV-3 infection and were significantly correlated with 7 differentially expressed genes (DEGs) in 7- and 21-day-old ducklings. 3 immunity-related pathways were significantly different between 7- and 21-day-old ducklings, especially for IFIH1-mediated induction of the interferon-alpha/beta pathway, which induces differential production of CD8(+) T cells and was influenced by a combination of differentially abundant microbiota and DEGs. We found that microbes in the ileum changed regularly with age. The intestinal microbiota was associated with the expression of genes in the liver through IFIH1-mediated induction of the interferon-alpha/beta pathway, which may partially explain why younger ducklings were more susceptible to DHAV-3 infection.

Effects of DHAV-3 infection on innate immunity, antioxidant capacity, and lipid metabolism in ducks with different DHAV-3 susceptibilities.

The aim of the experiment was to evaluate the status of innate immunity, oxidative status and lipid accumulation in ducklings exhibiting varying susceptibilities to DHAV-3 infection. In the experiment, ducklings with different DHAV-3 susceptibilities were used. Samples were collected at 6, 12, 15, and 24 h post infection (hpi), with 5 samples per time point. Plasma biochemistry, antioxidant enzyme activities, lipid content of liver and kidney were detected in the experiment. Elevated plasma level of total bilirubin, direct bilirubin, and creatinine indicated the injury of liver and kidney in susceptible ducklings (P < 0.05). The histopathological sections showed the injury in kidney. During the infection time, there was an increase in the concentrations of reactive oxygen species and oxidative damage markers (malondialdehyde and nitric oxide) in plasma of susceptible ducklings, particularly at 24 hpi (P < 0.05). Compared with the resistant ducklings, DHAV-3 infection resulted in a significant increase in the plasma total triglyceride (TG) level and a decrease in glucose level in susceptible ducklings. Gene expression of the innate immune response was both investigated in liver and kidney. In resistant ducklings, the expressions levels of pattern recognition receptors RIG-I, MDA5 remained constant. In contrast, the gene expressions peaked at 24 hpi in the susceptible ducklings. DHAV-3 infection promoted the expression of IFN, IL6, IL12ß, caspase-8 or caspase-9 in both liver and kidney of susceptible ducklings. In conclusion, DHAV-3 infection led to the mobilization of antioxidant defenses, alterations in lipid metabolism, and oxidative stress in susceptible ducklings during DHAV-3 infection.

Dietary riboflavin supplementation improves meat quality, antioxidant capacity, fatty acid composition, lipidomic, volatilomic, and proteomic profiles of breast muscle in Pekin ducks.

Our objective was to determine effects of supplemental dietary riboflavin on meat quality, antioxidant capacity, fatty acid composition, lipidomic, volatilomic, and proteomic profiling of duck breast muscle. The results showed that dietary riboflavin supplementation significantly increased growth performance, breast meat yield, intramuscular fat content, polyunsaturated fatty acid (PUFA), n3-PUFA, n6-PUFA, redness (a*), and pH24h, but decreased lightness (L*) and yellowness (b*). Furthermore, riboflavin supplementation significantly improved muscle antioxidant capacity based on various biochemical parameters. Lipidomic and volatilomic analyses revealed that riboflavin supplementation markedly increased breast meat phosphatidylglycerol and coenzyme Q contents and two favourable key odorants, citronellyl acetate and 3-(methylthio)-propanal. Proteomics analyses confirmed that riboflavin supplementation activated mitochondrial aerobic respiration, including fatty acid beta oxidation, the tricarboxylic acid cycle, and oxidative phosphorylation. In conclusion, supplementing duck diets with riboflavin enhanced breast meat quality, attributed to increases in antioxidant capacity and mitochondrial functions.

Changes in physical architecture and lipids compounds in skeletal muscle from Pekin duck and Liancheng white duck.

As a complex food, meat displays various biochemical properties that are determined to a great extent by physical architecture and lipid metabolites. Pekin duck and Liancheng white duck are elite breeds with distinct characteristics. Here, we explored the development of the muscle fibers from embryonic stage to 10-wk after birth, and muscle fibers grow slowly after 8-wk. We investigated the meat quality, ultrastructure, lipidomics profiling, and lipids spatial distribution of skeletal muscle at 8 wk. Pekin duck has lower Warner-Bratzler shear force (WBSF) (P < 0.05), high intramuscular fat (IMF) (P < 0.01), longer and wider sarcomere, and higher mitochondrial density (P < 0.001). Liancheng white duck with tighter collagen architecture. A total of 950 lipids from 6 lipid classes identified with lipidomics were analyzed, the levels of GP, GL, and PR were significantly higher in Pekin duck (P < 0.05), SL and ST were significantly higher in Liancheng white duck (P < 0.05). There were 333 significantly different lipids (|log2(Fold Change)| ≥ 1 and FDR < 0.05) screened, most lipids distributed in the muscle tissue were uniform, but some specifically distributed in connective tissue. To some extent, the results demonstrate the high lipid deposition capacity of Pekin duck and the high medicinal function of Liancheng white duck. Our study provides new insights into the relationship between skeletal muscle architecture and meat toughness, which increased the knowledge of lipidomic characteristics and provide a basis for duck meat authentication.

Plasma lipidome reveals susceptibility and resistance of Pekin ducks to DHAV-3.

Duck hepatitis A virus genotype 3 (DHAV-3) is the most popular pathogen of duck viral hepatitis (DVH) and has led to a huge economic threat to the Asian duck industry. In this work, we investigated the differences in the LC-MS/MS-based dynamic lipid profiles between susceptible and resistant Pekin duck lines with DHAV-3 infection. We found that the plasma lipidome of the two duck lines was characterized differently in expression levels of lipids during the infection, such as decreased levels of glycerolipids and increased levels of cholesteryl esters and glycerophospholipids in susceptible ducks compared with resistant ducks. By integrating lipidomics and transcriptomics analysis, we showed that the altered homeostasis of lipids was potentially regulated by a variety of differentially expressed genes including CHPT1, PI4K2A, and OSBP2 between the two duck lines, which could account for liver dysfunction, apoptosis, and illness upon DHAV-3 infection. Using the least absolute shrinkage and selection operator (LASSO) approach, we determined a total of 25 infection-related lipids that were able to distinguish between the infection states of susceptible and resistant ducks. This study provides molecular clues for elucidating the pathogenesis and therapeutic strategies of DHAV-3 infection in ducklings, which has implication for the development of resistance breeding.

Strategies to improve genomic predictions for 35 duck carcass traits in an F2 population.

BACKGROUND: Carcass traits are crucial for broiler ducks, but carcass traits can only be measured postmortem. Genomic selection (GS) is an effective approach in animal breeding to improve selection and reduce costs. However, the performance of genomic prediction in duck carcass traits remains largely unknown. RESULTS: In this study, we estimated the genetic parameters, performed GS using different models and marker densities, and compared the estimation performance between GS and conventional BLUP on 35 carcass traits in an F2 population of ducks. Most of the cut weight traits and intestine length traits were estimated to be high and moderate heritabilities, respectively, while the heritabilities of percentage slaughter traits were dynamic. The reliability of genome prediction using GBLUP increased by an average of 0.06 compared to the conventional BLUP method. The Permutation studies revealed that 50K markers had achieved ideal prediction reliability, while 3K markers still achieved 90.7% predictive capability would further reduce the cost for duck carcass traits. The genomic relationship matrix normalized by our true variance method instead of the widely used [Formula: see text] could achieve an increase in prediction reliability in most traits. We detected most of the bayesian models had a better performance, especially for BayesN. Compared to GBLUP, BayesN can further improve the predictive reliability with an average of 0.06 for duck carcass traits. CONCLUSION: This study demonstrates genomic selection for duck carcass traits is promising. The genomic prediction can be further improved by modifying the genomic relationship matrix using our proposed true variance method and several Bayesian models. Permutation study provides a theoretical basis for the fact that low-density arrays can be used to reduce genotype costs in duck genome selection.

Proteomic and phosphoproteomic analysis reveal threonine deficiency increases hepatic lipid deposition in Pekin ducks via reducing STAT phosphorylation.

Dietary threonine (Thr) deficiency enhances triglyceride (TG) deposition in the liver of Pekin ducks, which injures hepatic function and impairs growth performance. However, the underlying molecular mechanisms remain unclear. In the present study, we investigated the effects of dietary Thr deficiency on the expressions of proteins and phosphoproteins in liver of Pekin ducks, to identify the underlying molecular changes. A total of 300 one-day-old ducklings were divided into 3 groups with 10 replicates of 10 birds. All ducks were fed corn-wheat-peanut meal diets containing 0.46%, 0.71%, and 0.96% Thr, respectively, from 1 to 21 days of age. Growth performance, serum parameters, hepatic TG content, and expression of genes involved in lipid metabolism of Pekin ducks were determined. A Thr deficiency group (Thr-D, 0.46% Thr) and a Thr sufficiency group (Thr-S, 0.71% Thr) were selected for subsequent proteomic and phosphoproteomic analysis. The results showed that Thr-D reduced the growth performance (P < 0.001), and increased the plasma concentrations of cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and hepatic TG (P < 0.05). Thr-D increased gene expression related to fatty acid and TG synthesis (P < 0.05). A total of 176 proteins and 259 phosphosites (containing 198 phosphoproteins) were observed to be differentially expressed as a result of Thr-D. The upregulated proteins were enriched in the pathway related to amino acid metabolism, peroxisome. The downregulated proteins were enriched in linolenic and arachidonic acid metabolism, and the Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathway. The upregulated phosphoproteins were enriched in the pathways related to fatty acid biosynthesis, fructose and mannose metabolism, and glycolysis/gluconeogenesis. Thr-D reduced the phosphorylation of STAT1 at S729 and STAT3 at S728, and expression of STAT5B. In contrast, Thr-D increased non-receptor tyrosine-protein kinase (TYK2) expression and STAT1 phosphorylation at S649. Taken together, dietary Thr-D increased hepatic TG accumulation by upregulating the expression of genes and proteins, and phosphoproteins related to fatty acid and triglyceride synthesis. Furthermore, these processes might be regulated by the JAK-STAT signaling pathway, especially the phosphorylation of STAT1 and STAT3.

Metabolome-Based Genome-Wide Association Study of Duck Meat Leads to Novel Genetic and Biochemical Insights.

Meat is among the most consumed foods worldwide and has a unique flavor and high nutrient density in the human diet. However, the genetic and biochemical bases of meat nutrition and flavor are poorly understood. Here, 3431 metabolites and 702 volatiles in 423 skeletal muscle samples are profiled from a gradient consanguinity segregating population generated by Pekin duck × Liancheng duck crosses using metabolomic approaches. The authors identified 2862 metabolome-based genome-wide association studies (mGWAS) signals and 48 candidate genes potentially modulating metabolite and volatile levels, 79.2% of which are regulated by cis-regulatory elements. The level of plasmalogen is significantly associated with TMEM189 encoding plasmanylethanolamine desaturase 1. The levels of 2-pyrrolidone and glycerophospholipids are regulated by the gene expression of AOX1 and ACBD5, which further affects the levels of volatiles, 2-pyrrolidone and decanal, respectively. Genetic variations in GADL1 and CARNMT2 determine the levels of 49 metabolites including L-carnosine and anserine. This study provides novel insights into the genetic and biochemical basis of skeletal muscle metabolism and constitutes a valuable resource for the precise improvement of meat nutrition and flavor.

Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection.

BACKGROUND: Short-term, intense artificial selection drives fast phenotypic changes in domestic animals and leaves imprints on their genomes. However, the genetic basis of this selection response is poorly understood. To better address this, we employed the Pekin duck Z2 pure line, in which the breast muscle weight was increased nearly 3-fold after 10 generations of breeding. We denovo assembled a high-quality reference genome of a female Pekin duck of this line (GCA_003850225.1) and identified 8.60 million genetic variants in 119 individuals among 10 generations of the breeding population. RESULTS: We identified 53 selected regions between the first and tenth generations, and 93.8% of the identified variations were enriched in regulatory and noncoding regions. Integrating the selection signatures and genome-wide association approach, we found that 2 regions covering 0.36 Mb containing UTP25 and FBRSL1 were most likely to contribute to breast muscle weight improvement. The major allele frequencies of these 2 loci increased gradually with each generation following the same trend. Additionally, we found that a copy number variation region containing the entire EXOC4 gene could explain 1.9% of the variance in breast muscle weight, indicating that the nervous system may play a role in economic trait improvement. CONCLUSIONS: Our study not only provides insights into genomic dynamics under intense artificial selection but also provides resources for genomics-enabled improvements in duck breeding.

Genetic fine-mapping reveals single nucleotide polymorphism mutations in the MC1R regulatory region associated with duck melanism.

Birds are among the most colourful terrestrial vertebrates, with various plumage colours and patterns. We conducted a genome-wide association study (GWAS) on an intercross F2 population of Pekin ducks and mallards (n = 722) and identified a 1.57-Mb genetic region (Chr11: 20,176,480-21,750,101 bp) related to duck melanism. Fine mapping by linkage disequilibrium (LD) and FST analysis narrowed the final candidate region to a region of 22,500 bp (Chr11: 20,677,500-20,700,000 bp) including three coding genes, TCF25, MC1R and TUBB3. Combined with transcriptome and qRT-PCR analysis, MC1R was identified as the unique genetic locus responsible for black plumage in ducks, and it was significantly more highly expressed in the feather bulbs of black ducks. We also identified 52G > A (Chr11: 20,696,354G > A) and 376G > A (Chr11: 20,696,678G > A) mutations in the MC1R coding region that have been widely studied in ducks. In addition, structural variations (SVs) were screened by nanopore sequencing, and no significant SV was found to be associated with the duck black plumage trait. However, we identified four novel single nucleotide polymorphisms in the MC1R regulator region (Chr11: 20,678,412G > A, Chr11: 20,679,236G > A, Chr11: 20,692,496 A > G and Chr11: 20,692,791 A > G) that had a strong association with the black plumage phenotype of ducks and combined with potential changes in transcription binding affinities. The luciferase reporter gene assay demonstrated that Chr11: 20,678,412G > A and Chr11: 20,679,236G > A led to significant promoter activity changes. Our research emphasizes the importance of MC1R regulatory region mutation in determining the duck black plumage phenotype, and these results expand our understanding of the genetic mechanism underlying duck plumage colour.

Genomic characteristics, pathogenicity and viral shedding of a novel DVEV variant derived from goose.

Duck virus enteritis (DVE), caused by the DVE virus (DVEV), is an acute, septicemic, and contagious disease affecting ducks of different breeds, ages, and sexes. In late spring and summer 2019, several outbreaks of DVE were reported in areas with large waterfowl industries in central and southern China. A goose farm located in Jining County, Shandong Province, was impacted by an acute DVE outbreak in July 2019. The causative DVEV field strain (Goose/DVEV/SDJN/China/2019) was subsequently isolated from the liver specimens collected from acute cases of dead geese, which showed severe hemorrhagic lesions on the esophageal mucosal membranes of specimens collected from all the postmortem cases. Comparison of the genome sequence of this newly isolated field strain (Goose/DVEV/SDJN/China/2019) with the common DVEV strains revealed insertions or mutations in the gB and gC genes, which possibly caused the observed high morbidity and mortality in this acute outbreak. We conducted a trial among geese to evaluate the pathogenicity of this strain. Healthy experimental goslings aged 15 d old were inoculated with 10-5.53 ELD50/0.2 mL doses orally or through intramuscular injection. Clinical signs and esophageal erosion appeared in infected geese. Necropsy revealed hemorrhage and necrosis of the cloacal mucosa and liver. Detection of the virus using real-time PCR in the liver, brain, and spleen indicated that they were the hotspots of DVEV infections. One day after the DVEV infection, virus release and seroconvert were observed in infected geese. Thus, our studies demonstrate that DVEV is highly pathogenic and contagious in geese. To the best of our knowledge, this is the first study on the pathogenicity of mutant duck viral enteritis virus in goslings. This study serves as a foundation for further investigations into the pathophysiology of the recently identified variant DVEV strains.

Genome-wide association studies demonstrate the genes associated with perimysial thickness in ducks.

The thickness of the perimysium has an essential effect on the tenderness of the meat. However, the genetic basis underlying perimysial thickness has not been determined. The objective of this study was to explore the quantitative trait loci (QTL) that influence perimysial thickness in an F2 segregating population generated by Mallard × Pekin duck using the genome-wide association study (GWAS) method. Two QTL identified in chromosomes 27 and 13 displayed significant associations with perimysial thickness traits at the genome-wide level. The strongest association was the QTL located in chromosome 27, and this region had an effect on perimysial thickness and contained a promising candidate gene MAGI3 (Membrane-associated guanylate kinase, WW and PDZ domain containing 3). Meanwhile, association analysis showed that the top SNP within the MAGI3 gene was also associated with intramuscular fat content traits, which showed that perimysial thickness was positively correlated with intramuscular fat content. The second strongest association was the QTL region of chromosome 13. SUCLG2 (Succinate-CoA ligase GDP-forming subunit beta) is proximal to the top SNP and stood out as another candidate gene. Furthermore, the Transposase-Accessible Chromatin using Sequencing result showed that some key transcription factors (MYF5, MYOD1, KLF11) related to muscle development or energy metabolism might bind to the open regions of MAGI3 and SUCLG2. By analyzing the expression of different genotypes of the candidate gene, we speculate that different genotypes of MAGI3 may have an effect on breast muscle development, and then affect the thickness of the perimysium. This study maps two major genes of the duck breast muscle perimysial thickness trait, which helps to characterize muscle development and contributes to the genetic improvement of meat yield and quality in livestock.

Two variants of AUTS2 gene are associated with high lean meat percentage in Pekin ducks.

Duck meat is starting to receive more attention due to its unique meaty characteristics. Pekin duck is an important breed resource of meat duck, which has been used in meat production and product research. However, the study about whole genome resequencing analysis of ducks for meat production has not been reported and the underlying mechanisms of meat production remain undefined. Here, lines with high lean meat percentage (S, n = 30) and low lean meat percentage (Z, n = 30) were used to analyze. The values of body weight, breast meat weight and leg meat weight in S line (body weight: 3,071 ± 26.83 g), breast meat: 391.3 ± 6.670 g; leg meat: 121.1 ± 2.184 g) were significantly higher than those in Z line (body weight: 2,584 ± 38.53 g, breast meat: 263.9 ± 6.984 g; leg meat: 110.1 ± 3.645 g). The values of body size in Z line (26.47 ± 0.1571 cm) were significantly higher than that in S line (25.38 ± 0.2475 cm). A total of 14,220,037 SNPs were obtained from 19 individuals by whole-genome resequencing, and the separate analyses of FST (range from 0.30 to 0.52) and log2θπ ratio (range from 5.8 to 8.1) revealed 50 and 124 candidate genes in the top 0.1% regions respectively, which involved in 209 and 298 candidate regions. The integration of two approaches resulted in 7 overlapping genes. Notably, AUTS2 gene is related to activator of developmental regulator. As expected, we found that in the chr29:2.29-2.30 Mb region of AUTS2, the FST value is 0.32, and the S line (π = 7.3 × 10 -5) shows a very low level of π value compared with Z line (π = 8.8 × 10 -3). Genotyping and GWAS analysis showed that 2 candidate SNPs (chr29:2,296,787 and chr29:2,296,832) were associated with high meat percentage, which were verified by Sanger sequencing. Taken together, lean meat percentage was much higher in S line individuals by comparing with Z line. The integration of FST and θπ resulted in only 7 overlapping genes that in the top 0.1% candidate regions of them. The chr29:2,296,787 and chr29:2,296,832 in the AUTS2 gene could be important molecular markers for high lean meat adaptation selection in S line.

Genome-wide association study reveals the genetic determinism of serum biochemical indicators in ducks.

BACKGROUND: The serum is rich in nutrients and plays an essential role in electrolyte and acid-base balance, maintaining cellular homeostasis. In addition, serum parameters have been commonly used as essential biomarkers for clinical diagnosis. However, little is known about the genetic mechanism of the serum parameters in ducks. RESULTS: This study measured 18 serum parameters in 320 samples of the F2 segregating population generated by Mallard × Pekin duck. The phenotypic correlations showed a high correlation between LDH, HBDH, AST, and ALT (0.59-0.99), and higher coefficients were also observed among TP, ALB, HDL-C, and CHO (0.46-0.87). And then, we performed the GWAS to reveal the genetic basis of the 18 serum biochemical parameters in ducks. Fourteen candidate protein-coding genes were identified with enzyme traits (AST, ALP, LDH, HBDH), and 3 protein-coding genes were associated with metabolism and protein-related serum parameters (UA, TG). Moreover, the expression levels of the above candidate protein-coding genes in different stages of breast muscle and different tissues were analyzed. Furthermore, the genes located within the high-LD region (r2 > 0.4 and - log10(P) < 4) neighboring the significant locus also remained. Finally, 86 putative protein-coding genes were used for GO and KEGG enrichment analysis, the enzyme-linked receptor protein signaling pathway and ErbB signaling pathway deserve further focus. CONCLUSIONS: The obtained results can contribute to new insights into blood metabolism and provide new genetic biomarkers for application in duck breeding programs.

Genome-wide association analysis reveals 6 copy number variations associated with the number of cervical vertebrae in Pekin ducks.

As a critical developmental stage in vertebrates, the vertebral column formation process is under strict control; however, we observed variations in the number of cervical vertebrae in duck populations in our previous study. Here, we further explored the variations in the number of vertebrae in two duck populations: 421 Pekin duck × mallard F2 ducks and 850 Pekin ducks. Using resequencing data of 125 Pekin ducks with different numbers of cervical vertebrae and 352 Pekin duck × mallard F2 ducks with different numbers of thoracic vertebrae, we detected whole-genome copy number variations (CNVs) and implemented a genome-wide association study (GWAS) to identify the genetic variants related to the traits. The findings verified the existence of variations in the number of cervical vertebrae in duck populations. The number of cervical vertebrae in most ducks was 15, while that in a small number of the ducks was 14 or 16. The number of cervical vertebrae had a positive influence on the neck production, and one cervical vertebra addition could increase 11 g or 2 cm of duck neck. Genome-wide CNV association analysis identified six CNVs associated with the number of cervical vertebrae, and the associated CNV regions covered 15 genes which included WNT10A and WNT6. These findings improve our understanding of the variations in the number of vertebrae in ducks and lay a foundation for future duck breeding.