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.

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.

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.

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 reveal the genetic reasons affect melanin spot accumulation in beak skin of ducks.

BACKGROUND: Skin pigmentation is a broadly appearing phenomenon of most animals and humans in nature. Here we used a bird model to investigate why melanin spot deposits on the skin. RESULTS: Our result showed that growth age and the sunlight might induce melanin deposition in bird beak skin which was determined by genetic factors. GWAS helped us to identify two major loci affecting melanin deposition, located on chromosomes 13 and 25, respectively. The fine mapping works narrowed the candidate regions to 0.98 Mb and 1.0 Mb on chromosomes 13 and 25. The MITF and POU2F3 may be the causative genes and synergistically affect melanin deposition during duck beak skin. Furthermore, our data strongly demonstrated that the pathway of melanin metabolism contributes to melanin deposition on the skin. CONCLUSIONS: We demonstrated that age and sunlight induce melanin deposition in bird beak skin, while heredity is fundamental. The MITF and POU2F3 likely played a synergistic effect on the regulation of melanin synthesis, and their mutations contribute to phenotypic differences in beak melanin deposition among individuals. It is pointed out that melanin deposition in the skin is related to the pathway of melanin metabolism, which provided insights into the molecular regulatory mechanisms and the genetic improvement of the melanin deposition in duck beak.

Genomic divergence during artificial selection by feed conversion ratio in Pekin ducks.

Pekin ducks are world-famous for its fast growth and have become the majority of breeds rearing in duck industry. Feed conversion ratio (FCR) is an important trait in Pekin ducks breeding and production, and the underlying biological processes are complex. To gain an insight to the possible biological mechanism underlying the FCR in Pekin ducks, an artificial selection population (S) and a natural population (Z7) were used in this study. The FCR of S line decreased from 2.184 ± 0.057 in the first generation to 1.886 ± 0.063 in the eighth generation, which displays significantly low FCR (p = 0.0032) than that of the Z7 line (2.23 ± 0.046). Then, 9 samples from eighth generation of S line and 10 samples from Z7 were used for whole-genome resequencing. Analyses of FST, θπ and XP-EHH revealed 450, 479 and 356 candidate genes, which involved in 1,955, 1,933 and 1,964 candidate divergent regions (CDRs), respectively. And the integration of three approaches resulted in 30 overlapping genes. Functional analysis of 30 candidate genes revealed that variants of KCNQ1 and ADCY7, which were involved in the pancreatic secretion signal pathway, could be important molecular markers for high feed conversion efficiency in S line breeding.

Severe pantothenic acid deficiency induces alterations in the intestinal mucosal proteome of starter Pekin ducks.

BACKGROUND: Pantothenic acid deficiency (PAD) results in growth depression and intestinal hypofunction of animals. However, the underlying molecular mechanisms remain to be elucidated. Mucosal proteome might reflect dietary influences on physiological processes. RESULTS: A total of 128 white Pekin ducks of one-day-old were randomly assigned to two groups, fed either a PAD or a pantothenic acid adequate (control, CON) diet. After a 16-day feeding period, two ducks from each replicate were sampled to measure plasma parameters, intestinal morphology, and mucosal proteome. Compared to the CON group, high mortality, growth retardation, fasting hypoglycemia, reduced plasma insulin, and oxidative stress were observed in the PAD group. Furthermore, PAD induced morphological alterations of the small intestine indicated by reduced villus height and villus surface area of duodenum, jejunum, and ileum. The duodenum mucosal proteome of ducks showed that 198 proteins were up-regulated and 223 proteins were down-regulated (> 1.5-fold change) in the PAD group compared to those in the CON group. Selected proteins were confirmed by Western blotting. Pathway analysis of these proteins exhibited the suppression of glycolysis and gluconeogenesis, fatty acid beta oxidation, tricarboxylic acid cycle, oxidative phosphorylation, oxidative stress, and intestinal absorption in the PAD group, indicating impaired energy generation and abnormal intestinal absorption. We also show that nine out of eleven proteins involved in regulation of actin cytoskeleton were up-regulated by PAD, probably indicates reduced intestinal integrity. CONCLUSION: PAD leads to growth depression and intestinal hypofunction of ducks, which are associated with impaired energy generation, abnormal intestinal absorption, and regulation of actin cytoskeleton processes. These findings provide insights into the mechanisms of intestinal hypofunction induced by PAD.

A single nucleotide polymorphism variant located in the cis-regulatory region of the ABCG2 gene is associated with mallard egg colour.

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.

Genome-wide association studies demonstrate that TASP1 contributes to increased muscle fiber diameter.

Muscle fiber diameter is an economically important trait because it affects meat yield and quality. However, the genetic basis underlying muscle fiber diameter has not been determined. In this study, we collected THREE muscular histological phenotypes in 479 ducks from an F2 segregating population generated by mallard × Pekin duck crosses. We performed genome-wide association studies (GWAS) and identified a quantitative trait locus (QTL) significantly associated with muscle fiber diameter on chromosome 3. Then, we discovered the selection signatures using the fixation index among 40 mallards and 30 Pekin ducks in this QTL region. Furthermore, we characterized the recombination event in this QTL region and identified a 6-kb block located on TASP1 that was significantly associated with muscle fiber diameter. Finally, five SNPs were screened as potential causative mutations within the 6-kb block. In conclusion, we demonstrated that TASP1 contributes to an increase in muscle fiber diameter, which helps to characterize muscle development and contributes to the genetic improvement of meat yield and quality in livestock.

Genome-wide association and selective sweep analyses reveal genetic loci for FCR of egg production traits in ducks.

BACKGROUND: As a major economic trait in poultry, egg production efficiency attracts widespread interest in breeding and production. However, limited information is available about the underlying genetic architecture of egg production traits in ducks. In this paper, we analyzed six egg production-related traits in 352 F2 ducks derived from reciprocal crosses between mallard and Pekin ducks. RESULTS: Feed conversation ratio (FCR) was positively correlated with feed intake but negatively correlated with egg-related traits, including egg weight and egg production, both phenotypically and genetically. Estimates of pedigree-based heritability were higher than 0.2 for all traits investigated, except hip-width. Based on whole-genome sequencing data, we conducted genome-wide association studies to identify genomic regions associated with these traits. In total, 11 genomic regions were associated with FCR. No genomic regions were identified as significantly associated with hip-width, total feed intake, average daily feed intake, and total egg production. Analysis of selective sweeps between mallard and Pekin ducks confirmed three of these genomic regions on chromosomes 13, 3 and 6. Within these three regions, variants in candidate genes that were in linkage disequilibrium with the GWAS leader single nucleotide polymorphisms (SNPs) (Chr13:2,196,728, P = 7.05 × 10-14; Chr3:76,991,524, P = 1.06 × 10-12; Chr6:20,356,803, P = 1.14 × 10-10) were detected. Thus, we identified 31 potential candidate genes associated with FCR, among which the strongest candidates are those that are highly expressed in tissues involved in reproduction and nervous system functions of ducks: CNTN4, CRBR, GPR63, KLHL32, FHL5, TRNT1, MANEA, NDUFAF4, and SCD. CONCLUSIONS: For the first time, we report the identification of genomic regions that are associated with FCR in ducks and our results illustrate the genomic changes that occurred during their domestication and are involved in egg production efficiency.

Genetic variations for egg internal quality of ducks revealed by genome-wide association study.

Egg internal quality traits are important traits related to egg production in poultry industry. To better understand the genetic architecture of egg internal quality traits in ducks, we performed genetic parameters estimates and a genome-wide association study (GWAS). The phenotypic values of egg weight, yolk color, albumin height (AH), yolk weight, and Haugh unit (HU) were collected individually from 352 F2 laying ducks produced by reciprocal crosses between mallards and Pekin ducks, and their genotypes were assayed by whole genome re-sequencing. The results showed that the AH and HU traits have a clear coefficient of variance, around 15% for both mallards and Pekin ducks. The pedigree-based genetic parameters estimates rane from 0.26 to 0.71 for all eight egg quality traits, while the highest heritability was 0.71 for egg weight. The GWAS showed that a clear signal was associated with AH and HU traits. The locus zoom analysis and conditional GWAS helped to narrow the candidate region to ~5.8-Mb spanning from 14.7 to 20.5 Mb on Chromosome 5, which harbored 111 candidate genes. MUC6 and LDLRAD3 were finally promised as the major candidate genes affecting albumen composition. Our data revealed the egg internal quality traits for the first time in ducks, which provides a theoretical basis and technological support for improving duck egg internal quality.

Dynamic accumulation of fatty acids in duck (Anas platyrhynchos) breast muscle and its correlations with gene expression.

BACKGROUND: Fatty acid composition contributes greatly to the quality and nutritional value of meat. However, the molecular regulatory mechanisms underlying fatty acid accumulation in poultry have not yet been cleared. The aims of this study were to characterize the dynamics of fatty acid accumulation in duck breast muscle and investigate its correlations with gene expression. RESULTS: Here, we analyzed the fatty acid profile and transcriptome of breast muscle derived from Pekin ducks and mallards at the ages of 2 weeks, 4 weeks, 6 weeks and 8 weeks. Twenty fatty acids were detected in duck breast muscle, with palmitic acid (C16:0, 16.6%~ 21.1%), stearic acid (C18:0, 9.8%~ 17.7%), oleic acid (C18:1n-9, 15.7%~ 33.8%), linoleic acid (C18:2n-6, 10.8%~ 18.9%) and arachidonic acid (C20:4n-6, 11.7%~ 28.9%) as the major fatty acids. Our results showed that fatty acid composition was similar between the two breeds before 6 weeks, but the compositions diverged greatly after this point, mainly due to the stronger capacity for C16:0 and C18:1n-9 deposition in Pekin ducks. By comparing the multistage transcriptomes of Pekin ducks and mallards, we identified 2025 differentially expressed genes (DEGs). Cluster analysis of these DEGs revealed that the genes involved in oxidative phosphorylation, fatty acid degradation and the PPAR signaling pathway were upregulated in mallard at 8 weeks. Moreover, correlation analysis of the DEGs and fatty acid composition traits suggested that the DEGs involved in lipogenesis, lipolysis and fatty acid ß-oxidation may interact to influence the deposition of fatty acids in duck breast muscle. CONCLUSIONS: We reported the temporal progression of fatty acid accumulation and the dynamics of the transcriptome in breast muscle of Pekin ducks and mallards. Our results provide insights into the transcriptome regulation of fatty acid accumulation in duck breast muscle, and will facilitate improvements of fatty acid composition in duck breeding.

Selection response and estimation of the genetic parameters for multidimensional measured breast meat yield related traits in a long-term breeding Pekin duck line.

OBJECTIVE: This 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. METHODS: The 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. RESULTS: Estimated 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. CONCLUSION: The 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.

Severe riboflavin deficiency induces alterations in the hepatic proteome of starter Pekin ducks.

Suboptimal vitamin B2 status is encountered globally. Riboflavin deficiency depresses growth and results in a fatty liver. The underlying mechanisms remain to be established and an overview of molecular alterations is lacking. We investigated hepatic proteome changes induced by riboflavin deficiency to explain its effects on growth and hepatic lipid metabolism. In all, 360 1-d-old Pekin ducks were divided into three groups of 120 birds each, with twelve replicates and ten birds per replicate. For 21 d, the ducks were fed ad libitum a control diet (CAL), a riboflavin-deficient diet (RD) or were pair-fed with the control diet to the mean daily intake of the RD group (CPF). When comparing RD with CAL and CPF, growth depression, liver enlargement, liver lipid accumulation and enhanced liver SFA (C6 : 0, C12 : 0, C16 : 0, C18 : 0) were observed. In RD, thirty-two proteins were enhanced and thirty-one diminished (>1·5-fold) compared with CAL and CPF. Selected proteins were confirmed by Western blotting. The diminished proteins are mainly involved in fatty acid ß-oxidation and the mitochondrial electron transport chain (ETC), whereas the enhanced proteins are mainly involved in TAG and cholesterol biosynthesis. RD causes liver lipid accumulation and growth depression probably by impairing fatty acid ß-oxidation and ETC. These findings contribute to our understanding of the mechanisms of liver lipid metabolic disorders due to RD.

Genetic parameters for residual feed intake in a random population of Pekin duck.

OBJECTIVE: The feed intake (FI) and feed efficiency are economically important traits in ducks. To obtain insight into this economically important trait, we designed an experiment based on the residual feed intake (RFI) and feed conversion ratio (FCR) of a random population Pekin duck. METHODS: Two thousand and twenty pedigreed random population Pekin ducks were established from 90 males mated to 450 females in two hatches. Traits analyzed in the study were body weight at the 42th day (BW42), 15 to 42 days average daily gain (ADG), 15 to 42 days FI, 15 to 42 days FCR, and 15 to 42 days RFI to assess their genetic inter-relationships. The genetic parameters for feed efficiency traits were estimated using restricted maximum likelihood (REML) methodology applied to a sire-dam model for all traits using the ASREML software. RESULTS: Estimates heritability of BW42, ADG, FI, FCR, and RFI were 0.39, 0.38, 0.33, 0.38, and 0.41, respectively. The genetic correlation was high between RFI and FI (0.77) and moderate between RFI and FCR (0.54). The genetic correlation was high and moderate between FCR and ADG (-0.80), and between FCR and BW42 (-0.64), and between FCR and FI (0.49), respectively. CONCLUSION: Thus, selection on RFI was expected to improve feed efficiency, and reduce FI. Selection on RFI thus improves the feed efficiency of animals without impairing their FI and increase growth rate.

The research progress of farm animal genomics based on sequencing technologies.

Various farm animal breeds have been domesticated and bred for thousands years, and they provide adequate animal-derived proteins to meet the human nutrition requirement. Although quantitative genetics was applied in animal breeding, which launched a technological revolution in the past century, a number of complex traits remain difficult to be selected based on pedigree derived breeding, due to complicated animal genetics and development mechanisms. Farm animal's genetic potential hasn't yet to be fully exploited. The concept and technology from the Human Genome Project have greatly promoted farm animal genomic researches. It is possible to fine map the causal variations at the whole genome level and then exploit their biological functions, thus providing the theoretical basis for molecular designed breeding. In this review, we summarize the genomics research progress of main farm animals during the past decade, including pigs, cattle, yaks, goats, sheep, chickens, ducks and geese. We focus on the reference genome sequencing and follow-up population-level genomic studies based on high throughput resequencing technologies, and meanwhile envision the future work of farm animal genomics.

Effects of pyridoxine on growth performance and plasma aminotransferases and homocysteine of white pekin ducks.

A dose-response experiment with seven supplemental pyridoxine levels (0, 0.66, 1.32, 1.98, 2.64, 3.30, and 3.96 mg/kg) was conducted to investigate the effects of pyridoxine on growth performance and plasma aminotransferases and homocysteine of White Pekin ducks and to estimate pyridoxine requirement for these birds. A total of 336 one-day-old male White Pekin ducks were divided to 7 experimental treatments and each treatment contained 8 replicate pens with 6 birds per pen. Ducks were reared in raised wire-floor pens from hatch to 28 d of age. At 28 d of age, the weight gain, feed intake, feed/gain, and the aspartate aminotransferase, alanine aminotransferase, and homocysteine in plasma of ducks from each pen were all measured. In our study, the pyridoxine deficiency of ducks was characterized by growth depression, decreasing plasma aspartate aminotransferase activity and increasing plasma homocysteine. The ducks fed vitamin B6-deficient basal diets had the worst weight gain and feed/gain among all birds and this growth depression was alleviated (p<0.05) when pyridoxine was supplemented to basal diets. On the other hand, plasma aspartate aminotransferase and homocysteine may be the sensitive indicators for vitamin B6 status of ducks. The ducks fed basal diets had much lower aspartate aminotransferase activity and higher homocysteine level in plasma compared with other birds fed pyridoxine-supplemented diets (p<0.05). According to quadratic regression, the supplemental pyridoxine requirements of Pekin ducks from hatch to 28 days of age was 2.44 mg/kg for feed/gain and 2.08 mg/kg for plasma aspartate aminotransferase and the corresponding total requirements of this vitamin for these two criteria were 4.37 and 4.01 mg/kg when the pyridoxine concentration of basal diets was included, respectively. All data suggested that pyridoxine deficiency could cause growth retardation in ducks and the deficiency of this vitamin could be indicated by decreasing plasma aspartate aminotransferase activity and increasing plasma homocysteine.

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.

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.

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.