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.

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.

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.

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.

Effect of riboflavin deficiency on intestinal morphology, jejunum mucosa proteomics, and cecal microbiota of Pekin ducks.

This study was to determine the effects of riboflavin deficiency (RD) on intestinal development, jejunum mucosa proteome, cecal short-chain fatty acids (SCFA) profiling, and cecal microbial diversity and community of starter Pekin ducks. Male white Pekin ducks (1 d old, n = 240) were allocated into 2 groups, with 12 replicates and 10 birds per replicate in each group. For 21 d, all ducks had ad libitum access to either an RD or a riboflavin adequate (control, CON) diet, formulated by supplementing a basal diet with 0 or 10 mg riboflavin per kg of diet, respectively. Compared to the CON group, growth retardation, high mortality, and poor riboflavin status were observed in the RD group. Furthermore, RD reduced the villus height and the ratio of villus height to crypt depth of jejunum and ileum (P < 0.05), indicating morphological alterations of the small intestine. In addition, dietary RD enhanced relative cecum weight and decreased cecal SCFA concentrations (P < 0.05), including propionate, isobutyrate, butyrate, and isovalerate. The jejunum mucosa proteomics showed that 208 proteins were upregulated and 229 proteins were downregulated in the RD group compared to those in the CON group. Among these, RD mainly suppressed intestinal absorption and energy generation processes such as glycolysis and gluconeogenesis, fatty acid beta oxidation, tricarboxylic acid cycle, and oxidative phosphorylation, leading to impaired ATP generation. In addition, RD decreased the community richness and diversity of the bacterial community in the cecum of ducks. Specifically, RD reduced the abundance of butyrate-producing bacteria in the cecum (P < 0.05), such as Eubacterium coprostanoligenes, Prevotella and Faecalibacterium. Dietary RD resulted in growth depression and intestinal hypofunction of Pekin ducks, which could be associated with impaired intestinal absorption and energy generation processes in intestinal mucosa, as well as gut microbiota dysbiosis. These findings contribute to our understanding of the mechanisms of intestinal hypofunction due to RD.

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.

Comparative transcriptome reveals the effect of IFITM1 on differential resistance to duck hepatitis A virus genotype 3 in Pekin ducks.

BACKGROUND: Duck viral hepatitis (DVH) has a significant economic impact on duck industry, and duck hepatitis A virus genotype 3 (DHAV-3) is the most prevalent pathogen of DVH in Asian duck industry. The detailed study connecting differentially expressed genes (DEGs) and the differential resistance to DHAV-3 have not been accurately described, although a large numbers of DEGs have been identified by transcriptomic studies. RESULTS: Here, a resistant Pekin duck line (Z8R) and a susceptible Pekin duck line (Z8S) as models, high mortality and dramatically increased aspartate aminotransferase (AST), alanine aminotransferase (ALT) and the expression of immune-related genes of Z8S group were shown to be noticeable signs of cases caused by DHAV-3 infection. Compared with the control (Con) group, 1117 down-regulated DEGs and 612 up-regulated DEGs were found in the Z8S group and 37 down-regulated DEGs and 82 up-regulated DEGs were found in the Z8R group. Ultimately, the expression patterns of 10 DEGs were found to be diametrically opposite in Z8R and Z8S group. Functional analysis revealed that IFITM1 was associated with cell growth suppression, which was considered a key candidate gene. Results of flow cytometry showed that the conserved regions of IFITM1 (213-317 bp) could affected the cell cycle of duck embryo fibroblast (DEF) cells after infection with DHAV-3. Transcriptome and western blot analysis suggested that the CCND1, CCNE1 and CDK6 were significantly up-regulated in susceptible ducks by comparing with Con group. CONCLUSIONS: The hepatic injury and pathogenic outcomes caused by DHAV-3 infection were more severe in Z8S group compared to Z8R. Results of transcriptomics analysis and flow cytometry suggested that DHAV-3 infection can induce cell cycle changes that may be associated with IFITM1 expression level. These data will greatly enhance our understanding of the pathogenesis of DHAV-3 infection in ducklings and have implications for development of resistance breeding.

Integrated liver proteomics and metabolomics identify metabolic pathways affected by pantothenic acid deficiency in Pekin ducks.

Pantothenic acid deficiency (PAD) in animals causes growth depression, fasting hypoglycemia and impaired lipid and glucose metabolism. However, a systematic multi-omics analysis of effects of PAD on hepatic function has apparently not been reported. We investigated liver proteome and metabolome changes induced by PAD to explain its effects on growth and liver metabolic disorders. Pekin ducks (1-d-old, n = 128) were allocated into 2 groups, with 8 replicates and 8 birds per replicate. For 16 d, all ducks had ad libitum access to either a PAD or a pantothenic acid adequate (control, CON) diet, formulated by supplementing a basal diet with 0 or 8 mg pantothenic acid/kg of diet, respectively. Liver enlargement, elevated liver glycogen concentrations and decreased liver concentrations of triglyceride and unsaturated fatty acids were present in the PAD group compared to the CON group. Based on integrated liver proteomics and metabolomics, PAD mainly affected glycogen synthesis and degradation, glycolysis and gluconeogenesis, tricarboxylic acid (TCA) cycle, peroxisome proliferator-activated receptor (PPAR) signaling pathway, fatty acid beta oxidation, and oxidative phosphorylation. Selected proteins were confirmed by Western blotting. Downregulation of proteins and metabolites involved in glycogen synthesis and degradation, glycolysis and gluconeogenesis implied that these processes were impaired in PAD ducks, which could have contributed to fasting hypoglycemia, liver glycogen storage, insufficient ATP production, and growth retardation. In contrast, PAD also upregulated proteins and metabolites involved in fatty acid beta oxidation, the TCA cycle, and oxidative phosphorylation processes in the liver; presumably compensatory responses to produce ATP. We inferred that PAD decreased liver triglyceride and unsaturated fatty acids by activating fatty acid beta oxidation and impairing unsaturated fatty acid synthesis. These findings contributed to our understanding of the mechanisms of PAD-induced changes in hepatic metabolism.

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.

NOD1 Is Associated With the Susceptibility of Pekin Duck Flock to Duck Hepatitis A Virus Genotype 3.

Duck viral hepatitis (DVH) is an acute, highly lethal infectious disease of ducklings that causes huge losses in the duck industry. Duck hepatitis A virus genotype 3 (DHAV-3) has been one of the most prevalent DVH pathogen in the Asian duck industry in recent years. Here, we investigated the genetic basis of the resistance and susceptibility of ducks to DVH by comparing the genomes and transcriptomes of a resistant Pekin duck flock (Z8) and a susceptible Pekin duck flock (SZ7). Our comparative genomic and transcriptomic analyses suggested that NOD1 showed a strong signal of association with DVH susceptibility in ducks. Then, we found that NOD1 showed a significant expression difference between the livers of susceptible and resistant individuals after infection with DHAV-3, with higher expression in the SZ7 flock. Furthermore, suppression and overexpression experiments showed that the number of DHAV-3 genomic copies in primary duck hepatocytes was influenced by the expression level of NOD1. In addition, in situ RNAscope analysis showed that the localization of NOD1 and DHAV-3 in liver cells was consistent. Altogether, our data suggested that NOD1 was likely associated with DHAV-3 susceptibility in ducks, which provides a target for future investigations of the pathogenesis of DVH.

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.

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.

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.

Dynamic Transcriptome Reveals the Mechanism of Liver Injury Caused by DHAV-3 Infection in Pekin Duck.

Duck hepatitis A virus 3 (DHAV-3) is a wild endemic virus, which seriously endangers the duck industry in China. The present study aims to elucidate the mechanism of duck resistance to DHAV-3 infection. Both resistant and susceptible ducks were challenged with DHAV-3 in this experiment. The histopathological features and serum biochemical indices (ALT and AST) were analyzed to estimate liver injury status at 6, 12, 15, and 24 h post-infection (hpi). The dynamic transcriptomes of liver were analyzed to explain the molecular regulation mechanism in ducks against DHAV-3. The result showed that the liver injury in susceptible ducks was more serious than that in the resistant ducks throughout the four time points. A total of 2,127 differentially expressed genes (DEGs) were identified by comparing the transcriptome of the two populations. The expression levels of genes involved in innate immune response increased rapidly in susceptible ducks from 12 hpi. Similarly, the expression of genes involved in cytokine regulation also increased at the same time points, while the expression levels of these genes in resistant ducks remained similar between the various time points. KEGG enrichment analysis of the DEGs revealed that the genes involved in cytokine regulation and apoptosis were highly expressed in susceptible ducks than that in resistant ducks, suggesting that excessive cytokine storm and apoptosis may partially explain the mechanism of liver injury caused by DHAV-3 infection. Besides, we found that the FUT9 gene may contribute to resistance towards DHAV-3 in resistant ducklings. These findings will provide insight into duck resistance and susceptibility to DHAV-3 infection in the early phases, facilitate the development of a strategy for DHAV-3 prevention and treatment, and enhance genetic resistance via genetic selection in animal breeding.

Effects of pantothenic acid on growth performance and antioxidant status of growing male white Pekin ducks.

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

Proteomics reveals the effect of type I interferon on the pathogenicity of duck hepatitis A virus genotype 3 in Pekin ducks.

Duck hepatitis A virus genotypes 3 (DHAV-3) has become the most prevalent pathogen of duck viral hepatitis (DVH) in Asian duck industry in recent years. Previous studies on the pathogenic mechanism of DHAV-3 mainly focused on examine host gene expression levels. However, the study about host protein expression levels has not been reported. For this, proteomics analysis on livers of infected 7-day-old Pekin ducks with DHAV-3 112803 strain was performed to screen differentially expressed proteins. A total of 3,385 proteins were identified, and we found 39 proteins in the challenged group (CH) were significantly up-regulated and 15 proteins were significantly down-regulated in comparison with control group (CON). GO results showed that 9 of the top 20 GO terms were involved in type I interferon regulation, and the KEGG pathway enrichment results showed that innate immune responses were significantly enriched, such as RIG-1-like, Toll-like and NOD-like receptor signaling pathways. Notably, interaction between 11 up-regulation proteins promoted interferon-induced protein synthesis and supported viral genome replication, which could aggravate inflammatory response and liver damage. These findings, together with RT-qPCR verification of related genes, support the view that the type I interferon may play an extremely important role in the pathogenic mechanism of DHAV-3.

Effect of duck hepatitis A virus genotype 3 infection on glucose metabolism of Pekin ducklings and underlying mechanism.

Earlier works identified the second generation (Z8R2) of a resistant Pekin duck line to duck hepatitis A virus genotype 3 (DHAV-3), which displays significantly strong resistance than that of the second generation (Z8S2) of a susceptible Pekin duck line. To understand the genetic mechanisms that determine the different resistance/susceptibility of Z8R2 and Z8S2 to DHAV-3, transcriptome analysis on livers of infected Pekin ducklings was performed to screen differentially expressed genes (DEGs). We found that DHAV-3 infection has a great effect on metabolism of Z8S2 at the transcription level. Using a newly created fourth generation of the resistant Pekin duck line (Z8R4) and an unselected Pekin duck flock (Z7) as models, hypoglycemia and dramatically increased aspartate aminotransferase and alanine aminotransferase were shown to be noticeable signs of fatal cases caused by DHAV-3 infection. These findings, together with expression analysis and verification of DEGs, support the view that DHAV-3 infection results in glucose metabolic abnormalities in susceptible individuals and that there are significant differences in expression patterns of glucose metabolism-related DEGs between susceptible and resistant individuals. Notably, cytokines displayed a negative correlation with glucose synthesis in terms of expression in susceptible individuals following DHAV-3 infection. Mechanism analyses suggests that cytokines will activate PI3K-AKT pathway and/or JAK-STAT pathway by up-regulated expression of JAK2, and thereby causes down-regulated expression of G6PC and/or ACAT1. Cytokines can also cause down-regulated expression of HPGDS by JAK2. The present work contributes to the understanding of pathogenesis of DHAV-3 infection and the resistance breeding project against DHAV-3.

Fetal Calf Serum Exerts an Inhibitory Effect on Replication of Duck Hepatitis A Virus Genotype 1 in Duck Embryo Fibroblast Cells.

Among the causative agents of duck viral hepatitis, duck hepatitis A virus genotype 1 (DHAV-1) is the most common virus reported in most outbreaks worldwide. How to propagate DHAV-1 in cell cultures efficiently remains a problem to be explored. Here, we aimed to test the effect of serum type on DHAV-1 replication in duck embryo fibroblast (DEF) cells. Comparative studies involved virus culture and passage, observation of cytopathic effect (CPE), virus quantification, and plaque formation assay. From the results of these investigations, we conclude that use of chicken serum (CS) in maintenance medium allows DHAV-1 to establish productive, cytocidal infection in DEF cells, whereas FCS exerts inhibitory effects on DHAV-1 replication, CPE development, and plaque formation. By using a neutralization test, we found that the direct action of FCS on virions is likely to play a key role in inhibiting DHAV-1 replication in DEF cells. Mechanism analyses revealed that FCS inhibits DHAV-1 replication at virus adsorption and reduces extracellular virus yields. The present work may shed light on a new perspective for antiviral agent development, and have provided a virus-host cell system for further studies on molecular mechanism involved DHAV-1 replication and pathogenesis.

Host Differences Affecting Resistance and Susceptibility of the Second Generation of a Pekin Duck Flock to Duck Hepatitis A Virus Genotype 3.

Earlier work suggested the possibility to anti duck hepatitis A virus genotype 3 (DHAV-3) using the resistance breeding strategy. Here, we report the creation of the second generations of a resistant Pekin duck flock (designated Z8R2) and a highly susceptible Pekin duck flock (designated Z8S2) and the investigation of their responses to DHAV-3. Experimental infection with DHAV-3 at 7 days of age resulted in a high mortality (66.3%) in 11 susceptible Z8S2 families and an extremely low mortality rate (2.67%) in 32 Z8R2 families, indicating that Z8R2 exhibits strong resistance to DHAV-3, while Z8S2 is highly susceptible to the virus. Detection of DHAV-3 in the liver between 1 and 60 hours post inoculation (hpi) suggests that DHAV-3 can be replicated rapidly and efficiently in the liver of Z8S2, whereas the replication of the virus in the liver of Z8R2 is suppressed greatly. High levels of serum biochemical markers (e.g., ALT, AST, ALP and GGT) were detected in Z8S2 at 24 hpi, which were significantly higher than those in Z8R2. Analysis of transcripts in the liver revealed that the expression levels of several pattern recognition receptors (PRRs) (e.g., TLR4/7, RIG-1 and MDA5) and cytokines (e.g., IL-2, IL-6, IL-8, IFN-α, and IFN-γ) in Z8S2 were significantly higher than those in Z8R2 at 12 and 24 hpi. Together these findings suggest that Z8R2 and Z8S2 Pekin ducks, which were derived from the same Z8 line, exhibit disparate pathogenic outcomes following DHAV-3 infection. Therefore, it is possible to select a Pekin duck flock resistant to DHAV-3 employing the strategy described here. It is likely that the high viral load and the strong inflammatory response correlate with the high susceptibility of Z8S2 Pekin ducks to DHAV-3.

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.