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.

Clostridium perfringens α toxin damages the immune function, antioxidant capacity and intestinal health and induces PLCγ1/AMPK/mTOR pathway-mediated autophagy in broiler chickens.

Clostridium perfringens α toxin is generated by all types of C. perfringens and is closely related to necrotic enteritis in poultry. This study was conducted to investigate the effects of α toxin on immune function, antioxidant capacity, intestinal health and the underlying mechanisms in broiler chickens. A total of 144 twenty-day-old broiler chickens were randomly assigned to four treatments. On d 21, the birds were intraperitoneally injected with PBS (control group) or α toxin at 0.025, 0.1 or 0.4 U/kg of body weight. Samples were collected at 3 h and 24 h post injection (p.i.). Results showed that α toxin challenge linearly decreased the average daily gain during the 3 days after infection and decreased plasma IgA and IgM levels 3 h p.i. Plasma diamine oxidase and d-lactate levels were linearly elevated by α toxin challenge at 3 h p.i. and 24 h p.i. Alpha toxin challenge linearly decreased plasma and jejunal mucosal catalase, glutathione peroxidase and total superoxide dismutase activities at 3 h p.i. and linearly decreased glutathione peroxidase and total superoxide dismutase activities at 24 h p.i. The ileal villus height to crypt depth ratio decreased linearly with increasing α toxin levels at 3 h p.i. and 24 h p.i. Alpha toxin challenge linearly elevated jejunal IL-1ß, IL-6, IL-8 and tumor necrosis factor α mRNA expression at 3 h p.i. Additionally, α toxin challenge linearly reduced the jejunal claudin-1, claudin-3 and zonula occludens 1 mRNA expression at 3 h p.i. and the claudin-3, occludin and zonula occludens 1 mRNA expression at 24 h p.i. What's more, α toxin linearly increased the jejunal PLCγ1, AMPKα1 and ATG5 mRNA expression and linearly decreased the mTOR mRNA expression. In conclusion, C. perfringens α toxin challenge decreased body weight gain, impaired immune function, antioxidant capacity and intestinal health, and induced PLCγ1/AMPK/mTOR pathway-mediated autophagy. The recommended intraperitoneal injection dose for moderate injury was 0.1 U/kg of body weight and the recommended sampling time was 3 h p.i. in broiler chickens.

Effects of dietary vitamin K3 supplementation on production performance, egg quality, vitamin K-dependent proteins, and antioxidant properties in breeding geese during the laying period.

The aim of this work was to investigate the effects of dietary vitamin K3 (VK3) supplementation on production performance, egg quality, vitamin K-dependent proteins, and antioxidant properties in breeding geese during the laying period. A total of one hundred twenty 82-wk-old Wulong geese with similar body weights were randomly divided into 6 groups with 4 replicates and 5 geese each (1 male and 4 female). The geese in the control group were fed a basal diet, and the geese in the treatment groups were fed diets supplemented with different levels of VK3 (2.5, 5.0, 7.5, 10.0, and 12.5 mg/kg) for 11 wk. Dietary VK3 supplementation linearly and quadratically increased feed intake, egg mass, egg weight, and egg production (P < 0.05). Increasing VK3 levels linearly and quadratically increased albumen height, shell thickness and Haugh unit of eggs (P < 0.05). VK3 reduced osteocalcin (OC) and uncarboxylated osteocalcin (ucOC) levels in the serum. Dietary VK3 addition linearly decreased serum malondialdehyde (MDA) levels (P < 0.01). There was linear and quadratic effect in the activity of serum total superoxide dismutase (T-SOD) (P < 0.01), and linear effect in serum total antioxidant capacity (T-AOC) (P < 0.01). In conclusion, dietary VK3 supplementation enhanced the production performance, egg quality, vitamin K-dependent proteins, and antioxidant properties in breeding geese during the laying period. The optimal dose of dietary VK3 supplementation was 10.0 mg/kg.

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.

Effects of dietary arginine supplementation on production performance, serum biochemicals, antioxidant capacity, and immunity of laying Wulong geese.

This study investigated the effects of dietary arginine supplementation on the production performance, serum biochemicals, antioxidant capacity, and immunity of laying Wulong geese. A total of 150 Wulong geese (34-wk old) with similar body weights were randomly divided into 6 groups with 5 replicates and 5 geese each (1 male and 4 female). The geese in the control group were fed a corn-rapeseed meal basal diet, and the geese in the treatment groups were fed the basal diet supplemented with 0.1, 0.2, 0.3, 0.4, and 0.5% arginine. The experiment lasted for 17 wk. Our results showed that dietary arginine increased the egg production rate (LR) and average egg weight (AEW) of geese in a quadratic manner (P < 0.05). Dietary arginine had a quadratic effect on the contents of total protein (TP) and triglyceride (TG) (P < 0.05) in the serum. Dietary arginine quadratically decreased the content of malondialdehyde (MDA) and increased the activity of total superoxide dismutase (T-SOD) (P < 0.05). Dietary arginine supplementation linearly and quadratically increased the contents of immunoglobulin A (IgA) and immunoglobulin G (IgG), and linearly increased the content of nitric oxide (NO) (P < 0.05). In conclusion, dietary arginine supplementation can significantly improve the production performance, serum biochemicals, antioxidant capacity, and immunity of laying Wulong geese. Therefore, 0.3% arginine (actual content: 1.02%) is recommended in the diet.

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.

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 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.

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.

Effects of zinc and Bacillus subtilis on the reproductive performance, egg quality, nutrient digestion, intestinal morphology, and serum antioxidant capacity of geese breeders.

The effects of zinc (Zn) and Bacillus subtilis (B. subtilis) on reproductive performance, egg quality, nutrient digestion, intestine morphology, and antioxidant capacity were explored in geese breeders. Geese breeders (n = 120, 46-wk of age) were randomly assigned into 6 groups with 4 replicates of 5 birds each (1 male and 4 female). Breeders were fed diets with 2 levels of B. subtilis (2.5 × 109 and 5 × 109 CFU/kg) crossed with three levels of Zn (25, 45, and 65 mg/kg) for duration of 10-wk. The results showed that the egg laying rate (P < 0.05), fertility rate (P < 0.01), hatchability rate (P < 0.05), yolk color (P < 0.05), and the retentions of crude protein (P < 0.05), ether extract (P < 0.05) and phosphorus of geese breeders were improved by dietary supplementation of 5 × 109 CFU/kg B. subtilis and 25 mg or 45 mg/kg Zn. The serum T-SOD (P < 0.05) was increased by 45 mg/kg Zn supplementation. The serum T-AOC (P < 0.05) and retention of Zn (P < 0.05) were increased by 5 × 109 CFU/kg B. subtilis supplementation. The birds fed with 5 × 109 CFU/kg B. subtilis and 25 mg or 45 mg/kg Zn showed improved villus length (P < 0.01) and villus length/ crypt depth (P < 0.01) in both the jejunum and ileum. In conclusion, the combination of B. subtilis and Zn may have synergistic effects on these parameters, and dietary inclusion of 5 × 109 CFU/kg B. subtilis and 45 mg/kg Zn is recommended for improving the reproductive performance of geese breeders.

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.

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.

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.

Genome-wide DNA methylation analysis of Hashimoto's thyroiditis during pregnancy.

Hashimoto's thyroiditis (HT) during pregnancy is usually accompanied by an elevation of thyroid-stimulating hormone and a reduction of serum-free thyroxine during gestation, which may lead to abortion, preterm delivery, and reduced intellectual function of the offspring. Epigenetic alterations may provide important insights into genetic-environmental interactions in HT. Here, we examined global DNA methylation patterns in patients with HT during pregnancy. DNA was extracted from 13 women with HT during pregnancy (HTDP) and eight healthy pregnant women as a control group. Genome-wide methylation was detected with the use of an Illumina Human Methylation 850K Beadchip. A total of 652 differentially methylated positions (DMPs) and 27 differentially methylated regions (DMRs) were identified between the HTDP and control groups. GO analysis revealed that DMPs were significantly enriched in 540 GO terms, which included regulation of the differentiation of keratinocytes, T helper cell differentiation, and alpha-beta T-cell differentiation. Moreover, significant enrichment of KEGG pathways of the DMPs included mucin-type O-glycan biosynthesis, focal adhesion, and the insulin signaling pathway. The GO items associated with DMRs included muscle cell proliferation, response to biotic stimulus, anatomical structure formation involved in morphogenesis, and genes primarily involved in the FoxO signaling pathway. Finally, the DTNA gene was identified as the seed gene of functional epigenetic modules. In summary, the DNA methylation pattern of the HTDP group was distinct from that of the control group, and thus, changes in DNA methylation may influence the development of HT by regulation of the autoimmunity process.

Synergistic Effect of Diacylglycerol and Vitamin D in Ameliorating Dextran Sodium Sulfate-Induced Colitis in Rats.

Vitamin D (VD) has the function of antibacteria and protect intestinal mucosa. Diacylglycerol has the property of dissolving VD, anti-bacterial, and antioxidant effects. The purpose of this study was to explore the potentially synergistic effects of diacylglycerol and VD in ameliorating dextran sodium sulfate-induced colitis in rats. A 2 × 3 factorial design was used in this experiment, consisting of two levels of VD (2.5 and 5 µg/day) crossed with three levels of duck oil diacylglycerol (0.5, 1, and 2 mL/day). The experiment lasted for 2 weeks. Compared with the colitis group, the physiological indexes were altered in colitis rats treated with diacylglycerol and VD, the concentrations of the pro-inflammatory indices were significantly reduced, the antioxidant enzyme activities were significantly increased, the diversity of caecal microflora was significantly increased. Besides, the expression of PPARγ was up-regulated while the expression of NF-κBp65 was downregulated. The changes of all those measures were toward those in the Healthy Control, and the mostly appropriate combination was 1 mL/day of diacylglycerol plus 2.5 µg/day VD.