Identification of the genetic basis of the duck growth rate in multiple growth stages using genome-wide association analysis.

BACKGROUND: The genetic locus responsible for duck body size has been fully explained before, but the growth trait-related genetic basis is still waiting to be explored. For example, the genetic site related to growth rate, an important economic trait affecting marketing weight and feeding cost, is still unclear. Here, we performed genome wide association study (GWAS) to identify growth rate-associated genes and mutations. RESULT: In the current study, the body weight data of 358 ducks were recorded every 10 days from hatching to 120 days of age. According to the growth curve, we evaluated the relative and absolute growth rates (RGR and AGR) of 5 stages during the early rapid growth period. GWAS results for RGRs identified 31 significant SNPs on autosomes, and these SNPs were annotated by 24 protein-coding genes. Fourteen autosomal SNPs were significantly associated with AGRs. In addition, 4 shared significant SNPs were identified as having an association with both AGR and RGR, which were Chr2: 11483045 C>T, Chr2: 13750217 G>A, Chr2: 42508231 G>A and Chr2: 43644612 C>T. Among them, Chr2: 11483045 C>T, Chr2: 42508231 G>A, and Chr2: 43644612 C>T were annotated by ASAP1, LYN and CABYR, respectively. ASAP1 and LYN have already been proven to play roles in the growth and development of other species. In addition, we genotyped every duck using the most significant SNP (Chr2: 42508231 G>A) and compared the growth rate difference among each genotype population. The results showed that the growth rates of individuals carrying the Chr2: 42508231 A allele were significantly lower than those without this allele. Moreover, the results of the Mendelian randomization (MR) analysis supported the idea that the growth rate and birth weight had a causal effect on the adult body weight, with the growth rate having a greater effect size. CONCLUSION: In this study, 41 SNPs significantly related to growth rate were identified. In addition, we considered that the ASAP1 and LYN genes are essential candidate genes affecting the duck growth rate. The growth rate also showed the potential to be used as a reliable predictor of adult weight, providing a theoretical reference for preselection.

Transcriptomic analyses of the HPG axis-related tissues reveals potential candidate genes and regulatory pathways associated with egg production in ducks.

BACKGROUND: Egg production is one of the most important economic traits in the poultry industry. The hypothalamic-pituitary-gonadal (HPG) axis plays an essential role in regulating reproductive activities. However, the key genes and regulatory pathways within the HPG axis dominating egg production performance remain largely unknown in ducks. RESULTS: In this study, we compared the transcriptomic profiles of the HPG-related tissues between ducks with high egg production (HEP) and low egg production (LEP) to reveal candidate genes and regulatory pathways dominating egg production. We identified 543, 759, 670, and 181 differentially expressed genes (DEGs) in the hypothalamus, pituitary, ovary stroma, and F5 follicle membrane, respectively. Gene Ontology (GO) analysis revealed that DEGs from four HPG axis-related tissues were enriched in the "cellular component" category. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that the neuroactive ligand-receptor interaction pathway was significantly enriched based on DEGs commonly identified in all four HPG axis-related tissues. Gene expression profiles and Protein-Protein Interaction (PPI) network were performed to show the regulatory relationships of the DEGs identified. Five DEGs encoding secreted proteins in the hypothalamus and pituitary have interaction with DEGs encoding targeted proteins in the ovary stroma and F5 follicle membrane, implying that they were these DEGs might play similar roles in the regulation of egg production. CONCLUSIONS: Our results revealed that neuroactive ligand-receptor interaction pathway and five key genes(VEGFC, SPARC, BMP2, THBS1, and ADAMTS15) were identified as the key signaling pathways and candidate genes within the HPG axis responsible for different egg production performance between HEP and LEP. This is the first study comparing the transcriptomic profiles of all HPG axis-related tissues in HEP and LEP using RNA-seq in ducks to the best of our knowledge. These data are helpful to enrich our understanding of the classical HPG axis regulating the egg production performance and identify candidate genes that can be used for genetic selection in ducks.

Effect of thermal manipulation during embryogenesis on the promoter methylation and expression of myogenesis-related genes in duck skeletal muscle.

Avian embryos are an ideal system to investigate the effect of incubation temperature on embryonic development, but the characteristics and mechanisms of temperature effects on poultry embryonic myogenesis are unclear. In this study, we investigated the effect of increasing the incubation temperature by 1 °C on the expression of nine myogenesis-related genes in ducks and then explored the correlation between the alteration of promoter methylation and the expression of two of the nine genes under thermal manipulation (TM). The qRT-PCR results showed that TM during embryonic days (ED) 1-10 promoted (P < 0.05) the expression of genes in breast muscle (PAX3, PAX7, MYOG, MCK, SIX1, TNNC1) and leg muscle (MYOD, MYOG, MYF5, MCK, AKIRIN2, TNNC1). TM during ED10-20 promoted the expression of PAX3, MYF5 and MCK and inhibited AKIRIN2 expression in breast muscle (P < 0.05); however, it inhibited the expression of PAX3, PAX7, MYOD, MYOG, MYF5, SIX1, AKIRIN2 and TNNC1 and promoted MCK expression in leg muscle (P < 0.05). TM during ED20-27 inhibited the expression of genes in breast muscle (PAX7) and leg muscle (MYOD, MYOG, MYF5, TNNC1) and promoted MCK expression in breast and leg muscle (P < 0.05). Furthermore, with the Sequenom MassARRAY platform, it was observed that the average methylation level of AKIRIN2 (ED10) and TNNC1 (ED20) in leg muscle decreased (P < 0.05) after TM. Notably, we found significant (P < 0.05) inverse correlations between the methylation and mRNA levels of AKIRIN2 under TM during ED1-10 (r = - 0.969) and ED10-20 (r = - 0.805). Taken together, TM during ED1-10 was more favorable for improving duck myogenesis-related gene expression than TM during ED10-20 and ED20-27. TM during duck embryogenesis seemed to have a greater effect on the development of leg muscle than breast muscle and might alter AKIRIN2 expression by changing its promoter methylation status. These findings may be helpful to understand temperature effects on the muscle development of avian embryos and to explore the role of epigenetic regulation during this process.

Evidence in duck for supporting alteration of incubation temperature may have influence on methylation of genomic DNA.

Incubation temperature has an immediate and long-term influence on the embryonic development in birds. DNA methylation as an important environment-induced mechanism could serve as a potential link between embryos' phenotypic variability and temperature variation, which reprogrammed by DNA (cytosine-5)-methyltransferases (DNMTS) and Methyl-CpG binding domain proteins (MBPS) 3&5 (MBD3&5). Five genes in DNMTS and MBPS gene families were selected as target genes, given their important role in epigenetic modification. In this study, we aimed to test whether raising incubation temperature from 37.8°C to 38.8°C between embryonic days (ED) 1-10, ED10-20 and ED20-27 have effect on DNA methylation and whether DNMTS, MBPS play roles in thermal epigenetic regulation of early development in duck. Real-time quantitative PCR analysis showed that increased incubation temperature by 1°C has remarkably dynamic effect on gene expression levels of DNMTS and MBPS. Slight changes in incubation temperature significantly increased mRNA levels of target genes in breast muscle tissue during ED1-10, especially for DNMT1, DNMT3A and MBD5. In addition, higher temperature significantly increased enzyme activities of DNMT1 in leg muscle during ED10-20, liver tissue during ED1-10, ED20-27 and DNMT3A in leg muscle and breast muscle tissue during ED10-20. These results suggest that incubation temperature has an extended effect on gene expression levels and enzyme activities of DNMTS and MBPS, which provides evidence that incubation temperature may influence DNA methylation in duck during early developmental stages. Our data indicated that DNMTS and MBPS may involved in thermal epigenetice regulation of embryos during the early development in duck. The potential links between embryonic temperature and epigenetic modification need further investigation.

Impact of thermal stress during incubation on gene expression in embryonic muscle of Peking ducks (Anasplatyrhynchos domestica).

Changes in temperature will influence poultry embryonic muscle development. However, little is known about the changes in molecular processes impacted by incubation temperature in avians. In this study, we investigated the effects of increasing the incubation temperature by 1°C from day 11-20 on the embryonic and posthatch skeletal muscle development of the Peking duck, and identified the differentially expressed genes using RNA-seq of leg muscle tissues. The results showed that altering the incubation temperature had immediate and long-lasting effects on phenotypic changes in the embryonic and post-hatching muscle development. It was shown that expression levels of total 1370 genes were altered in muscle tissues by the thermal treatments. The gene ontology (GO) analyses indicated that cellular processes including metabolism, cell cycle, catalytic activity, and enzyme regulatory activity may have involved in the muscle mass impacted by thermal manipulation. TGF-beta and insulin pathways as two classical muscle development related pathways may also involve in regulating muscle mass. These data may be helpful for understanding the physiological and biochemical processes of muscle development under environmental treatments in embryonic avians.

Gene expression patterns, and protein metabolic and histological analyses for muscle development in Peking duck.

In this study, we aimed to use duck breast muscle and leg muscle, the 2 main productive muscle organs, as a model to elucidate the molecular mechanism controlling how the 2 muscles have different deposition capabilities, and to analyze the mechanisms facilitating duck muscle development posthatching. Peking duck breast muscle and leg muscle were collected 3, 7, and 16 wk posthatching. The morphology of the myofibers was observed by paraffin sectioning the muscles. The expression of genes involved in protein metabolism [mammalian target of rapamycin (mTOR), RPS6-p70-protein kinase (S6K), forkhead box O1 (FoxO1), muscle RING finger 1 (MuRF1), and atrogin-1 (MAFbx)] was detected using real-time quantitative PCR and Western blot assays, and the results indicated that breast muscle had a stronger capacity for both protein synthesis and protein degradation compared with leg muscle. Satellite cell frequency declined during muscle development in both tissues, and the expression of Pax3/7, satellite cell marker genes, was not significantly different between breast muscle and leg muscle. No notable apoptosis was observed in either tissue. The results of this study suggest that protein metabolism signaling is the main reason promoting duck skeletal muscle mass gain.

Influence of in ovo thermal manipulation on lipid metabolism in embryonic duck liver.

The growth and development of poultry embryos are easily affected by environmental factors, such as the incubation temperature and humidity. Metabolism, including lipid metabolism, during the embryonic stage is also important for the growth and development of poultry. Our study aimed to investigate the effects of incubation temperature on embryonic lipid metabolism in the liver of ducks. To fully evaluate the effects, thermal treatment was given between embryonic ages 11 and 24 days with a 1 °C higher incubation temperature than the control group, and lipid metabolism parameters in the liver and blood serum were analyzed both at embryonic stage day 20 and 2 weeks post-hatching. Our results showed no significant changes in the embryonic stage in total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C) in the blood serum (P>0.05). Additionally, the mRNA expression levels and enzyme activities of fatty acid synthase (FAS), acetyl CoA carboxylase (ACC), and elongase of very long chain fatty acids (ELOVL) did not show significant changes either in the embryonic stage or at hatching day 20 (P>0.05). However, there were significant changes in the gene expression and enzyme activities of TC, LDL-C and FAS at post-hatching stages (P≤0.05). These results may indicate that the thermal treatment has less influence on lipid metabolism in the embryonic stage but has a much stronger effect in the post-hatching stage.

Research Note: Integrated transcriptomic and metabolomic analysis reveals potential candidate genes and regulatory pathways associated with egg weight in ducks.

Egg weight is an important indicator of egg phenotypic traits, which directly affects the economic benefits of the poultry industry. In the present research, laying ducks were classified into high egg weight (HEW) and light egg weight (LEW) groups. To reveal the underlying mechanism that may be responsible for the egg weight difference, the integrated analysis of transcriptomes and serum metabolomics was performed between the two groups. The results showed extremely significant differences (P < 0.01) in the total egg weight at 300 d, and average egg weight between the HEW and LEW groups. 733, 591, 82, and 74 differentially expressed genes (DEGs) were identified in the liver, magnum, F1, and F5 (hierarchical follicles) follicle membrane, respectively. The candidate genes were screened further from the perspective of forming an egg. In terms of egg yolk formation, the functional analysis revealed fatty acid metabolism-related pathways account for 36% of the liver's top pathways, including fatty acid biosynthesis, folate biosynthesis, fatty acid metabolism, and glycerol lipid metabolism pathways. FASN gene was identified as the key candidate gene by comprehensive analysis of gene expression and protein-protein interaction (PPI) network. In the follicle membrane, the DEGs were mainly enriched in protein processing in the endoplasmic reticulum, and MAPK signaling pathway, and HSPA2, HSPA8, BAG3 genes were identified as crucial candidate genes. In terms of egg white formation, the functional analysis revealed protein metabolism-related pathways account for 40% of the magnum's top pathways, which includes protein processing in the endoplasmic reticulum pathway. HSP90AA1 and HSPA8 genes were identified as key candidate genes. In addition, the integrated transcriptomic and metabolomic analysis showed that arginine and proline metabolism pathways could contribute to differences in egg weight. Thus, we speculated that the potential candidate genes, regulatory pathways, and metabolic biomarkers mentioned above might be responsible for the egg weight difference. These findings might provide a theoretical basis for improving the egg weight of ducks.

[Automatic classification of lip color based on SVM in traditional Chinese medicine inspection].

The lip color of a person is closely related to his or her health in the visual diagnosis of traditional Chinese medicine (TCM). The traditional method to judge the color of lips is through observing by a TCM doctor. The diagnosis result is affected not only by the doctor's knowledge and diagnosis experience, but also by the light, temperature and other environmental impacts. For these reasons, sometimes different doctors may make different judgement for the same lips. So it is urgently needed that an objective evaluation as reference for doctors can be obtained. A method based on support vector machine (SVM) that classifies lip color by computer automatically is presented in the present paper. Firstly, nine features of lip color in Hue, Saturation and Intensity (HSI) color space were extracted. Then, according to different combinations of these features five different experiments were conducted. By comparing the results of these experiments, it was discovered that the mean value is one of the most important features for the lip color. The overall effect of classification is better when the mean value and variance of HSI were chosen than other characteristics. In addition, experiments results demonstrated that the accuracy rate of classification is not improved when more features were adopted. The objective of the present paper is to select the appropriate characteristics and to combine them effectively to classify lip colors.

Evolutionary Pattern and Regulation Analysis to Support Why Diversity Functions Existed within PPAR Gene Family Members.

Peroxisome proliferators-activated receptor (PPAR) gene family members exhibit distinct patterns of distribution in tissues and differ in functions. The purpose of this study is to investigate the evolutionary impacts on diversity functions of PPAR members and the regulatory differences on gene expression patterns. 63 homology sequences of PPAR genes from 31 species were collected and analyzed. The results showed that three isolated types of PPAR gene family may emerge from twice times of gene duplication events. The conserved domains of HOLI (ligand binding domain of hormone receptors) domain and ZnF_C4 (C4 zinc finger in nuclear in hormone receptors) are essential for keeping basic roles of PPAR gene family, and the variant domains of LCRs may be responsible for their divergence in functions. The positive selection sites in HOLI domain are benefit for PPARs to evolve towards diversity functions. The evolutionary variants in the promoter regions and 3' UTR regions of PPARs result into differential transcription factors and miRNAs involved in regulating PPAR members, which may eventually affect their expressions and tissues distributions. These results indicate that gene duplication event, selection pressure on HOLI domain, and the variants on promoter and 3' UTR are essential for PPARs evolution and diversity functions acquired.

Transcriptional Profiling Identifies Location-Specific and Breed-Specific Differentially Expressed Genes in Embryonic Myogenesis in Anas Platyrhynchos.

Skeletal muscle growth and development are highly orchestrated processes involving significant changes in gene expressions. Differences in the location-specific and breed-specific genes and pathways involved have important implications for meat productions and meat quality. Here, RNA-Seq was performed to identify differences in the muscle deposition between two muscle locations and two duck breeds for functional genomics studies. To achieve those goals, skeletal muscle samples were collected from the leg muscle (LM) and the pectoral muscle (PM) of two genetically different duck breeds, Heiwu duck (H) and Peking duck (P), at embryonic 15 days. Functional genomics studies were performed in two experiments: Experiment 1 directly compared the location-specific genes between PM and LM, and Experiment 2 compared the two breeds (H and P) at the same developmental stage (embryonic 15 days). Almost 13 million clean reads were generated using Illumina technology (Novogene, Beijing, China) on each library, and more than 70% of the reads mapped to the Peking duck (Anas platyrhynchos) genome. A total of 168 genes were differentially expressed between the two locations analyzed in Experiment 1, whereas only 8 genes were differentially expressed when comparing the same location between two breeds in Experiment 2. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes pathways (KEGG) were used to functionally annotate DEGs (differentially expression genes). The DEGs identified in Experiment 1 were mainly involved in focal adhesion, the PI3K-Akt signaling pathway and ECM-receptor interaction pathways (corrected P-value<0.05). In Experiment 2, the DEGs were associated with only the ribosome signaling pathway (corrected P-value<0.05). In addition, quantitative real-time PCR was used to confirm 15 of the differentially expressed genes originally detected by RNA-Seq. A comparative transcript analysis of the leg and pectoral muscles of two duck breeds not only improves our understanding of the location-specific and breed-specific genes and pathways but also provides some candidate molecular targets for increasing muscle products and meat quality by genetic control.