Genome-wide association analysis identifies candidate genes for carcass yields in Peking ducks.

Poultry meat, particularly Peking ducks, holds a significant global market share, prized for their high meat yield and fat content. However, understanding of the molecular genetic mechanisms influencing carcass yield in ducks is limited. This research aims to use genome-wide association analysis to uncover single-nucleotide polymorphisms influencing carcass yield in Peking ducks, followed by identifying candidate genes linked to carcass traits. In this study, we analyzed seven traits of 643 Peking ducks at age 42 days and identified novel loci associated with these traits. A total of 35 significant loci were detected, with eight SNPs reaching genome-wide significance. KIF20B, AGBL5, SGSM1, MRO, PLAG1, XKR4, and TGS1 were considered as important candidate genes influencing carcass yield in ducks. This study adds to the list of genes affecting Peking duck body traits, aiding marker-assisted breeding and enhancing economic yield.

Application of transcriptome in time analysis and donor characterization in blood samples.

As an effective supplement to the current forensic DNA typing and one of the research hotpots in forensic science, the in-depth mining and characterization of biological evidence can provide rich and reliable clues for case investigation. In this study, the time-dependent variations of transcriptome were confirmed in in vitro blood samples within 0-168 days and a random forest model was established to realize the classification of blood samples with different TSD (time since deposition). Meanwhile, significant differences were observed in the transcripts of blood samples with different smoking habits and genders within a certain time period. HLA-DRB1, HLA-DQB1 and HLA-DQA2 were identified as markers for smoking habit identification, while the transcripts for RPS4Y1 and EIF1AY from the non-recombining region of the Y chromosome (NRY) were identified as markers for male sex identification. Thus, this study provides a theoretical foundation and experimental strategy for establishing a transcriptome-based method for characterizing blood sample retention time and donor characteristics in the field of forensic investigation.

Genome-wide association study reveals novel loci associated with feeding behavior in Pekin ducks.

BACKGROUND: Feeding behavior traits are an essential part of livestock production. However, the genetic base of feeding behavior traits remains unclear in Pekin ducks. This study aimed to determine novel loci related to feeding behavior in Pekin ducks. RESULTS: In this study, the feeding information of 540 Pekin ducks was recorded, and individual genotype was evaluated using genotyping-by-sequencing methods. Genome-wide association analysis (GWAS) was conducted for feeding behavior traits. Overall, thirty significant (P-value < 4.74E-06) SNPs for feeding behavior traits were discovered, and four of them reached the genome-wide significance level (P-value < 2.37E-07). One genome-wide significance locus associated with daily meal times was located in a 122.25 Mb region on chromosome 2, which was within the intron of gene ubiquitin-conjugating enzyme E2 E2 (UBE2E2), and could explain 2.64% of the phenotypic variation. This locus was also significantly associated with meal feed intake, and explained 2.72% of this phenotypic variation. CONCLUSIONS: This study is the first GWAS for feeding behavior traits in ducks. Our results provide a list of candidate genes associated with feeding behavior, and also help to better understand the genetic mechanisms of feeding behavior patterns in ducks.

Genome-wide association study of the level of blood components in Pekin ducks.

Blood components are considered to reflect nutrient metabolism and immune activity in both humans and animals. In this study, we measured 12 blood components in Pekin ducks and performed genome-wide association analysis to identify the QTLs (quantitative trait locus) using a genotyping-by-sequencing strategy. A total of 54 QTLs were identified for blood components. One genome-wide significant QTL for alkaline phosphatase was identified within the intron-region of the OTOG gene (P = 1.31E-07). Moreover, 21 genome-wide significant SNPs for the level of serum cholinesterase were identified on six different scaffolds. In addition, for serum calcium, one genome-wide significant QTL was identified in the upstream region of gene RAB11B. These results provide new markers for functional studies in Pekin ducks, and several candidate genes were identified, which may provide additional insights into specific mechanisms for blood metabolism in ducks and their potential application for duck breeding programs.

Genome-wide association study of bone quality and feed efficiency-related traits in Pekin ducks.

Feeding and bone traits are vital for breeding and reproduction in the commercial duck industry. In this study, we performed a genome-wide association study for feeding and bone traits in a population of 540 lean-type Pekin ducks, followed by genotyping-by-sequencing procedures. The genetic parameters of feeding and bone traits were also estimated using genomic information. In total, seventy-eight significant SNPs were determined, and eleven of them reached the genome-wide significant level for 7 traits except for body weight at 42-day old. A peak of genome-wide significant SNPs was detected on chromosome 2 for feed conversion ratio (P-value = 7.46E-11), and the top SNP (P-value = 2.23E-08) for bone-breaking strength was also obtained in the upstream of gene RAPGEF5. This study provided a list of novel markers and candidate genes associated with feeding and bone traits in Pekin ducks, which could contribute to the genetic selection in duck breeding.

Genome-wide association study reveals novel loci associated with body size and carcass yields in Pekin ducks.

BACKGROUND: Pekin duck products have become popular in Asia over recent decades and account for an increasing market share. However, the genetic mechanisms affecting carcass growth in Pekin ducks remain unknown. This study aimed to identify quantitative trait loci affecting body size and carcass yields in Pekin ducks. RESULTS: We measured 18 carcass traits in 639 Pekin ducks and performed genotyping using genotyping-by-sequencing (GBS). Loci-based association analysis detected 37 significant loci for the 17 traits. Thirty-seven identified candidate genes were involved in many biological processes. One single nucleotide polymorphism (SNP) (Chr1_140105435 A > T) located in the intron of the ATPase phospholipid transporting 11A gene (ATP11A) attained genome-wide significance associated with five weight traits. Eight SNPs were significantly associated with three body size traits, including the candidate gene plexin domain containing 2 (PLXDC2) associated with breast width and tensin 3 (TNS3) associated with fossil bone length. Only two SNPs were significantly associated with foot weight and four SNPs were significantly associated with heart weight. In the gene-based analysis, three genes (LOC101791418, TUBGCP3 (encoding tubulin gamma complex-associated protein 3), and ATP11A) were associated with four traits (42-day body weight, eviscerated weight, half-eviscerated weight, and leg muscle weight percentage). However, no loci were significantly associated with leg muscle weight in this study. CONCLUSIONS: The novel results of this study improve our understanding of the genetic mechanisms regulating body growth in ducks and thus provide a genetic basis for breeding programs aimed at maximizing the economic potential of Pekin ducks.

De novo transcriptome assembly and identification of genes associated with feed conversion ratio and breast muscle yield in domestic ducks.

Breast muscle yield and feed conversion efficiency are the major breeding aims in duck breeding. Understanding the role of specific transcripts in the muscle and small intestine might lead to the elucidation of interrelated biological processes. In this study, we obtained jejunum and breast muscle samples from two strains of Peking ducks that were sorted by feed conversion ratio (FCR) and breast muscle percentage into two-tailed populations. Ten RNA-Seq libraries were developed from the pooled samples and sequenced using the Hiseq2000 platform. We created a reference duck transcript database using de novo assembly methods, which included 16 663 irredundant contigs with an N50 length of 1530 bp. This new duck reference cDNA dataset significantly improved the mapping rate for RNA-Seq data, from 50% to 70%. Mapping and annotation were followed by Gene Ontology analysis, which showed that numerous genes were differentially expressed between the low and high FCR groups. The differentially expressed genes in the jejunum were enriched in biological processes related to immune response and immune response activation, whereas those in the breast muscle were significantly enriched in biological processes related to muscle cell differentiation and organ development. We identified new candidate genes, that is, PCK1, for improving the FCR and breast muscle yield of ducks and obtained much better reference duck transcripts. This study suggested that de novo assembly is essential when applying transcriptome analysis to a species with an incomplete genome.

Genome-Wide Association Analysis Identifies Important Haplotypes and Candidate Gene XKR4 for Body Size Traits in Pekin Ducks.

Body size is an important growth indicator in ducks and is a primary selection criterion for physical improvement. An excessively rapid growth rate in meat ducks can result in excessive body size, which may hinder subsequent processing and slaughter operations. However, only a few molecular markers related to body size have been studied in meat ducks. In this study, we performed a genome-wide association study (GWAS) to identify candidate genes and QTLs affecting body length (BL), keel bone length (KBL), neck length (NL), and breast width (BrW) in Pekin ducks (Anas platyrhynchos domestica). Our results indicate the significant SNP for NL is located within a pseudogene, whereas the significant SNP for BrW is located in an intergenic region. More importantly, our analysis identified a haplotype that was significantly associated with both BL and KBL. This haplotype, containing 48 single-nucleotide polymorphisms (SNPs), is localized within the XKR4 gene. The identification of this haplotype suggests that XKR4 may be a key candidate gene influencing BL and KBL in Pekin ducks. These findings have important implications for the breeding and genetic improvement of Pekin ducks, and provide valuable insights into the genetic architecture of body size traits in this species.

Genome-Wide Association Analysis and Genetic Parameters for Egg Production Traits in Peking Ducks.

Egg production traits are crucial in the poultry industry, including age at first egg (AFE), egg number (EN) at different stages, and laying rate (LR). Ducks exhibit higher egg production capacity than other poultry species, but the genetic mechanisms are still poorly understood. In this study, we collected egg-laying data of 618 Peking ducks from 22 to 66 weeks of age and genotyped them by whole-genome resequencing. Genetic parameters were calculated based on SNPs, and a genome-wide association study (GWAS) was performed for these traits. The SNP-based heritability of egg production traits ranged from 0.09 to 0.54. The GWAS identified nine significant SNP loci associated with AFE and egg number from 22 to 66 weeks. These loci showed that the corresponding alleles were positively correlated with a decrease in the traits. Moreover, three potential candidate genes (ENSAPLG00020011445, ENSAPLG00020012564, TMEM260) were identified. Functional enrichment analyses suggest that specific immune responses may have a critical impact on egg production capacity by influencing ovarian function and oocyte maturation processes. In conclusion, this study deepens the understanding of egg-laying genetics in Peking duck and provides a sound theoretical basis for future genetic improvement and genomic selection strategies in poultry.

Icariin ameliorates behavioral deficits and neuropathology in a mouse model of multiple sclerosis.

Multiple sclerosis (MS) is a systemic inflammatory illness of the central nervous system that involves demyelinating lesions in the myelin-rich white matter and pathology in the grey matter. Despite significant advancements in drug research for MS, the disease's complex pathophysiology makes it difficult to treat the progressive forms of the disease. In this study, we identified a natural flavonoid compound icariin (ICA) as a potent effective agent for MS in ameliorating the deterioration of symptoms including the neurological deficit score and the body weight in a murine experimental autoimmune encephalomyelitis (EAE) model. These improvements were associated with decreased demyelination in the corpus callosum and neuron loss in the hippocampus and cortex confirmed by immunohistochemistry analysis. Meanwhile, it was observed that the activation of microglia in cerebral cortex and hippocampus were inhibited followed by the neuroinflammatory cytokines downregulation such as IL-1ß, IL-6 and TNF-α after ICA treatment, which was probably attributable to the suppression of microglial NLRP3 inflammasome activation. Additionally, molecular docking also revealed the binding force of ICA to NLRP3 inflammasome protein complexes in vitro. Taken together, our findings have demonstrated that ICA, as pleiotropic agent, prevents EAE-induced MS by improving demyelination and neuron loss, which interferes with the neuroinflammation via microglial NLRP3 inflammasome activation.

Tetrahydroxy stilbene glycoside ameliorates neuroinflammation for Alzheimer's disease via cGAS-STING.

Alzheimer's disease (AD), also known as senile dementia, is the most common degenerative disease of the central nervous system. Neuroinflammation is currently believed to be a crucial factor in the progression of AD, while its exact mechanism remains unclear. In this study, we demonstrated that AD transgenic mice exhibited cognitive deficits accompanied by the elevated serum and brain inflammation. Treating with a natural active ingredient tetrahydroxy stilbene glucoside (TSG) from the Chinese herb Polygonum multiflorum that has been well known for its unique anti-aging effect, learning-memory ability of AD mice was distinctly improved. Meanwhile, it was observed that the expressions of serum inflammatory cytokines and the activation of microglia in cerebral cortex and hippocampus were suppressed after TSG treatment, which was probably attributable to the decrease of cyclic GMP-AMP synthase (cGAS) and stimulator of interferon genes (STING) triggered immune response and NLRP3 inflammasome activation. Furthermore, cell culture experiments employing LPS combined with IFN-γ induced microglia activation showed that TSG reversed the polarization status of M1-type microglia to restore the quiescence, and cGAS-STING elevation was observed in the activated microglia and normalized by TSG incubation. In addition, TSG suppressed the production of inflammatory cytokines such as IL-1ß, IL-6, TNF-α, IFN-α and IFN-ß, as well as the expression of IFN regulatory proteins such as IFIT1 and IRF7 in the LPS/IFN-γ-stimulated inflammatory response in BV2 cell. Finally, it was also verified that TSG are, in part, through a cGAS-STING dependent pathway and triggered NLRP3 inflammasome activation to inhibit neuroinflammation through interfering with cGAS-STING inhibitors. Taken together, our findings highlight the health benefits of TSG and its potential application in preventing cognitive disorders by inhibiting neuroinflammation through cGAS-STING signaling pathway in AD.

Exploration in the Mechanism of Zhisou San for the Treatment of Cough Variant Asthma Based on Network Pharmacology.

Background: Cough variant asthma (CVA) has no definitive diagnosis or pathogenic causes, and there is currently no effective and safe treatment. Methods: The network pharmacology was employed to investigate possible targets of Zhisou San (ZSS) in CVA treatment. The main chemical constituents of seven herbs in ZSS were collected based on the TCMSP. To explain the main mechanism, we sequentially screened the targets of each active ingredient and constructed the network of "herb-ingredient-target-disease." The core targets of ZSS were further confirmed by the molecular docking analysis. Furthermore, pulmonary function, histopathology, and biochemical assays in mice were used to investigate the effect of ZSS on the treatment of CVA. Results: A total of 137 active ingredients and 86 potential targets for the ZSS in the treatment of CVA were screened, which were connected with the regulation of inflammatory response and immune balance, such as IL-17 signaling pathway, Th17 cell differentiation, TNF signaling pathway, Toll-like receptor signaling pathway, MAPK signaling pathway, T-cell receptor signaling pathway, Th1 and Th2 cell differentiation, and other signaling pathways closely related to the pathogenesis of CVA. Thereinto, 29 core targets contained 8 of the highest scores and could evidently bind to components such as stigmasterol, quercetin, stemoninine B, luteolin, and ß-sitosterol predicted by molecular docking. Furthermore, experiments in vivo were conducted for further validation that ZSS had essential effects on lung function and histopathology as well as the inflammatory state in CVA mice, which was significantly related to regulating the Th17/Treg immune balance to reduce inflammation as the important pharmacological mechanism. Conclusion: This study revealed that ZSS has multicomponent and multipathway characteristics of ZSS in the treatment of CVA, which was primarily associated with inflammation and Th17/Treg immune balance. This study provides a scientific foundation for systematically elaborating the pharmacological activities and mechanism of ZSS, as well as explaining the reliability of the TCM compatibility theory.

Tetrahydroxy stilbene glucoside alters neurogenesis and neuroinflammation to ameliorate radiation-associated cognitive disability via AMPK/Tet2.

Along with the extensive application of radiation in medical, military and other fields, human beings carry a greater risk of exposure to radiation environment that causes a range of physical injure, particularly to the brain in cognition. However, the radiation-associated cognitive disability is poorly understood and there is no effective prevention or long-term treatment. Here, we demonstrate that neurogenesis and neuroinflammation disorder are primarily involved in the pathophysiological basis of irradiation-induced cognitive decline. Furthermore, we discovered that tetrahydroxy stilbene glucoside (TSG), a natural active ingredient from Heshouwu that has been well known for its unique anti-aging effect as the Chinese herb, can be a promising mitigator to improve learning-memory ability by facilitating the neurogenesis in the proliferation and differentiation of the surviving neural progenitor cells via AMPK/Tet2, and attenuating the neuroinflammation in the microglial NLRP3 inflammasomes activation via AMPK in vivo. Additionally, TSG was also revealed to activate AMPK by molecular docking and kinase enzyme system assay in vitro. Taken together, our findings identify TSG, as the AMPK activator, prevents radiation-induced cognitive dysfunction by regulating neurogenesis and neuroinflammation via AMPK/Tet2 in rodents, and represents a very promising candidate for developing drugs that can be used for radiation-associated brain injury.

Comparison of carcass and meat quality traits between lean and fat Pekin ducks.

OBJECTIVE: According to market demand, meat duck breeding mainly includes 2 breeding directions: lean Pekin duck (LPD) and fat Pekin duck (FPD). The aim of the present study was to compare carcass and meat quality traits between 2 strains, and to provide basic data for guidelines of processing and meat quality improvement. METHODS: A total of 62 female Pekin ducks (32 LPDs and 30 FPDs) were slaughtered at the age of 42 days. The live body weight and carcass traits were measured and calculated. Physical properties of breast muscle were determined by texture analyzer and muscle fibers were measured by paraffin sections. The content of inosine monophosphate (IMP), intramuscular fat (IMF) and fatty acids composition were measured by high-performance liquid chromatography, Soxhlet extraction method and automated gas chromatography respectively. RESULTS: The results showed that the bodyweight of LPDs was higher than that of FPDs. FPDs were significantly higher than LPDs in subcutaneous fat thickness, subcutaneous fat weight, subcutaneous fat percentage, abdominal fat percentage and abdominal fat shear force (p<0.01). LPDs were significantly higher than FPDs in breast muscle thickness, breast muscle weight, breast muscle rate and breast muscle shear force (p<0.01). The muscle fiber average area and fiber diameter of LPDs were significantly higher than those of FPDs (p<0.01). The muscle fiber density of LPDs was significantly lower than that of FPDs (p<0.01). The IMF of LPDs in the breast muscle was significantly higher than that in the FPDs (p<0.01). There was no significant difference between the 2 strains in IMP content (p>0.05). The polyunsaturated fatty acid content of LPDs was significantly higher than that of FPDs (p<0.01), and FPDs had higher saturated fatty acid and monounsaturated fatty acid levels (p<0.05). CONCLUSION: Long-term breeding work resulted in vast differences between the two strains Pekin ducks. This study provides a reference for differences between LPD and FPD that manifest as a result of long-term selection.

Selection response and genetic parameter estimation of feeding behavior traits in Pekin ducks.

Body weight-related traits and feeding behavior traits are important in poultry breeding and production. To investigate the heritability of feeding behavior and their genetic correlation with body weight-related traits in Pekin ducks, 5,594 Pekin ducks were selected. The information about body weight-related traits and feeding behavior from 3 to 6 wk of age were recorded by automatic electronic feeders. The heritability estimates for body weight, residual feed intake, and feeding behavior traits are relatively high (ranging from 0.29 to 0.65). We observed that total feed intake, meal feed intake, body weight at the age of 3 wk, and daily body weight gain had strong positive genetic correlations with body weight at the age of 6 wk. Moreover, body weight at the age of 3 wk also showed a positive genetic correlation with the feed conversion ratio (0.33). Total feeding time, daily feed intake, and feeding rate had significant positive phenotypic correlations with feed efficiency. However, the average interval between meals, the number of daily visits, and the number of meals all had a low genetic or phenotypic relationship with body weight and feed efficiency. In conclusion, our study revealed that body weight, residual feed intake, and feeding behavior traits were all highly heritable traits, and the selection for certain feeding behaviors could improve feed efficiency in Pekin ducks. This study is the first report about genetic parameter estimates about feeding behaviors in ducks based on large datasets and provides solid data for genetic study in ducks.

Genome-Wide Association Study of Growth and Feeding Traits in Pekin Ducks.

Growth rate and feeding efficiency are the most important economic traits for meat animals. Pekin duck is one of the major global breeds of meat-type duck. This study aims to identify QTL for duck growth and feeding efficiency traits in order to assist artificial selection. In this study, the growth and feeding related phenotypes of 639 Pekin ducks were recorded, and each individual genotype was evaluated using a genotyping-by-sequencing (GBS) protocol. The genetic parameters for growth and feeding efficiency related traits were estimated. Genome-wide association analysis (GWAS) was then performed for these traits. In total, 15 non-overlapping QTLs for the measured traits and 12 significant SNPs for feed efficiency traits were discovered using a mixed linear model. The most significant loci of feed intake (FI) is located in a 182Mb region on Chr1, which is downstream of gene RNF17, and can explain 2.3% of the phenotypic variation. This locus is also significantly associated with residual feed intake (RFI), and can explain 3% of this phenotypic variation. Among 12 SNPs associated with the feed conversion ratio (FCR), the most significant SNP (P-value = 1.65E-06), which was located in the region between the 3rd and 4th exon of the SORCS1 gene on Chr6, explained 3% of the phenotypic variance. Using gene-set analysis, a total of two significant genes were detected be associated with RFI on Chr1. This study is the first GWAS for growth and feeding efficiency related traits in ducks. Our results provide a list of candidate genes for marker assisted selection for growth and feeding efficiency, and also help to better understand the genetic mechanisms of feed efficiency and growth in ducks.

In vivo prediction of the carcass fatness using live body measurements in Pekin ducks.

The purpose of this study was to evaluate the correlation between live body measurements and several fat traits in Pekin ducks, and ultimately to formulate multiple regression equations for the in vivo estimation of the carcass fatness of Pekin ducks. Several traits were measured in a total of 208 Pekin ducks aged 6 wk (107 males and 101 females). All ducks were weighed and measured for a set of body measurements including live body weight, body slope length, breast muscle thickness, skin fat thickness, chest width, keel length, and neck length. The breast muscle thickness and skin fat thickness was measured using B-scan sonography. Carcass information, including eviscerated weight, subcutaneous fat with skin weight, and abdominal fat weight, was collected after slaughter. Our results revealed that sex effects on most traits were significant (P < 0.05), and that the weight of subcutaneous fat with skin was significantly correlated with live body weight (r = 0.57 to 0.71, P < 0.01). Four additional traits of males were closely correlated with the weight of subcutaneous fat with skin, namely breast muscle thickness (r = 0.20, P < 0.01), skin fat thickness (r = 0.43, P < 0.01), chest width (r = 0.24, P < 0.01), and neck length (r = 0.20, P < 0.05). The abdominal fat weight, percentage of fat, and percentage of subcutaneous fat with skin of ducks were significantly correlated with live body weight (r = 0.38 to 0.43, P < 0.01), and skin fat thickness (r = 0.38 to 0.49, P < 0.01). These traits provided the basis for constructing regression equations to predict weight (or percentage) of subcutaneous fat and abdominal fat with high values of coefficients of multiple correlation (R) between the dependent variable and the independent variables. Two equations were verified to be applicable in other duck groups, with high accuracy, as more than 80% of estimated values were within the margin of error (<10%), compared with the actual values.

[Polymorphisms analysis of mitochondrial DNA in coding area].

OBJECTIVE: To analyze mitochondrial DNA (mtDNA) polymorphisms in coding area and provide a theoretical basis for applying in forensic science. METHODS: The primers of 8162F/8483R and 13070F/13299R were designed according to the Anderson's sequence. Using PCR-sequencing method to detect polymorphisms of mtDNA nt8162-8483 and nt13070-13299. RESULTS: The lengths of the amplicons were 322 bp and 230 bp respectively. There were 24 mitochondrial haplotypes defined by 21 variable positions in both regions. The gene diversity was estimated at 0.751 1, and the probability of two randomly selected individuals having identical mtDNA types was 0.256 4. CONCLUSION: The polymorphic sites within mtDNA coding area can be useful in combination with mtDNA control region in order to increase the discrimination power.