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Previous studies have shown that the feather growth rate of chicks is determined by two alleles located on the sex chromosome Z; however, in chicken production, feathering is usually not consistently controlled by the sex chromosome. To identify whether the feathering rate is related to autosomal inheritance, whole-genome resequencing was performed in eight chickens with slow- and fast-feathering rate. A total of 54,984 autosomal single nucleotide polymorphisms (SNPs) were identified, including 393 and 376 exonic SNPs in slow-feathering and fast-feathering chickens, respectively. Mutated genes were mainly involved in response to stimuli and growth and reproduction processes. Mutated genes related to slow-feathering rate were mainly involved in wingless-type MMTV integration site signaling pathway and mitogen-activated protein kinase signaling pathway, whereas mutated genes associated with fast-feathering rate were primarily enriched in autophagy, calcium signaling pathway, extracellular matrix-receptor interaction, and Focal adhesion processes. Importantly, two SNPs, involved in feather development, were found in the exonic regions of Wnt signaling genes. These results shed new light on the relationship between genetic mutation and feather growth rate from the perspective of autosomal inheritance and may have economic significance in chicken breeding. [ABSTRACT FROM AUTHOR]

Functional studies have revealed miRNAs play pivotal roles in ovulation and ovary development in mammalians, whereas little is known about the miRNA function in ducks. In this study, miRNA deep sequencing in the ovary tissues was carried out to obtain the miRNA profile from ovaries before oviposition (BO) and after oviposition (AO) in Jinding duck. Overall, an average of 23,128,075 and 26,020,523 reads were identified in the BO and AO samples, respectively, and 6739 miRNAs were identified from them through further mapping and analysis. Besides, 1570 miRNAs were identified as differentially expressed miRNAs compared with BO, including 493 miRNAs up-regulated and 1077 down-regulated in AO. Moreover, 2291 target genes were predicted from 443 significantly differentially expressed miRNAs. In addition, GO and KEGG pathway analysis indicated that target genes were enriched in some basic cell metabolism pathways as well as the productive pathways such as MAPK signaling pathway, gonadotropin-releasing hormone signaling pathway, TGF-beta signaling pathway which had been significantly changed. Our results helped to replenish the duck miRNA database and illustrate the potential mechanism of miRNA function in duck ovary development and reproduction process. [ABSTRACT FROM AUTHOR]

Highlights • Turbulence flow contributes to the excessive convective heat losses for the birds. • Uniform indoor air movement reduce the temperature at the end of the poultry house. • Side-wall air inlets placed at the middle of the house reduce the temperature at the end of the house. • Side-wall windows have strong effects on the indoor environmental parameters. Abstract Ventilation system is crucial for poultry houses to control the indoor climate and air quality. The tunnel ventilation system is widely applied for large-scale poultry buildings in China but only limited scientific researches regarding the flow pattern, temperature distribution and design criteria are available in the literature. Thanks to the fast development of computer technology, Computational Fluid Dynamics (CFD) techniques were used in present study to investigate the indoor air movement, air temperature and relatively humidity. A three-dimensional CFD model was built according to the real dimensions of a laying hen house and the model was validated by comparing the simulation results with the field measurements at 30 positions. Meanwhile, statistical analysis was performed to determine the differences between different boundary conditions regarding the agreement between measured and CFD simulated results. Optimization of air inlet configurations was performed by using the validated CFD model and it was found that the uniformity of indoor air movement could prevent excessive local convective heat losses and reduce the temperature at the end of the house. Furthermore, the air inlets placed at the middle of the side wall could significantly reduce the high temperature expected at the end of the building without using extra energy, which is especially important for large-scale poultry farms with long buildings. The performance of side-wall windows was also examined and preliminary guidance was provided to effectively regulate the indoor climate by using these windows with the help of environmental monitoring systems. The present study contributes to the understanding and design of the tunnel ventilation system used in poultry houses. [ABSTRACT FROM AUTHOR]

Studies have shown that prebiotics can affect meat quality; however, the underlying mechanisms remain poorly understood. This study aimed to investigate whether prebiotics affect the flavor of chicken meat via the gut microbiome and metabolome. The gut content was collected from chickens fed with or without prebiotics (galacto-oligosaccharides or xylo-oligosaccharides) and subjected to microbiome and metabolome analyses, whereas transcriptome sequencing was performed using chicken breast. Prebiotic supplementation yielded a slight improvement that was not statistically significant in the growth and production performance of chickens. Moreover, treatment with prebiotics promoted fat synthesis and starch hydrolysis, thus increasing meat flavor by enhancing lipase and α-amylase activity in the blood of broiler chickens. The prebiotics altered the proportions of microbiota in the gut at different levels, especially microbiota in the phyla Bacteroidetes and Firmicutes, such as members of the Alistipe s, Bacteroides , and Faecalibacterium genera. Furthermore, the prebiotics altered the content of cecal metabolites related to flavor substances, including 8 types of lysophosphatidylcholine (lysoPC) and 4 types of amino acid. Differentially expressed genes (DEG s) induced by prebiotics were significantly involved in fatty acid accumulation processes, such as lipolysis in adipocytes and the adipocytokine signaling pathway. Changes in gut microbiota were correlated with metabolites, for example, Bacteroidetes and Firmicutes were positively and negatively correlated with lysoPC, respectively. Finally, DEGs interacted with cecal metabolites, especially meat-flavor-related amino acids and their derivatives. The findings of this study integrated and incorporated associations among the gut microbiota, metabolites, and transcriptome, which suggests that prebiotics affect the flavor of chicken meat. Chickens fed with the galacto-oligosaccharide or xylo-oligosaccharide prebiotics exhibited alterations in their growth and production performance, metabolites, microbiota, and transcriptome. [Display omitted] [ABSTRACT FROM AUTHOR]

Reducing abdominal fat (AF) accumulation and increasing the level of intramuscular fat (IMF) simultaneously is a major breeding goal in the poultry industry. To explore the different molecular mechanisms underlying AF and IMF, gene expression profiles in the breast muscle (BM) and AF from three chicken breeds were analyzed. A total of 4737 shared DEGs were identified between BM and AF, of which 2602 DEGs were upregulated and 2135 DEGs were downregulated in the BM groups compared with the AF groups. DEGs involved in glycerophospholipid metabolism and glycerolipid metabolism were potential regulators, resulting in the difference in lipid metabolite accumulation between IMF and AF. The PPAR signaling pathway was the most important pathway involved in tissue-specific lipid deposition. Correlation analysis showed that most representative DEGs enriched in the PPAR signaling pathway, such as FABP5, PPARG, ACOX1, and GK2, were negatively correlated with PUFA-enriched glycerophospholipid molecules. Most DEGs related to glycerophospholipid metabolism, such as GPD2, GPD1, PEMT, CRLS1, and GBGT1, were positively correlated with glycerophospholipid molecules, especially DHA- and arachidonic acid (ARA)-containing glycerophospholipid molecules. This study elucidated the molecular mechanism underlying tissue-specific lipid deposition and poultry meat quality. [ABSTRACT FROM AUTHOR]

• The mode of action on fatty acid composition and volatile flavor components of chicken meat were determined. • Fatty acids were significantly correlated with the volatile flavor compounds. • Module eigengenes 2 and 11 were more responsible for the age-dependent variation of fatty acid. Chicken meat is accompanied by physicochemical alterations during the process of growth and development, resulting in differences of nutritional value and meat flavor. The primary objective in the present study was to determine the mode of action on intramuscular fat content, serum lipid levels, fatty acid composition, and volatile flavor components of chicken meat. Negative correlations were observed between PUFA and aldehyde compounds and positive correlations were observed between PUFA and heterocyclic compounds. Intramuscular fat was correlated with only three volatile flavor compounds, indicating that the generation of volatile compounds was more dependent on the fatty acid composition rather than total intramuscular fat content. To explore the potential valuable biomarkers for sensorial and nutritional quality of chicken meat, a total of 12 temporal gene expression patterns were identified by transcriptomics. Module eigengenes 2 and 11 were significantly correlated with C14:0, C16:0, C18:1 cis-9, C18:2 cis-6, C18:3 n-3, C20:2, C20:3 n-6, C20:4 n-6, C22:6 n-3, C24:0, C24:0, C24:1, EFA, MUFA, PUFA, PUFA n-6 contents, and MUFA/SFA ratio, while were only significantly correlated with 1-octanol and 2-ethylhexyl glycidyl ether, respectively. Moreover, functional analysis of correlated-trait module eigengenes provided information on the explanation for the age-dependent variations for fatty acid composition and sensory quality of chicken meat. [ABSTRACT FROM AUTHOR]

Simple Summary: Hourly manure coverage proportion and area on the manure belt are key parameters for estimating ammonia emissions in poultry houses in order to provide environmental control suggestions and achieve the goals of precision poultry farming. In this study, experimental measurements were performed, and binary images were applied to provide new insights into the projected hourly manure coverage area on the manure belt at different layer hen ages. It was demonstrated that manure coverage proportion and area measured at different laying hen ages showed similar trends and values with four distinct stages within 48 h. In addition, statistical analyses found no significant correlation between the hourly increment of manure weight and the hourly increment of manure coverage proportion. The results from the present study are expected to serve as a fundamental input parameter for ammonia emission modeling to more accurately simulate the hourly indoor environment and provide effective mitigation strategies. The main advantage of having livestock, for example, the laying hens, in a controlled environment is that the optimum growth conditions can be achieved with accuracy. The indoor air temperature, humidity, gases concentration, etc., would significantly affect the animal performance, thus should be maintained within an acceptable range. In order to achieve the goals of precision poultry farming, various models have been developed by researchers all over the world to estimate the hourly indoor environmental parameters so as to provide decision suggestions. However, a key parameter of hourly manure area in the poultry house was missing in the literature to predict the ammonia emission using the recently developed mechanistic model. Therefore, in order to fill the gap of the understanding of hourly manure coverage proportion and area on the manure belt, experimental measurements were performed in the present study using laying hens from 10 weeks age to 30 weeks age. For each test, six polypropylene (pp) plates were applied to collect the manure dropped by the birds every hour, and photographs of the plates were taken at the same time using a pre-fixed camera. Binary images were then produced based on the color pictures to determine the object coverage proportion. It was demonstrated that for laying hens of stocking density around 14 birds/m2, the manure coverage proportion at the 24th hour after the most recent manure removal was about 60%, while the value was approximately 82% at the 48th hour. Meanwhile, for laying hens at different ages, the hourly increment of manure coverage proportion showed a similar pattern with four distinct stages within 48 h. The statistical analyses demonstrated no significant correlation between the hourly increment of manure weight and the hourly increment of manure coverage proportion. Finally, prediction models for estimating the hourly manure coverage proportion on the manure belt in typical laying hen houses were provided. [ABSTRACT FROM AUTHOR]

Simple Summary: A customized thermal-dynamic model was developed in the present study based on the ISO13790 Standard to predict the energy consumption of poultry houses with indoor environment control. A validation test was performed in a layer house by applying sensors and meters to record the indoor environmental parameters including temperature, relative humidity, gas concentrations and energy consumption. The validation results indicated that the simulated environmental parameters agree well with the measured data showing a similar overall trend with limited discrepancies. Meanwhile, the difference in total energy consumption between the predicted and measured value was only about 10.6%, indicating the model was able to accurately estimate the energy demand during poultry farming. The proposed model enables farmers to quickly check and optimize their management strategies to achieve precision livestock farming from the energy consumption perspective. Indoor environmental control is usually applied in poultry farming to ensure optimum growth conditions for birds. However, these control methods represent a considerable share of total energy consumption, and the trend of applying new equipment in the future for precision livestock farming would further increase energy demand, resulting in an increase in greenhouse gas emissions and management costs. Therefore, to ensure optimum efficiency of both energy use and livestock productivity, a customized hourly model was developed in the present study to interpret and analyze the electronically collected data. The modules for estimating indoor gas concentrations were incorporated into the present model, as this has not been properly considered in previous studies. A validation test was performed in a manure-belt layer house using sensors and meters to measure the indoor environmental parameters and energy consumption. The predicted results, including indoor temperature, relative humidity, carbon dioxide and ammonia concentrations, showed good agreement with the measured data, indicating a similar overall trend with acceptable discrepancies. Moreover, the corresponding differences between the measured and simulated energy consumption for heating, tunnel ventilation and base ventilation were 13.7, 7.5, and 0.1%, respectively. The total energy demand estimated by the model showed a limited discrepancy of approximately 10.6% compared with that measured in reality. Although human factors, including inspection, cleaning, vaccination, etc., were not included in the model, the validation results still suggested that the customized model was able to accurately predict the indoor environment and overall energy consumption during poultry farming. The validated model provides a tool for poultry producers to optimize production planning and management strategies, increase the production rate of unit energy consumption and achieve precision livestock farming from an energy consumption standpoint. [ABSTRACT FROM AUTHOR]

Simple Summary: The current work evaluated the breast muscle performance, meat quality traits, and myofiber characteristics of Da-Heng meat type birds with 60, 90, 120, 150, 180 days of age. Older chickens often presented a higher pH, lower drip loss, higher shear force, darker, and redder breast meat. The correlation coefficients showed that myofiber characteristics played an important role in breast pH values, drip loss, and meat color. Due to the increasing demand for producing chickens with high meat quality, there is a need to determine its mode of action on chicken meat quality traits across a wider age spectrum. In this study, five groups of 200 male Da-Heng meat type birds were reared until slaughter age of 60, 90, 120, 150, 180 days old and breast muscle performance, meat quality traits, and myofiber characteristics were evaluated. The larger body weight and breast weight of chicken are based on larger myofiber diameter and area, less myofiber density for the older birds than younger birds. There was an age effect on all meat quality traits of chicken breast muscle (p < 0.05). Older chickens often presented a higher pH, lower drip loss, higher shear force, darker, and redder breast meat. The correlation coefficients showed that myofiber characteristics played an important role in breast pH values, drip loss, and meat color (p < 0.05). Besides, significant correlations were also found between meat quality traits (p < 0.05). Further studies are needed to explore the biochemical character and potential molecular mechanism of chicken breast muscle to determine the factors that causes these age-related differences in meat quality in the current study. [ABSTRACT FROM AUTHOR]

Chicken Mx1 gene, as a positive antiviral gene, has been reported to provide resistance to several viruses especially avian influenza virus. In present research, the genotype frequency contributions of chicken Mx1 polymorphisms were characterized in five lowly selected as well as one moderately selected Sichuan native chicken populations and two highly selected commercial chicken breeds. Together with two newly-identified mutation sites (r.8A > G and r.1257T > C), a total of 13 single nucleotide polymorphisms (SNPs), including seven nonsynonymous mutation and six synonymous mutation, were found in the coding region of chicken Mx1 gene. Local Chinese chicken populations exhibited higher nucleotide diversity than commercial populations. Moreover, amino acid substitution sites as well as positive selection sites were located only in the domain not determined and GTPase domain, implying that amino acids mutations were likely needed in the modulatory and structural regions to better adapt the environment. Collectively, our results suggest that different selection pressures greatly influenced the genotype frequency contributions of chicken Mx1 gene. Understanding the interaction between genetic diversity and artificial selection may help us to better select and breed superior domestic chickens. [ABSTRACT FROM AUTHOR]

Steroid hormones play a crucial role in the growth and maturation of poultry ovarian follicles, with progesterone secretion by granulosa cells (GC) being essential. According to our previous transcriptome analysis, it apparented that miR-146a-5p expressions were upregulated in the follicles undergoing atresia. In this study, we delved the depth to explore the underlying mechanisms by miR-146a-5p in the regulation of follicle functions in chicken. The study demonstrated that miR-146a-5p suppressed cell growth, lipids accumulation, and progesterone biosynthesis in chicken GC. Through targeting association validations, we identified delta 4-desaturase, sphingolipid 1 (DEGS1) as capable of interacting with miR-146a-5p. Co-transfection experiments further confirmed that DEGS1 reversed the impairment of GC functions by miR-146a-5p. Moreover, we discovered that miR-146a-5p suppressed AKT phosphorylation, while DEGS1 enhanced AKT phosphorylation. Phosphatidylinositol-3 kinase (PI3K) inhibitor (LY294002) studies showed that miR-146a-5p would inhibit AKT phosphorylation by governing the DEGS1/AKT pathway, which in turn regulates GC function. In summary, the findings revealed that miR-146a-5p suppressed cell growth, lipid deposition, and progesterone biosynthesis via the DEGS1 / AKT pathway. These results may further enrich our understandings of how non-coding RNA regulates productive performance in chickens. • miRNA regulates granulosa cells functions by targeting gene expressions in the DEGS1/AKT signaling pathway. • The DEGS1/AKT pathway is associated with lipid synthesis and progesterone production. • The inhibitory effect of miR-146a-5p on the DEGS1/AKT pathway was validated by pharmacological inhibitors. [ABSTRACT FROM AUTHOR]

In diploid organisms, interactions between alleles determine phenotypic variation. In previous experiments, only MYH1F was found to show both ASE (spatiotemporal allele-specific expression) and TRD (allelic transmission ratio distortion) characteristics in the pectoral muscle by comparing the genome-wide allele lists of hybrid populations (F1) of meat- and egg- type chickens. In addition, MYH1F is a member of the MYH gene family, which plays an important role in skeletal muscle and non-muscle cells of animals, but the specific expression and function of this gene in chickens are still unknown. Therefore, qRT-PCR was used to detect the expression of MYH1F in different tissues of chicken. Proliferation and differentiation of chicken skeletal muscle satellite cells (SMSCs) have been detected by transfection of MYH1F-specific small interfering RNA (siRNA). The results showed that the expression of MYH1F in chicken skeletal muscle was higher than that in other tissues. Combined with CCK-8 assay, EdU assay, immunofluorescence, and Western blot Assay, it was found that MYH1F knockdown could significantly suppress the proliferation of chicken SMSCs and depress the differentiation and fusion of the cells. These results suggest that MYH1F plays a critical role in myogenesis in poultry, which is of great significance for exploring the regulatory mechanisms of muscle development and improving animal productivity. [ABSTRACT FROM AUTHOR]

Broodiness, a maternal behavior, is accompanied by the atresia of follicles and the serious degradation of poultry reproductive performance. The comparison of follicles between brooding and laying hens is usually an ideal model for exploring the regulation mechanism of follicle atresia. In this study, we selected three brooding hens and three laying hens to collect their follicles for whole transcriptome sequencing. The results demonstrated different expression patterns between the follicles of brooding hens and laying hens. In the top 10 differentially expressed genes with the highest expression, MMP10 was relatively low expressed in the follicles of brooding hens, but other nine genes were relatively highly expressed, including LRR1, RACK1, SPECC1L, ABHD2, COL6A3, RPS17, ATRN, BIRC6, PGAM1 and SPECC1L. While miR-21-3p, miR-146a-5p, miR-142-5p and miR-1b-3p were highly expressed in the follicles of brooding hen, miR-106-5p, miR-451, miR-183, miR-7, miR-2188-5p and miR-182-5p were lowly expressed in brooding hen. In addition, we identified 124 lncRNAs specifically expressed in the follicles of brooding hens and 147 lncRNAs specifically expressed in the follicles of laying hens. Our results may provide a theoretical basis for further exploration of the molecular mechanism of broodiness in broilers. [ABSTRACT FROM AUTHOR]

Granulosa cell (GC) apoptosis is the main trigger of follicular atresia. MicroRNAs (miRNAs) are 18–22 nt RNAs whose function is primarily determined by their extended seed region and are considered to be involved in the biological functions of follicular development, including follicular atresia, folliculogenesis, and oogenesis. MiR-138-5p is known to act on chicken GCs. In this study, we found that miR-138-5p was enriched in reproductive organs, such as the uterus and ovaries. To examine whether miR-138-5p could regulate the biological process of GCs, miR-138-5p was examined by transfection of cells with a mimic or inhibitor of miR-138-5p. Expression levels of caspase-3 and caspase-9 mRNA and protein were markedly increased or decreased after transfection of the mimic or inhibitor, respectively. Furthermore, following miR-138-5p inhibition, SIRT1, one of the target genes of miR-138-5p, was found to increase the mRNA, which is correlated with the increased levels of BCL2 expression, an anti-apoptotic gene in the chicken GCs. These results suggest that miR-138-5p promotes apoptosis in chicken GCs by targeting SIRT1. [ABSTRACT FROM AUTHOR]

Objective: The goal of this study was to investigate the mechanisms of muscle growth and development of three chicken breeds. Participants: Eighteen chickens, including three different breeds with different growth speeds (White Broiler, Daheng, and Commercial Layers of Roman), were used. Methods: Total RNA from breast muscle of these chickens was subjected to a gene expression microarray. Differentially expressed genes (DEGs) were screened and functional enrichment analysis was performed using DAVID. Seven DEGs were confirmed by quantitative reverse transcription PCR. Results: Overall, 8,398 DEGs were found among the different lines. The DEGs between each two lines that were unique for a developmental stage were greater than those that were common during all stages. Functional analysis revealed that DEGs across the entire developmental process were primarily involved in positive cell proliferation, growth, cell differentiation, and developmental processes. Genes involved in muscle regulation, muscle construction, and muscle cell differentiation were upregulated in the faster-growing breed compared to the slower-growing breed. DEGs including myosin heavy chain 15 (MYH15), myozenin 2 (MYOZ2), myosin-binding protein C (MYBPC3), insulin-like growth factor 2 (IGF2), apoptosis regulator (BCL-2), AP-1 transcription factor subunit (JUN), and AP-1 transcription factor subunit (FOS) directly regulated muscle growth or were in the center of the protein–protein interaction network. Pathways, including the extracellular matrix (ECM)-receptor interaction, mitogen-activated protein kinase (MAPK) signaling pathway, and focal adhesion, were the most enriched DEGs between lines or within lines under different developmental stages. Conclusions: Genes involved in muscle construction and cell differentiation were differentially expressed among the three breeds. [ABSTRACT FROM AUTHOR]

Skeletal muscle can undergo a regenerative process in response to injury or disease to maintain muscle quality and function. Myogenesis depends on the proliferation and differentiation of myoblasts, and miRNAs can maintain the balance between them by precisely regulating many key factors in the myogenic network. Here, we found that miR‐136‐5p was significantly upregulated during the proliferation and differentiation of C2C12 cells. We demonstrate that miR‐136‐5p acts as a myogenic negative regulator during the development of mouse C2C12 myoblasts. In terms of mechanism, miR‐136‐5p inhibits the formation of β‐catenin/LEF/TCF DNA‐binding factor transcriptional regulatory complex by targeting FZD4, a gating protein in the Wnt signaling pathway, thereby enhancing downstream myogenic factors and finally promoting myoblast proliferation and differentiation. In addition, in BaCl2‐induced muscle injury mouse model, miR‐136‐5p knockdown accelerated the regeneration of skeletal muscle after injury, and further led to the improvement of gastrocnemius muscle mass and muscle fiber diameter, while being suppressed by shFZD4 lentivirus infection. In summary, these results demonstrate the essential role of miR‐136‐5p/FZD4 axis in skeletal muscle regeneration. Given the conservation of miR‐136‐5p among species, miR‐136‐5p may be a new target for treating human skeletal muscle injury and improving the production of animal meat products. [ABSTRACT FROM AUTHOR]

The hypothalamic-pituitary-adrenal (HPA) axis and hypothalamic-pituitary-gonadal (HPG) axis plays a central role in mediating physiological responses related to the reproductive system under any stressful condition. However, the molecular mechanism underlying the effects of stress on physiology still needs to be elucidated. This study demonstrated that increasing the stocking density from 4 to 8 birds/m2 during the laying period decreased the egg production rate of laying ducks by 13.04 − 63.55% and feed intake by 7.40 − 23.44%. Transcriptome analysis between high- and low-feeding-density laying ducks revealed 469, 509, 428 and 210 differentially expressed genes (DEGs) in the hypothalamus, pituitary, ovary and follicular membrane, respectively. Gene ontology (GO) and KEGG enrichment analysis showed that the DEGs in the hypothalamus and pituitary were primarily enriched in the biostimulation and dopamine secretion pathways. The major enrichment pathways in the ovarian and follicular membranes involved lipid metabolism, negative regulation of inflammatory response, and steroid hormone biosynthesis. Among the DEGs in the HPG system, POMC and GnRH1 were identified, which may be manifesting their crucial roles in regulating the stress response and reproduction. Our data showed that a high stocking density as environmental stress negatively affects the reproductive performance in ducks through transcriptional changes in the HPG axis. Raising the stocking density from 4 to 8 birds/m2 decreased the egg production rate and feed intake in laying ducks. The transcriptome indicated that stocking density affects the stress response of laying ducks through the hypothalamus-pituitary. The stress signals are subsequently transmitted to affect gene expression related to the reproduction process in laying ducks' ovarian and follicular tissues. The hypothalamic expression of POMC and GnRH1 may play a central role in integrating stress signals and the reproductive processes of laying ducks. [ABSTRACT FROM AUTHOR]

Probiotics are expected to be an ideal alternative for antibiotics in the poultry industry. This study aimed to investigate the effect of Lactobacillus plantarum on growth traits, slaughter performance, serum markers and intestinal bacterial community of Daheng broilers. A total of 2400 healthy one‐day‐old Daheng broilers were randomly divided into 5 groups with 6 replicates per group and 40 individuals per replicate. Birds in control group were fed a basal diet, and others were fed basal diets supplemented with 105, 106, 107 and 108 CFU/kg Lactobacillus plantarum, respectively. It turned out that adding Lactobacillus plantarum to diet could significantly improve the serum immune performance of broilers (p < 0.05), enhance the antioxidant capacity to a certain extent (p > 0.05), but had no significant effect on growth traits and slaughter performance. Moreover, Lactobacillus plantarum could improve the diversity of intestinal bacterial community, but with the increase of addition concentration, the diversity would gradually decrease. In conclusion, Lactobacillus plantarum can be used as feed additive in broiler production, but whether it is more effective than antibiotics needs further investigation. [ABSTRACT FROM AUTHOR]

Background: The egg production performance of chickens is affected by many factors, including genetics, nutrition and environmental conditions. These factors all play a role in egg production by affecting the development of follicles. MicroRNAs (miRNAs) are important non-coding RNAs that regulate biological processes by targeting genes or other non-coding RNAs after transcription. In the animal reproduction process, miRNA is known to affect the development and atresia of follicles by regulating apoptosis and autophagy of granulosa cells (GCs). Results: In this study, we identified potential miRNAs in the atretic follicles of broody chickens and unatretic follicles of healthy chickens. We identified gga-miR-30a-5p in 50 differentially expressed miRNAs and found that gga-miR-30a-5p played a regulatory role in the development of chicken follicles. The function of miR-30a-5p was explored through the transfection test of miR-30a-5p inhibitor and miR-30a-5p mimics. In the study, we used qPCR, western blot and flow cytometry to detect granulosa cell apoptosis, autophagy and steroid hormone synthesis. Confocal microscopy and transmission electron microscopy are used for the observation of autophagolysosomes. The levels of estradiol (E2), progesterone (P4), malondialdehyde (MDA) and superoxide dismutase (SOD) were detected by ELISA. The results showed that miR-30a-5p showed a negative effect on autophagy and apoptosis of granulosa cells, and also contributed in steroid hormones and reactive oxygen species (ROS) production. In addition, the results obtained from the biosynthesis and dual luciferase experiments showed that Beclin1 was the target gene of miR-30a-5p. The rescue experiment conducted further confirmed that Beclin1 belongs to the miR-30a-5p regulatory pathway. Conclusions: In summary, after deep miRNA sequencing on healthy and atretic follicles, the results indicated that miR-30a-5p inhibits granulosa cell death by inhibiting Beclin1. [ABSTRACT FROM AUTHOR]

Intramuscular fat (IMF) is one of the crucial factors determining meat quality. IMF deposition depends on the hyperplasia and hypertrophy of intramuscular preadipocytes, in which genes and noncoding RNAs play an important regulatory role. According to previous transcriptome analysis, ANXA6 and miR-24-3p were identified as involved in lipid metabolism in breast muscle. In this study, we further investigated their function in the proliferation and differentiation of chicken intramuscular preadipocytes. The results indicated that overexpression of ANXA6 inhibited proliferation and promoted differentiation of intramuscular preadipocytes, while knockdown of ANXA6 promoted cell proliferation and inhibited adipogenic differentiation. miR-24-3p was proved to directly bind to the 3′ untranslated region (3′UTR) of ANXA6 by dual-luciferase reporter assay. The regulatory effect of miR-24-3p on the proliferation and differentiation of intramuscular preadipocytes was opposite to that of ANXA6. Besides, the overexpression vector of ANXA6 eliminated the impact of miR-24-3p mimics on intramuscular preadipocytes. In brief, we revealed that miR-24-3p promoted proliferation but inhibited differentiation of intramuscular preadipocytes by blocking ANXA6 expression, thus dominating IMF deposition in broilers. These findings may provide a novel target for improving chicken meat quality. [ABSTRACT FROM AUTHOR]

Thiram, an agricultural insecticide, has been demonstrated to induce tibial dyschondroplasia (TD) in avian species. Circular RNA (circRNAs), a novel class of functional biological macromolecules characterized by their distinct circular structure, play crucial roles in various biological processes and diseases. Nevertheless, the precise regulatory mechanism underlying non-coding RNA involvement in thiram-induced broiler tibial chondrodysplasia remains elusive. In this study, we established a broiler model of thiram exposure for 10 days to assess TD and obtain a ceRNA network by RNA sequencing. By analyzing the differentially expressed circRNAs network, we id entify that circ_003084 was significantly upregulated in TD cartilage. Elevated circ_003084 inhibited TD chondrocytes proliferation and differentiation in vitro but promote apoptosis. Mechanistically, circ_003084 competitively binds to miR-130c-5p and prevents miR-130c-5p to decrease the level of BMPR1A, which upregulates the expression of apoptosis genes Caspase 3, Caspase 9, Bax and Bcl 2 , and finally facilitates cell apoptosis. Taken together, these findings imply that circ_003084/miR-130c-5p/BMPR1A interaction regulated TD chicken chondrocyte proliferation, apoptosis, and differentiation. This is the first work to reveal the mechanism of regulation of circRNA-related ceRNA on thiram-induced TD, offering a key reference for environmental toxicology. [Display omitted] • Thiram exposure causes tibial chondrodysplasia and the changes of circRNA profiles in broilers cartilage. • Circ_003084 was the direct target of miR-130c-5p. • Circ_003084 up-regulates BMPR1A expression in TD chondrocytes by competitively binding to miR-130c-5p. • Circ_003084/miR-130c-5p/BMPR1A axis is involved in the regulation of thiram-induced TD chondrocytes differentiation and proliferation. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are ∼22 nt RNAs that direct post-transcriptional repression of mRNA targets in diverse eukaryotic lineages. Granulosa cells (GCs) are the earliest differentiated follicular somatic cells. From the initiation of primordial follicles, their differentiation and growth are closely related to the development of follicles. The research on follicular development mostly focused on the granular layer, as well as the hormone synthesis induced by granulosa cell differentiation before and after follicular selection. In this study, we evaluated the effects of miR-23b-3p on chicken granulosa cells, including granulosa cell proliferation and steroid hormone synthesis. Elevated expression of miR-23b-3p significantly inhibited granulosa cell proliferation and steroid hormone synthesis, but did not affect apoptosis. Furthermore, it was observed that the forecast growth differentiation factor 9 (GDF9) is a target gene of miR-23b-3p and miR-23b-3p can down-regulate expression of GDF9. Overall, this study demonstrated that miR-23b-3p can regulate the proliferation and steroid hormone synthesis of chicken granulosa cells by inhibiting the expression of GDF9. • miR-23b-3p is highly expressed in chicken propagative organ. • miR-23b-3p targets GDF9 in chickens. • miR-23b-3p regulates cell proliferation in chicken granulosa cells. • miR-23b-3p regulates steroid hormone synthesis in chicken granulosa cells. [ABSTRACT FROM AUTHOR]

The Tibetan chicken (Gallus gallus) provides high quality protein and iron for humans, which shows many phenotypic adaptations to the low oxygen. Study of the genetic mechanisms of circular RNAs (circRNAs) in hypoxia adaptation has not been reported. Four embryonic heart tissue samples from Tibetan chickens and Daheng broilers were collected. Differentially expressed circRNAs (DEcircRNAs) were identified via high-throughput sequencing. Bioinformatic analysis was used to indicate the functions and pathways of the DEcircRNAs. A total of 29 DEcircRNAs were identified between 4 Tibetan chickens and 4 Daheng broilers, including 15 upregulated and 14 downregulated DEcircRNAs in Tibetan chickens. GO analysis revealed that the DEcircRNAs were mainly involved in lung development or oxygen metabolism, such as ubiqunegative regulation of mesenchymal cell proliferation involved in lung development, oxidoreductase activity, and peroxisome. Pathway analysis showed that DEcircRNAs were mainly enriched in oxidative phosphorylation, tight junction, VEGF/MAPK/PPAR/Ras/PI3K-Akt signaling pathway. We also constructed a circRNA-miRNA-mRNA-pathway network to visualize the regulatory relationship associated with hypoxia adaptation of the tight junction pathways. The circRNA expression profile was obtained to complement the current Tibetan chicken circRNA database and provides new information for future studies into biological adaptation to hypoxic stress in the Tibetan chicken. [ABSTRACT FROM AUTHOR]

The feather growth rate in chickens included early and late feathering. We attempted to characterize the genes and pathways associated with the feather growth rate in chickens that are not in agreement with Mendelian inheritance. Gene expression profiles in the hair follicle tissues of late-feathering cocks (LC), early-feathering cocks (EC), late-feathering hens (LH), and early-feathering hens (EH) were acquired using RNA sequencing (RNA-seq), mass spectrometry (MS), and quantitative reverse transcription PCR (qRT‑PCR). A total of 188 differentially expressed genes (DEGs) were ascertained in EC vs. LC and 538 DEGs were identified in EH vs. LH. We observed that 14 up-regulated genes and 9 down-regulated genes were screened both in EC vs. LC and EH vs. LH. MS revealed that 41 and 138 differentially expressed proteins (DEPs) were screened out in EC vs. LC and EH vs. LH, respectively. Moreover, these DEGs and DEPs were enriched in multiple feather-related pathways, including JAK-STAT, MAPK, WNT, TGF-β, and calcium signaling pathways. qRT-PCR assay showed that the expression of WNT8A was decreased in LC compared with EC, while ALK and GRM4 expression were significantly up-regulated in EH relative to LH. This study helps to elucidate the potential mechanism of the feather growth rate in chickens that do not conform to genetic law. [ABSTRACT FROM AUTHOR]

• An energy-recovery system for poultry houses was designed and tested. • 13.5% of the energy used for ventilation fans could be recovered. • The reduction of GHG emissions is estimated to be 3.01gCO2eq/egg∙year. • The system energy and GHG payback time is 3.36 years and 1.17 years, respectively. New and renewable energies are being applied in the field of livestock farming in order to reduce the increasing energy demand and to some extent provide potential alternative profits for producers. In this study, a preliminary ventilation energy-recovery system for poultry houses was investigated. The air flow that generated by the ventilation fans was accelerated by a flow-convergence configuration and the wind turbine located at the outlet of the flow tunnel was applied to recover the energy together with other electronic components. A maximum of 270 W power output from the wind turbine was steadily recorded for this small-scale experimentally-oriented system recovering 13.5 % of the energy used for ventilation. Meanwhile, about 2074kWh renewable energy per year could be produced by the system, accounting for about 10.2% of total energy requirement for poultry farming and reducing approximately 3.01 g C O 2 e q / e g g ∙ y e a r greenhouse gas emissions. Furthermore, a 3.7 % reduction of volumetric ventilation rate was also observed due to the additional pressure load from the wind turbine and no apparent difference in the power consumptions of ventilation fans was found. Furthermore, a life cycle assessment (LCA) was also performed in order to quantify the impacts of applying this system on the environment during its lifespan from 'cradle to grave'. It was demonstrated that the energy and greenhouse gas payback time were 3.36 years and 1.17 years respectively, demonstrating a 'green' and environmentally-friendly system considering the lifespan of the system was 20 years. This study suggests new ideas for the future design of poultry houses combining renewable energy and power generation technology, which is technically and environmentally feasible. [ABSTRACT FROM AUTHOR]

Salmonella enteritidis can cause significant morbidity and mortality in humans and economic loss in the animal industry. Improving the innate immunity is an effective method to prevent S. enteritidis infection. Pediococcus pentosaceus is a Gram-positive coccus which had probiotics properties. Numerous previously published studies reported that probiotics were beneficial to gut microbiota by changing the intestinal flora structure and inhibiting the harmful microbial growth to enhance the innate immunity. We investigated the immunological effects of P. pentosaceus on Salmonella-infected chickens by the following experiment. A total of 120 broilers from AA line were fed and divided into 2 groups (treated and control groups) for the experiment from day 1. The control group was fed with the basic diet, while the treated group was fed with the basic diet adding P. pentosaceus microcapsule with the bacterial concentration of 1 g/kg in the feed and bacterial counts 2.5 × 10 9 CFU/g. All the birds were given with 0.5 ml of S. enteritidis bacterial suspension (109 CFU/ml) through oral cavity at day 9. The number of dead birds was recorded and used in the analysis. The bacterial culture method and quantitative real-time PCR analysis were used to evaluate the effects of P. pentosaceus on chickens infected with S. enteritidis and to ascertain the mechanism of the effect. The results showed that the P. pentosaceus could restrain the pathogenicity of S. enteritidis and reduce the death rate from 44.4% to 23.3%. The flora in the caecum exhibited "rising-declining" trends, and the gene (TLR4, MyD88, TRAF6 NF-κB, IFN-β, TNF-a, IL6, and IL8) expression pattern was different between the experimental and control group. P. pentosaceus as a probiotic may competitively inhibit the growth of S. enteritidis and control the inflammatory response through regulating the gene expression which involved in the toll-like receptor pathway and inflammation pathway. [ABSTRACT FROM AUTHOR]

• High concentrations of bio-aerosols are expected at the rear part of the tunnel-ventilated houses. • Turbulent flow resulting from ventilation configuration enhances the dispersion of bio-aerosols. • Local disturbed flow region contributes to the local high concentrations of bio-aerosols. • Small-scale (≤ 10 μ m) bio-aerosols have similar dispersion and deposition behavior in poultry houses. Bio-aerosol concentrations in poultry houses must be controlled to provide adequate air quality for both birds and workers. High concentrations of airborne bio-aerosols would affect the environmental sustainability of the production and create environmental hazards to the surroundings via the ventilation systems. Previous studies demonstrate that several factors including the age of the birds, the housing configuration, the humidity and temperature would strongly affect the indoor concentration of bio-aerosols. However, limited studies are performed in the literature to investigate the bio-aerosol dispersion pattern inside poultry buildings. In order to fill a gap of the understanding of the bio-aerosol dispersion behavior, experimental measurements of the indoor bio-aerosol distribution are performed in a tunnel-ventilated poultry house in this paper. Meanwhile a three-dimensional computational fluid dynamics (CFD) model is built and validated to further investigate the effect of flow pattern, turbulence and vortex on the dispersion and deposition of the bio-aerosols. Furthermore, bio-aerosols with various diameters are also examined in the CFD model. It is found that higher concentrations of bio-aerosols are detected at the rear part of the house and strong turbulent flow resulting from the ventilation inlets enhances the diffusion and dispersion of bio-aerosols. Local vortex or disturbed flow is responsible for higher local concentration due to the re-suspension of settled bio-aerosols, which suggests that careful attentions should be paid to these locations during cleaning and disinfection. Results from present study contribute to the optimization of design and operation of the poultry houses from the standing point of reducing airborne bio-aerosol concentrations. [ABSTRACT FROM AUTHOR]

Hypoxia affects the physiology of cells and organisms; however, the mechanisms associated with hypoxia adaptation remain unknown in Tibetan chickens. In this study, we aimed to identify long noncoding RNAs (lncRNAs) involved in hypoxia adaptation in Tibetan chickens and Daheng broilers, to provide insights into the mechanisms underlying hypoxia induction. RNA sequencing results revealed that a total of 5504 lncRNAs and 16,779 microRNAs were differentially expressed in four Tibetan chickens and four Daheng broilers; 70 lncRNAs were up-regulated and 113 lncRNAs were down-regulated in the Tibetan chickens compared to the expression levels in the Daheng broilers. The differentially expressed lncRNAs (DElncRNAs) were enriched in the following Gene ontology terms: protein complex localization, small-molecule metabolic process, and RNA splicing. Kyoto Encyclopedia of Genes and Genomes analyses revealed that the DElncRNAs were mainly enriched in pathways that regulate cell junctions and intercellular spaces and oxygen or energy metabolism, mainly involved in hypoxic adaption. Moreover, a predicted ceRNA network with five DElncRNAs interacted with three miRNAs that acted on 42 pathways through 19 target genes. Quantitative real-time polymerase chain reaction was used to verify that the expression levels of ENSGALG00000008047, ENSGALG00000050044, and ENSGALG00000053982 were significantly lower in Tibetan chickens than in the Daheng broilers, consistent with the RNA sequencing results. We obtained lncRNA expression profiles for the heart tissue of Tibetan chickens for the first time and have provided novel data that may aid research on biological adaptation to hypoxic stress. [ABSTRACT FROM AUTHOR]

Sichuan mountainous black‐bone (SMB) chicken is a small‐sized black‐feathered chicken breed with low amount of meat, while Dahen (DH) chicken has a larger body size and a faster growth rate. MicroRNAs (miRNAs) are involved in various physiological processes, but their role in chicken muscle growth remains unclear. We aimed to investigate the miRNAs and pathways participating in the muscle growth of chicken. MiRNA profiles of four SMB chickens and four DH chickens were detected by small RNA sequencing. A total of 994 known miRNAs were identified, among which gga‐miR‐1a‐3p, gga‐miR‐148‐3p and gga‐miR‐133a‐3p exhibited the highest enrichment in both breeds of chickens. Thirty‐two miRNAs were differently expressed between SMB and DH chickens. The differently expressed miRNAs were mainly associated with fatty acid metabolism, immunity and MAPK activation‐related processes. Kyoto encyclopaedia of genes and genomes (KEGG) analysis showed that miRNAs were involved in the immunity‐related and MAPK signalling pathways. Moreover, miR‐204 was downregulated in DH chicken compared with SMB chicken, and significantly inhibited the expression of MAP3K13, which is involved in the MAPK pathway. It was confirmed through luciferase reporter assays that miR‐204 specifically inhibited the activity of MAP3K13. Our results helped demonstrate the potential molecular mechanisms of muscle growth in chickens and provide valuable information for chicken breeding. [ABSTRACT FROM AUTHOR]

Previous studies reported that the Myoz1 gene plays a crucial role in signal transduction and muscle fibre type differentiation. This finding suggests that the Myoz1 gene is a potential candidate for affecting carcase and meat quality traits in animals. Therefore, this study aimed to detect genetic variations in Avian and Yellow Bantam chickens and to evaluate the effects of these variations on economically important carcase and meat-quality traits. Expression analysis using quantitative real-time PCR indicated that Myoz1 was broadly expressed in all four studied tissues (liver, heart, breast muscle and leg muscle). Expression of Myoz1 was significantly higher in both leg muscle and breast muscle compared to the liver and heart. Then, using direct sequencing, a total of five single nucleotide polymorphisms (SNPs) were identified within the Myoz1 gene in two breeds of chickens. These breeds included three non-synonymous SNPs (SNP1: g. 16022512 G > T, SNP3: g. 16022560 C > T and SNP5: g.16023903 A > G) corresponding to A103S, H119Y and S189G, respectively. Statistical analyses indicated that SNP2 (g. 16022529 T > C), SNP3, SNP4 (g.16023878 A > C) and SNP5 significantly influenced some carcase and meat quality traits. Meanwhile, we did not find any association between the constructed haplotype and carcase traits in the Avian nor Yellow Bantam chickens. In conclusion, SNPs in the Myoz1 gene could be used for marker-assisted selection in chicken breeding. [ABSTRACT FROM AUTHOR]

Background: Tibetan chickens living at high altitudes show specific adaptations to high-altitude conditions, but the epigenetic modifications associated with these adaptations have not been characterized. Results: We investigated the genome-wide DNA methylation patterns in Tibetan chicken blood by using whole genome bisulfite sequencing. Generally, Tibetan chickens exhibited analogous methylation patterns to that of lowland chickens. A total of 3.92% of genomic cytosines were methylcytosines and 51.22% of cytosines in CG contexts were methylated, which was less than those in lowland chicken (55.69%). Moreover, the base adjacent to the methylcytosines of mCHGs in Tibetan chickens had a preference for T, which was different from that in lowland chickens. In Tibetan chickens, the methylation levels in the promoter were relatively low, while the gene body was also maintained in a hypomethylated state. DNA methylation levels in regions upstream of the transcription start site of genes were negatively correlated with the level of gene expression, and DNA methylation of gene body regions was also negatively related to gene expression. Conclusions: We generated the genome-wide DNA methylation patterns in Tibetan chickens and our results will be helpful for future epigenetic studies related to adaptations to high-altitude conditions. [ABSTRACT FROM AUTHOR]

Peroxisome proliferator activated receptor-alpha (PPARα) and Egl nine homolog 3 (EGLN3) play critical roles in facilitating the adaptation to a hypoxic environment. However, the relationship between EGLN3 and PPARα variants and hypoxic adaptation remains poorly understood in Tibetan chickens. To better understand the effects of genetic variation, we sequenced exons of PPARα and EGLN3 in 138 Lowland chickens (LC) from 7 breeds that were located in Emei, Miyi, Shimian, Wanyuan, Pengxian, and Muchuan in the Sichuan province, and Wenchang in the Hainan province (altitudes for these locations are below 1800 meters). Total 166 Tibetan chickens (TC) from 7 subpopulations that were located in Shigatse, Lhoka, Lhasa, Garze, Aba, Diqing and Yushu in the Tibetan area were also sequenced (altitudes greater than 2700 meters). One single-nucleotide polymorphism (rs316017491, C > T) was identified in EGLN3 and was shared by TC and LC with no significant difference for allele frequencies between them (P > 0.05). Six single-nucleotide polymorphisms (SNP1, A29410G; SNP2, rs13886097; SNP3, T29467C; SNP4, rs735915170; SNP5, rs736599044; and SNP6, rs740077421) including one non-synonymous mutation (SNP2, T > C) were identified in PPARα. This is the first report of SNP1 and SNP3. There was a difference between TC and LC for allele frequencies (P <0.01), except for SNP1, SNP4, and SNP5) The fix index statistic test indicated that there was population differentiation between TC and LC for SNP2, SNP3, and SNP6 in PPARα (P < 0.05). Phylogenetic analysis showed that the genetic distance among chickens, finch and great tit were close for both EGLN3 and PPARα. Bioinformatics analysis of PPARα showed that SNP2 leads to an amino acid substitution of Ile for Met, which results in the protein being more likely to be hydrolyzed. Thus, genetic variation in PPARα may play a role in the ability of TC to adapt to a high altitude environment; however we were unable to identify a relationship between polymorphisms in EGLN3 and environmental adaptability. [ABSTRACT FROM AUTHOR]

Salmonella enterica serovar ( S. enteritidis ) is a pathogenic bacterium that can cause symptoms of food poisoning, leading to death of poultry, resulting in serious economic losses. The MyD88 and TRIF signalling pathways play important roles in activating innate and adaptive immunity in chickens infected with S. enteritidis . The objective of the present study was to characterize in vivo mRNA expressions, protein levels and methylation levels of genes in the above two pathways in both Tibetan chickens and DaHeng S03 chickens infected with S. enteritidis . MyD88-dependent and TRIF-dependent signalling pathway were activated by infection, and the MyD88 signalling pathway induced cytokines LITAF and IL-8 played important roles in fighting against the S. enteritidis infection in vivo . The TLR4 methylation might alter expression of genes involved in the MyD88 signalling pathway, and thus different breeds of chickens might show differences in susceptibility to the S. enteritidis . The increased expression of INF β was activated by S. enteritidis , but its expressions were different in levels of mRNA and protein in Tibetan chickens and DaHeng chickens, suggesting its functions on the resistance to S. enteritidis infection in chickens. This study contributes to the understanding of two pathways activated in response to S. enteritidis infection, and gives indications on the mechanisms underlying resistance of Tibetan chickens and DaHeng chickens to S. enteritidis . [ABSTRACT FROM AUTHOR]

• The growth rate of hybrid broilers increased significantly after 28 days. • Effects of different factors on gene expression were that tissue > age > sex. • Cell cycle pathway was closely related to the growth of breast muscle. In China, the production mode of hybrid broilers with meat-type chicken as male parent and egg-type chicken as female parent is common, but few studies pay attention to the economic characteristics of hybrid broilers. In this experiment, we constructed a full-sib F1 population (n = 57) from male Recursive White broiler and female Lohmann Pink layer. Total 6, 6 and 7 hybrid broilers at days 1, 28 and 56 were selected randomly to collect breast muscle and liver tissues, respectively. After performing strand-specific RNA-Seq on these samples, we obtained 252.12 Gb sequencing data. Principal component analysis presented that the effects of different factors on gene expression were as below: tissue difference > age difference > sex difference. The ten genes with the highest expression in breast muscle were GAPDH , ACTA1 , ATP2B3 , COII , ATP6 , COX3 , COX1 , MYL1 , TNNI2 and ENSGALG00000042024. Through the analysis of differentially expressed transcripts (DETs) between different ages, we found that the number of DETs decreased progressively with the prolongation of ages in breast muscle. The same results were also observed in liver. GO enrichment analysis of DETs demonstrated that total 11 BP terms closely related to growth and development of breast muscle were annotated, such as cardiac muscle contract, muscle contract, cell division and so on. KEGG annotation presented that total 5 pathways related to growth and development were determined in breast muscle, including Cell cycle, Insulin signaling pathway, FoxO signaling pathway, Focal adhesion and Adrenergic signaling in cardiomyocytes. Our results may provide theoretical foundation for hybrid broiler production. [ABSTRACT FROM AUTHOR]

It is generally accepted the gut microbiota have a profound effect on the nutrition, health, and production in poultry. To deeply understand the gut microbiota composition with the dietary fiber level in broilers, we evaluated the cecal microbiota profiles feeding on different dietary fiber level with alfalfa as additive in Dahen broilers based on 16S rRNA gene sequencing and gas chromatography. As a result, the gut microbiota diversity was greatly accelerated with the dietary fiber level. The dietary fiber stimulated the growth of many intestinal communities such as Rikenellaceae RC9 gut group, Faecalibacterium, Prevotellaceae UCG 001 and Ruminococcaceae UCG 014, and led to an altered microbial function such as Carbohydrate metabolism and Genetic information processing. Meanwhile, we found the genera Anaerofilum and Dielma were significantly correlated with the production of short chain fatty acids (SCFAs). All these results provide a reference for the broilers gut microbiota changes with different dietary fiber level. The key role of the altered microbiota with the dietary fiber may mediate beneficial effects in broiler production, which also reflect the substantial potential of dietary fiber level in poultry. [ABSTRACT FROM AUTHOR]

Knowledge of the breed-specific and tissue-specific lipid molecular composition is helpful to understanding the complicated mechanisms of lipid deposition. In this study, a liquid chromatography (LC)-mass spectrometry (MS)-based lipidomics approach was used to discriminate chicken meat and abdominal fat from different sources. OxPC (16:0-20:4+1O(1Cyc)) and PC (18:2/20:5) were determined as the discriminatory markers for the meat of Guangyuan grey chicken, Jiuyuan black chicken and Tibetan chicken. A total of 209 lipid molecules were commonly determined as marker candidates for abdominal fat and intramuscular fat authentication, among which glycerophospholipids was the dominant class. Acylcarnitine (Acar), ceramides (Cer), cardiolipin (CL), fatty acid (FA), glucosylceramides (GlcCer), phosphatidic acids (PA), phosphatidylcholines (PC), phosphatidylethanolamines (PE), phosphatidylglycerols (PG), phosphatidylinositols (PI), phosphatidylserines (PS), sphingomyelines (SM), triacylglycerols (TAG) contributed significantly to these differences. The higher abundance of sphingolipid and PUFA-enriched glycerophospholipids in the intramuscular fat elucidated its beneficial roles in imparting a characteristic flavor and nutritional value to meat. Future investigation is required to combine these lipid metabolites with underlying molecular mechanisms to regulate and optimize body fat distribution in chickens. ● Breed-specific and tissue-specific lipid molecular composition was characterized ● Glycerophospholipids were the most dominant class in both tissues ● 209 lipid molecules were determined as discriminatory markers for abdominal fat and intramuscular fat authentication ● The chicken meat had higher sphingolipid and PUFA-enriched glycerophospholipids [ABSTRACT FROM AUTHOR]

[Display omitted] • Untargeted metabolomic profile of chicken meat was performed. • Significant differences in metabolic composition of chicken meat were observed during five growth and development periods. • The dynamic alterations of metabolites influencing meat quality were performed. • Chicken meat at 180 days of age has more umami and antioxidant compounds. • We identified key genes responsible for specific metabolite accumulation. To explore the chemical composition of chicken meat during different growth and development periods, the dynamic alterations of the metabolite composition were determined using LC-MS/MS-based metabolomics. Together, 573 metabolites were identified in chicken meat from five age stages. Generally, pentadecanoic acid, stearic acid, creatine, carnosine, IMP, L-histidine and L-isoleucine presented an upward trend with age, while anserine, DHA, L-aspartic acid, LPA 18:1 and LPI 18:1 decreased with age. The main pathways of chicken meat metabolism affected by age were fructose and mannose metabolism, arachidonic acid metabolism, steroid hormone biosynthesis, riboflavin metabolism, biosynthesis of unsaturated fatty acids, and linoleic acid metabolism. Using transcriptomic profiling data, we conducted Pearson correlation analysis between gene expression and metabolite profile data in each age comparison. Integration analysis of metabolome and transcriptome would be helpful to understand the biological processes underlying the development of meat quality and explore valuable biomarkers for specific metabolite accumulation. [ABSTRACT FROM AUTHOR]

Follicular atresia is an important cause of reproductive decline in egg-laying hens. Therefore, a better understanding of the regulation mechanism of follicle atresia in poultry is an important measure to maintain persistent high egg performance. However, how the role of the regulatory relationship between autophagy and apoptosis in the intrafollicular environment affects the follicular atresia of chickens is remain unclear. The objective of this study was to explore the regulatory molecular mechanisms in regard to follicular atresia. 20 white leghorn layers (32-wk-old) were equally divided into 2 groups. The control group was fed freely, and the experimental group induced follicular atretic by fasting for 5 d. The results showed that the expression of prolactin (PRL) levels was significantly higher in the fasted hens, while the levels of luteinizing hormone (LH) and follicle stimulating hormone (FSH) were lower. Most importantly, RNA sequencing, qPCR, and Western blotting detected significantly elevated levels of autophagy and apoptosis markers in atresia follicles. Interestingly, we found that fibromodulin (FMOD) levels was significantly lower in follicles from fasted hens and that this molecule had an important regulatory role in autophagy. FMOD silencing significantly promoted autophagy and apoptosis in granulosa cells, resulting in hormonal imbalance. FMOD was found to regulate autophagy via the transforming growth factor beta (TGF-β) signaling pathway. Our results suggest that the increase in autophagy and the imbalance in internal homeostasis cause granulosa cell apoptosis, leading to follicular atresia in the chicken ovary. This finding could provide further insight into broodiness in chicken and provide avenues for further improvements in poultry production. [ABSTRACT FROM AUTHOR]

The yield and quality of the skeletal muscle are important economic traits in livestock and poultry production. The musculoskeletal embryonic nuclear protein 1 (MUSTN1) gene has been shown to be associated with embryonic development, postnatal growth, bone and skeletal muscle regeneration; however, its function in the skeletal muscle development of chicken remains unclear. Therefore, in this study, we observed that the expression level of MUSTN1 increased in conjunction with the proliferation of chicken skeletal muscle satellite cells (SMSCs). Knockdown of MUSTN1 in SMSCs downregulated the expression of cell proliferation genes as Pax7 , CDK-2 and differentiation-relate genes including MyoD , MyoG , MyHC and MyH1B , whereas it upregulates the expression of cell apoptosis gene (Caspase-3) (P < 0.05). However, the combined analysis of CCK-8 and EdU showed that the cell vitality and EdU-positive cells of the si-MUSTN1 transfected group were significantly lower than those of the negative siRNA group (P < 0.05). In addition, the knockdown of MUSTN1 significantly increased the cell population in the G0/G1 phase and significantly decreased the cell population in the G2/M phase (P < 0.05), whereas the overexpression of MUSTN1 showed opposite effect. Taken together, our findings indicates that MUSTN1 is an important molecular factor that is responsible for regulating muscle growth and development in chickens, particularly, proliferation and differentiation of SMSCs. [ABSTRACT FROM AUTHOR]

The adaptation to hypoxia in high altitude areas has great research value in the field of biological sciences. Tibetan chicken has unique adaptability to high-altitude, low pressure and anoxic conditions, and served as a biological model to search for genetic diversity of hypoxia adaption. The whole genome re-sequencing technology was conducted to investigate the genetic diversity. In this study, we obtained quantity genetic resource, contained 5164926 single nucleotide polymorphisms (SNPs), 237504 Insertion/Deletion (InDel), 55606 structural variation types in all chromosomes of Tibetan chicken. Moreover, 17154 non-synonymous mutations, 45763 synonymous mutations, 258 InDel mutations and 9468 structural mutations were detected in coding sequencing (CDS) region. Furthermore, SNPs occur in 591 genes, including HIF1A, VEGF, MAPK 8/9/10/11, PPARA/D/G, NOTCH2, and ABCs, which were involved in 14 hypoxia-related pathways, such as VEGF signaling pathway, MAPK signaling pathway, PPAR signaling pathway and Notch signaling pathway. Among them, 19 genes with non-synonymous SNP variation in CDS were identified. Moreover, structure variation in CDS also occurred in the mentioned above genes with SNPs. This study provides useful targets for clarifying the hypoxia adaptability of the domestication of chickens in Tibetan and may help breeding efforts to develop improved breeds for the highlands. [ABSTRACT FROM AUTHOR]

The proliferation and differentiation of skeletal muscle satellite cells (SMSCs) play an important role in the development of skeletal muscle. Our previous sequencing data showed that miR-21-5p is one of the most abundant miRNAs in chicken skeletal muscle. Therefore, in this study, the spatiotemporal expression of miR-21-5p and its effects on skeletal muscle development of chickens were explored using in vitro cultured SMSCs as a model. The results in this study showed that miR-21-5p was highly expressed in the skeletal muscle of chickens. The overexpression of miR-21-5p promoted the proliferation of SMSCs as evidenced by increased cell viability, increased cell number in the proliferative phase, and increased mRNA and protein expression of proliferation markers including PCNA, CDK2, and CCND1. Moreover, it was revealed that miR-21-5p promotes the formation of myotubes by modulating the expression of myogenic markers including MyoG, MyoD, and MyHC, whereas knockdown of miR-21-5p showed the opposite result. Gene prediction and dual fluorescence analysis confirmed that KLF3 was one of the direct target genes of miR-21-5p. We confirmed that, contrary to the function of miR-21-5p, KLF3 plays a negative role in the proliferation and differentiation of SMSCs. Si-KLF3 promotes cell number and proliferation activity, as well as the cell differentiation processes. Our results demonstrated that miR-21-5p promotes the proliferation and differentiation of SMSCs by targeting KLF3. Collectively, the results obtained in this study laid a foundation for exploring the mechanism through which miR-21-5p regulates SMSCs. [ABSTRACT FROM AUTHOR]

As a ubiquitous heavy metal, cadmium (Cd) is highly toxic to various organs. However, the effects and molecular mechanism of Cd toxicity in the chicken heart remain largely unknown. The goal of our study was to investigate the cardiac injury in chickens' exposure to Cd. We detected the levels of oxidative stress–related molecules in the Cd-induced chicken heart, and assessed the histopathological changes by hematoxylin and eosin staining. RNA sequencing was performed to identify differentially expressed mRNAs between the Cd-induced group and control group. The expression of candidate genes involved in oxidative stress was certified by quantitative reverse transcription PCR. Our results showed that the expression of glutathione, peroxidase, and superoxide dismutase was significantly decreased and malondialdehyde was increased in the heart of chickens by Cd induction. The disorderly arranged cardiomyocytes, swelled and enlarged cells, partial cardiomyocyte necrosis, blurred morphological structure, and notable inflammatory cell infiltration were observed in the Cd-induced chicken heart. RNA sequencing identified 23 upregulated and 11 downregulated mRNAs in the heart tissues of the chicken in the Cd-induced group, and functional pathways indicated that they were associated with oxidative stress. Moreover, CREM, DUSP8, and ITGA11 expressions were significantly reduced, whereas LAMA1 expression was induced in heart tissue of chickens by Cd treatment. Overall, our findings revealed that oxidative stress and pathological changes in the chicken heart could be triggered by Cd. The mRNA transcriptional profiles identified differentially expressed genes in the chicken heart by Cd induction, revealing oxidative stress–related key genes and enhancing our understanding of Cd toxicity in the chicken heart. [ABSTRACT FROM AUTHOR]

• The number and density of informative genes are opposite on autosomes. • ASE ratio varies with tissues and time points in chickens. • The majority of ASE genes in chickens are tissue-specific and time-dependent. In diploid organisms, each gene locus is composed of two parental alleles, which would interact with each other for determining the phenotypic variation. Better understanding of the allele-specific expression (ASE) in farm animals is much important to explore the genetic basis underlying economically important traits, which have been poorly understood yet. In this study, genome-wide analysis was applied to explore the spatiotemporal pattern of ASE in the F1 hybrids of chicken. First, meat- and egg-type chickens were selected for producing a full-sib F1 hybrid population (n = 57). Then, genome resequencing of two parents and 38 offspring were performed and liver and breast muscle samples (n = 38) were subjected to strand-specific RNA sequencing (ssRNA-seq) for ASE detection at 1, 28, and 56 days of age, respectively. The results accurately identified a total of 465 informative genes that could be distinguished with respect to their parental origins. There were 0.4% − 4.1% of informative genes showing ASE, and 57 of them were found across different tissues and time points. Besides, most ASE genes in chickens were tissue-specific, and no matter what the time-point pattern of one ASE gene, the same parental allele of this gene almost showed consistently higher or lower expression across all time points in the same type tissue. In conclusion, this study indicated that most of ASE genes were tissue-specific and time-dependent. [ABSTRACT FROM AUTHOR]

PGC-1β-shRNA vector were transfected into chicken preadipocytes, and translocated into nucleus. PGC-1β expression abundance was decreased and its coactivations with Sterol Regulatory Element Binding Protein 1c (SREBP-1c) and Peroxisome Proliferator-activated Receptor-gamma (PPARγ) were suppressed and further impeded the activation of Fatty Acid Synthetase (FAS), which finally blocked the fatty acid synthesis in cytoplasm of adipocytes. • PGC-1β-shRNA decreased the mRNA and protein abundances of PGC-1β in adipocytes. • Interference decreased preadipocytes differentiation, not proliferation. • Interference impeded TAG deposition and PPARγ, SREBP-1c, and FAS expression. • PGC-1β modulated the differentiation and TAG accumulation of chicken adipocytes. To study the influence of the PGC-1β gene on chicken adipocyte proliferation and differentiation, we constructed RNA interference (RNAi) vectors that target the PGC-1β gene and transfected these vectors into adipocytes. Oil Red O staining and a CCK-8 cell kit were used to determine cell triglyceride accumulation status and cell proliferation after transfection, respectively. The mRNA abundances of PGC-1β and adipocyte-differentiation-related genes (PPARγ , C/EBPα , SREBP-1c , FAS, and A-FABP) were detected by real-time PCR. The results showed that the mRNA and protein abundances of PGC-1β in PGC-1β-shRNA transfected adipocytes were significantly lower than those in the control. Interference decreased cell differentiation, but did not depress the cell proliferation. PGC-1β interference impeded the triglyceride accumulation, the mRNA expression levels of nuclear receptors PPARγ and SREBP-1c, and fatty acid synthetase (FAS) , and both proteins PPARγ and SREBP-1c, and the fatty acids transporting protein A-FABP. Generally, PGC-1β modulated the cell differentiation and triglyceride accumulation in chicken adipocytes. [ABSTRACT FROM AUTHOR]

Problem: The oviduct plays an indispensable role in the formation of eggs, especially the magnum and uterus. The identification of oviduct development in different stages will help to target candidate genes and pathways in regulation of albumen and eggshell formation, as well as defense mechanism in oviduct and egg. Methods: To identify the function differences and the molecular defense mechanism of the oviduct and egg, we performed transcriptome sequencing analysis of the magnum and uterus in 120‐d‐old and 300‐d‐old Lohmann layers, three birds in each group. Results: With fold changes (log2 ratio) ≥ 2 and false discovery rate (FDR) < 0.01, RNA‐Seq revealed 1,040 genes expressed differentially in the magnum and 595 genes in the uterus. By combining GO enrichment and KEGG pathway analysis, it served to show that gene activities of the magnum and uterus in prelaying chickens were more likely to concentrate on growth and development, and after egg‐laying, they were mainly inclined to enhance the substances transmembrane transport and secretion activities. We further characterized 1579 new genes, while only 803 of them were functionally annotated. A complex mixture of proteins related to defense was measured in this study. A subset of avian β‐defensins (AvBDs) and ovodefensins (OvoDs), that is, AvBD12, AvBD11, AvBD10, OvoDA1, OvoDB1, OvoDA2, OvoDA3, and OvoDBβ, was detected to express in the magnum of laying hens at high levels. Conclusion: Collectively, the identification and functional analysis of these differentially expressed genes (DEGs), as well as specific expression of avian defensins, may contribute to understand the development and defense mechanisms of oviduct and eggs. [ABSTRACT FROM AUTHOR]