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Background: The impact of chickens on maintaining the economy and livelihood of rural communities cannot be overemphasized. In recent years, mycoplasmosis has become one of the diseases that affect the success of South African chicken production. Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS) are the most prevalent strains of Mycoplasma in South Africa. MG and MS are significant respiratory pathogens affecting the productivity of chickens. The present study aimed to molecularly detect using qPCR and characterize the presence of MG and MS using phylogenetic analysis. The phylogenetic analysis was utilized to clarify general evolutionary relationships between related taxa of different MG and MS observed in tracheal swabs from South African chicken breeds. Methods: Forty-five tracheal swabs of the Lohmann Brown (n = 9), Rhode Island Red (n = 9), Ovambo (n = 9), Venda (n = 9), and Potchefstroom Koekoek (n = 9) breeds were collected from symptomatic chickens present in the commercial farm. To detect MG and MS, DNA was extracted from tracheal swabs and faecal samples, and qPCR was performed with a 16 s rRNA (310 bp) and vlhA (400 bp) gene fragment. Following the sequencing of all the amplicons, MG, and MS dendrograms showing the evolutionary relationships among the five South African chicken breeds and the GeneBank reference population were constructed. Results: The qPCR revealed the presence of MG and MS in 22% (2/9) of the tracheal swab samples tested for MS only in Rhode Island Red breeds; 66.6% (6/9) and 33% (3/9) of the tested samples in Ovambo breeds; and 11.1% (1/9) and 44.4% (4/9) of the tested samples in Venda breeds. No MG or MS were detected in the Lohmann Brown or Potchefstroom Koekoek breed. Furthermore, qPCR revealed the presence of MG in pooled faecal samples from Lohmann Brown and Ovambo breeds. Eight different bacterial isolates were recognized from both samples. Four isolates were of the 16 s ribosomal ribonucleic acid (rRNA) gene (named PT/MG51/ck/00, PT/MG48/ck/00, PT/MG41/ck/00 and PT/MG71/ck/00) gene of Mycoplasma gallisepticum, and the other was Mycoplasma Synoviae variable lipoprotein hemagglutinin A (vlhA) gene (named PT/MSA22/ck/01, PT/MS41/ck/01, PT/MS74/ck/01 and PT/MS46/ck/01) which were available in GenBank. These isolates were successfully sequenced with 95–100% similarity to the isolates from the gene bank. Conclusion: The study revealed the presence of both MG and MS in the chicken breeds sampled. Furthermore, the different breeds of chicken were found to be susceptible to infection under the intensive or commercial management system. Therefore, continuous surveillance is encouraged to prevent the spread and outbreak of MG and MS in the poultry industry in South Africa. [ABSTRACT FROM AUTHOR]

Simple Summary: Improving the health of chickens is becoming of increasing importance as consumer expectations of cage-free and free-range housing result in more potential disease challenges while approved antibiotic treatments are decreasing. Antibodies are part of the immune response of chickens. Natural antibodies are present even though the bird has never been exposed to the specific antigen, and adaptive antibodies are produced after vaccination or exposure to a pathogen. This study looks for regions of the genome that influence both natural and adaptive antibody levels in three different breeds of commercially utilized egg production chickens. The genome regions that resulted in differential antibody-level production were identified with a high incidence of immune-related genes. Genetic influence (heritability) for antibody levels was also found. However, the genome regions and the level of heritability were different for different lines and different antigens, suggesting that there are not just a small number of genetic factors that influence overall antibody production. This study provides supporting evidence that overall health of chickens can be improved by genetic selection, though the exact genes and genomic regions still require further investigation, especially considering that the specific region can vary for different antigens and different chicken lines. Selection of livestock for disease resistance is challenging due to the difficulty in obtaining reliable phenotypes. Antibodies are immunological molecules that provide direct and indirect defenses against infection and link the activities of both the innate and adaptive compartments of the immune system. As a result, antibodies have been used as a trait in selection for immune defense. The goal of this study was to identify genomic regions associated with natural and induced antibodies in chickens using low-pass sequencing. Enzyme-linked immunosorbent assays were used to quantify innate (natural) antibodies binding KLH, OVA, and PHA and induced (adaptive) antibodies binding IBD, IBV, NDV, and REO. We collected plasma from four White Leghorn (WL), two White Plymouth Rock (WPR), and two Rhode Island Red (RIR) lines. Samples numbers ranged between 198 and 785 per breed. GWAS was performed within breed on data pre-adjusted for Line-Hatch-Sex effects using GCTA. A threshold of p = 10−6 was used to select genes for downstream annotation and enrichment analysis with SNPEff and Panther. Significant enrichment was found for the defense/immunity protein, immunoglobulin receptor superfamily, and the antimicrobial response protein in RIR; and the immunoglobulin receptor superfamily, defense/immunity protein, and protein modifying enzyme in WL. However, none were present in WPR, but some of the selected SNP were annotated in immune pathways. This study provides new insights regarding the genetics of the antibody response in layer chickens. [ABSTRACT FROM AUTHOR]

Simple Summary: Various kinds of yellow-feathered chickens are crossbred from Chinese local native chicken breeds and introduced broilers. The individual parts of yellow-feathered chickens are less suitable for sale after slaughtering than those of broilers, and they have mainly been sold as live whole chickens. With the establishment of cold chain logistics for chicken in China, chilled-type and processed yellow-feathered chicken products have appeared in the market. Xueshan chicken, a yellow-feathered chicken breed, which has high meat quality and good taste, is bred to meet the diversified needs of the market by Jiangsu Lihua Breeding Company. The present study used Xueshan chicken as an experimental model to determine the effect of sex on the slaughtering performance and meat quality. This study provides valuable breeding references for poultry producers by determining the basic production phenotypes of yellow-feathered chickens. The demand for high-quality chilled chicken has continued to increase in China. Chickens are sexually dimorphic, and to better understand the specific differences in chicken production based on sex, we examined how sex affects growth performance, carcass traits, and meat quality of yellow-feathered chickens. Male and female Xueshan chickens were used as the experimental model. Although males exhibited better growth performance, including body weight (BW), body slope, keel, shank length, and shank girth (p < 0.05), as well as carcass traits, such as dressed weight, leg muscle, and lean meat, females had higher carcass and breast muscle yields (p < 0.05). Males had higher follicle density and yellowness (b*) of the skin and better skin than females (p < 0.05). Among blood biochemical parameters, the serum content of corticosterone (CORT) was higher in males, while those of superoxide dismutase (SOD), glutathione peroxidase (GSH-PX), total antioxidant capacity (T-AOC), and catalase (CAT) were lower in males than in females (p < 0.05). The pH levels, shear force, and moisture content quality were better in male breast meat, while the intramuscular fat content (IMF) was lower in males than in females (p < 0.05). The redness (a*) and moisture content were higher in male leg meat, while the pH, water-loss rate (WLR), lightness (L*), and IMF were lower (p < 0.05). The muscle fiber diameter and cross-sectional area were also higher in males (p < 0.05). Consumers felt that soup of male chicken was better than female (p < 0.05), while mouthfeel and tenderness acceptance of breast meat were different between the sexes. These results indicate that female chickens can be marketed as a whole carcass, while males are more suitable for processed carcass products. This study provides significant insights into the production and processing methodologies of yellow-feathered chickens. [ABSTRACT FROM AUTHOR]

Qingyuan partridge chicken is a renowned indigenous yellow broiler breed in China. Egg production traits are important economic traits for chickens. With the decreasing cost of whole genome resequencing, identifying candidate genes with more precision has become possible. In order to identify molecular markers and candidate genes associated with egg production traits, we conducted genome‐wide association studies based on the resequencing data of 287 female Qingyuan partridge chickens. For each hen, age at first egg and egg laying rate were recorded and calculated, respectively. With a univariate linear mixed model, we detected one genome‐wide significant single nucleotide polymorphism (SNP) and three chromosome‐wide significant SNPs associated with egg laying rate. MTA2 is highly likely to be a functional gene for egg laying rate. Our study identifies MTA2 as the first time to be associated with egg laying rate. Findings in our study will advance our understanding of the genetic basis of egg production and have the potential to improve the efficiency of genomic selection in chickens. [ABSTRACT FROM AUTHOR]

Campylobacter hepaticus, the causative agent of Spotty Liver Disease (SLD) is an important disease in cage-free egg producing chickens causing mortality and production drops. C. hepaticus is a slow growing Campylobacter easily overgrown by fecal bacteria. It is currently only reliably isolatable from bile samples. A selective media for isolation from feces or environment would assist diagnosis and impact assessment. Growth of five Australian C. hepaticus isolates was studied using Horse blood agar (HBA), sheep blood agar (SBA), Bolton, Preston and Brain Heart Infusion (BHI) base media. Blood and/or bile were added to Bolton, Preston and BHI medias. C. jejuni was used as a positive control. Plates were incubated in duplicate under microaerophilic conditions at 42°C for 10 days and examined at days 3–5 and 7–10 of incubation. Each isolate was examined for sensitivity to 14 antimicrobials using HBA sensitivity plates. Growth was inhibited by BHI and by added bile, while blood improved growth. Further replicates using SBA, HBA, Bolton and Preston media showed best growth on Bolton agar with blood. All five C. hepaticus isolates were resistant to trimethoprim and vancomycin, while four were also resistant to rifampicin and bacitracin. Media based upon Bolton plus blood supplemented with vancomycin and trimethoprim might be used as the most appropriate media for selective growth of C. hepaticus. The addition of bile to media for C. hepaticus isolation and growth will inhibit growth and is not advised. [ABSTRACT FROM AUTHOR]

Background: Indigenous chickens were developed through a combination of natural and artificial selection; essentially, changes in genomes led to the formation of these modern breeds via admixture events. However, their confusing genetic backgrounds include a genomic footprint regulating complex traits, which is not conducive to modern animal breeding. Results: To better evaluate the candidate regions under domestication in indigenous chickens, we considered both runs of homozygosity (ROHs) and selective signatures in 13 indigenous chickens. The genomes of Silkie feather chickens presented the highest heterozygosity, whereas the highest inbreeding status and ROH number were found in Luhua chickens. Short ROH (< 1 Mb), were the principal type in all chickens. A total of 291 ROH islands were detected, and QTLdb mapping results indicated that body weight and carcass traits were the most important traits. An ROH on chromosome 2 covering VSTM2A gene was detected in 12 populations. Combined analysis with the Tajima's D index revealed that 18 genes (e.g., VSTM2A, BBOX1, and RYR2) were under selection and covered by ROH islands. Transcriptional analysis results showed that RYR2 and BBOX1 were specifically expressed in the heart and muscle tissue, respectively. Conclusion: Based on genome-wide scanning for ROH and selective signatures, we evaluated the genomic characteristics and detected significant candidate genes covered by ROH islands and selective signatures. The findings in this study facilitated the understanding of genetic diversity and provided valuable insights for chicken breeding and conservation strategies. [ABSTRACT FROM AUTHOR]

Background: The chicken body louse is an obligate ectoparasite of domestic chickens. Chicken body lice feed on feathers, and infestation with this louse is linked to decreases in egg production, hen weight, and feed conversion efficiency. However, it is unknown how chicken body lice impact egg-laying chickens in cage-free environments. Welfare and behavior metrics were collected from flocks of egg-laying chickens either infested with chicken body lice or left uninfested. Methods: In two trials, two flocks of cage-free commercial egg-laying chickens were infested with chicken body lice or maintained as uninfested controls. At three timepoints, behavior and welfare of all chickens was measured. On-animal sensors were used to quantify pecking, preening, and dustbathing behavior. Other animal-based welfare metrics included recording comb wounds and skin lesions. Results: Birds infested with chicken body lice exhibited significantly more preening behaviors than uninfested birds, even at low louse levels. Moderate or severe skin lesions were detected on birds that were moderately infested with chicken body lice while skin lesions were never detected on uninfested birds. Conclusions: The welfare of chickens was impacted by the chicken body louse, a chewing louse that primarily feather feeds. Evidence of skin lesions on infested birds suggests that lice may cause more damage to birds than previously thought, and further evaluation of louse economic damage is necessary. [ABSTRACT FROM AUTHOR]

Simple Summary: Lines of White Leghorn chickens divergently selected for high or low antibody response to sheep red blood cells (SRBC) have undergone selection for 50 generations. These lines have allowed for insights into understanding the phenotypic and genotypic changes occurring under phenotypic selection for this single trait. When collecting organ samples from 18-day embryos of generation 48, a difference was seen in the size of the spleen. This observation led to the question of whether the growth of organs associated with immunity had changed after almost 50 generations of selection. Body weights and weights of immune organs representing both primary and secondary immune systems were taken at nine time points. The results showed that divergent selection for the response to SRBC and relaxation of selection resulted in differences in spleen and bursa weights during the later stages of embryonic development and early post-hatch. Long-term divergent selection from a common founder population for a single trait—antibody response to sheep erythrocytes 5 days post-injection—has resulted in two distinct lines of White Leghorn chickens with a well-documented difference in antibody titers: high (HAS)- and low (LAS)-antibody selected lines. Subpopulations—high (HAR)- and low (LAR)-antibody relaxed—were developed from generation 24 of the selected lines to relax selection. The objective of the current experiment was to determine if this long-term selection and relaxation of selection impacted the growth of two organs important to chicken immunity: the spleen and the bursa of Fabricius. Spleens and bursae were obtained from ten chickens per line at nine timepoints (E18, D0, D6, D13, D20, D35, D49, D63, and D91) throughout their rapid growth phase and presented as a percent of body weight. Significance was set at p ≤ 0.05. For the spleen, all lines consistently increased in size relative to body weight to D49, followed by a consistent decline. All lines had a similar growth pattern, but HAS spleens grew faster than LAS spleens. For the bursa, LAS was smaller than the other three lines as an embryo and also smaller than HAS through D63. In the selected lines, bursa weight peaked at D35, whereas the relaxed lines peaked at D49. By D91, there was no difference between lines. Artificial and natural selection, represented by the long-term selected and relaxed antibody lines, resulted in differences in the growth patterns and relative weights of the spleen and bursa of Fabricius. [ABSTRACT FROM AUTHOR]

Gumboro disease is a viral poultry disease that causes immune suppression on the infected birds leading to poor production, mortality, and exposure to secondary infections, hence a major threat in the poultry industry worldwide. A mathematical model of the transmission dynamics of Gumboro disease is developed in this paper having four compartments of chicken population and one compartment of Gumboro pathogen population. The basic reproduction number R og is derived, and the dynamical behaviors of both the disease-free equilibrium (DFE) and endemic equilibrium are analyzed using the ordinary differential equation theory. From the analysis, we found that the system exhibits an asymptotic stable DFE whenever R og < 1 and an asymptotic stable EE whenever R og > 1. The numerical simulation to verify the theoretical results was carried out using MATLAB ode45 solver, and the results were found to be consistent with the theoretical findings. [ABSTRACT FROM AUTHOR]

The genetic complexity of polygenic traits represents a captivating and intricate facet of biological inheritance. Unlike Mendelian traits controlled by a single gene, polygenic traits are influenced by multiple genetic loci, each exerting a modest effect on the trait. This cumulative impact of numerous genes, interactions among them, environmental factors, and epigenetic modifications results in a multifaceted architecture of genetic contributions to complex traits. Given the well-characterized genome, diverse traits, and range of genetic resources, chicken (Gallus gallus) was employed as a model organism to dissect the intricate genetic makeup of a previously identified major Quantitative Trait Loci (QTL) for body weight on chromosome 1. A multigenerational advanced intercross line (AIL) of 3215 chickens whose genomes had been sequenced to an average of 0.4x was analyzed using genome-wide association study (GWAS) and variance-heterogeneity GWAS (vGWAS) to identify markers associated with 8-week body weight. Additionally, epistatic interactions were studied using the natural and orthogonal interaction (NOIA) model. Six genetic modules, two from GWAS and four from vGWAS, were strongly associated with the studied trait. We found evidence of both additive- and non-additive interactions between these modules and constructed a putative local epistasis network for the region. Our screens for functional alleles revealed a missense variant in the gene ribonuclease H2 subunit B (RNASEH2B), which has previously been associated with growth-related traits in chickens and Darwin's finches. In addition, one of the most strongly associated SNPs identified is located in a non-coding region upstream of the long non-coding RNA, ENSGALG00000053256, previously suggested as a candidate gene for regulating chicken body weight. By studying large numbers of individuals from a family material using approaches to capture both additive and non-additive effects, this study advances our understanding of genetic complexities in a highly polygenic trait and has practical implications for poultry breeding and agriculture. [ABSTRACT FROM AUTHOR]

Marek's disease (MD) is an important neoplastic disease caused by serotype 1 Marek's disease virus (MDV-1), which results in severe economic losses worldwide. Despite vaccination practices that have controlled the MD epidemic, current increasing MD-suspected cases indicate the persistent viral infections circulating among vaccinated chicken farms in many countries. However, the lack of available information about phylogeny and molecular characterization of circulating MDV-1 field strains in Taiwan reveals a potential risk in MD outbreaks. This study investigated the genetic characteristics of 18 MDV-1 strains obtained from 17 vaccinated chicken flocks in Taiwan between 2018 and 2020. Based on the sequences of the meq oncogene, the phylogenetic analysis demonstrated that the circulating Taiwanese MDV-1 field strains were predominantly in a single cluster that showed high similarity with strains from countries of the East Asian region. Because the strains were obtained from CVI988/Rispens vaccinated chicken flocks and the molecular characteristics of the Meq oncoprotein showed features like vvMDV and vv+MDV strains, the circulating Taiwanese MDV-1 field strains may have higher virulence compared with vvMDV pathotype. In conclusion, the data presented demonstrates the circulation of hypervirulent MDV-1 strains in Taiwan and highlights the importance of routine surveillance and precaution strategies in response to the emergence of enhanced virulent MDV-1. [ABSTRACT FROM AUTHOR]

Background: Triatoma infestans, Triatoma brasiliensis, Triatoma pseudomaculata and Rhodnius prolixus are vectors of Trypanosoma cruzi, the etiological agent of Chagas disease. Chickens serve as an important blood food source for triatomines. This study aimed to assess the insecticidal activity of fluralaner (Exzolt®) administered to chickens against triatomines (R. prolixus, T. infestans, T. brasiliensis and T. pseudomaculata). Methods: Twelve non-breed chickens (Gallus gallus domesticus) were randomized based on weight into three groups: negative control (n = 4); a single dose of 0.5 mg/kg fluralaner (Exzolt®) (n = 4); two doses of 0.5 mg/kg fluralaner (Exzolt®) (n = 4). Nymphs of 3rd, 4th and 5th instars of R. prolixus, T. infestans, T. brasiliensis and T. pseudomaculata (all n = 10) were allowed to feed on chickens before treatment, and at intervals of 1, 7, 14, 21, 28, 35 and 56 days after treatment, with insect mortality determined. Results: Treatment with two doses of fluralaner showed higher insecticidal efficacy against R. prolixus, T. infestans and T. brasiliensis compared to the single-dose treatment. Similar insecticidal efficacy was observed for T. pseudomaculata for one and two doses of fluralaner. Insecticidal activity of fluralaner (Exzolt®) against triatomine bugs was noted up to 21 and 28 days after treatment with one and two doses of fluralaner, respectively. Conclusions: The results demonstrate that treatment of chickens with fluralaner (Exzolt®) induces insecticidal activity against triatomines for up to 28 days post-treatment, suggesting its potential use as a control strategy for Chagas disease in endemic areas. [ABSTRACT FROM AUTHOR]

In recent years, the scale of poultry breeding in China is gradually expanding, and the demand for feed raw materials is also rising. At present, the poultry industry is facing the problem of shortage of protein feed resources, so it is urgent to find high-quality and sustainable protein feed raw materials. The edible insect black soldier fly (Hermetia illucens L., BSF) has become a potential sustainable new protein feed, which can replace traditional protein feed materials such as soybean meal and fish meal. BSF is a saprophytic insect, which mainly feeds on organic waste, and has the characteristics of rapid growth and reproduction, extensive feeding and high feed conversion rate. The larvae or pre-pupae of BSF are rich in protein, fat, minerals, and trace elements, and their content of essential amino acids is comparable to that of fish meal and soybean meal. They also contain bioactive substances such as lauric acid, antimicrobial peptides, and chitin. Based on the nutritional characteristics of BSF larvae and processed products, this paper reviewed the research progress of BSF in poultry breeding, in order to provide a reference for the wide application of BSF in poultry production. [ABSTRACT FROM AUTHOR]

At present, the global concern about food safety and environmental pollution is increasing day by day. Reducing the use of toxic and harmful additives such as antibiotics, hormones, and chemicals in livestock and poultry feed, developing green, safe, efficient, and low-residue additives, ensuring consumers' health, and improving the ecological environment are the focus of animal husbandry at present. Flavonoids are secondary metabolites of plants, which widely exist in bark, root, stem, leaf, fruit, and seeds of plants. They have many biological activities such as anti-inflammation, anti-oxidation, reducing oxidative stress, protecting intestinal mucosa, improving intestinal flora structure, promoting growth, and regulating immunity, etc. They can improve animal production performance and product quality, and have potential development value to enhance the economic benefits of farms. In this paper, the role of flavonoids and their application in livestock and poultry breeding were reviewed, and the application research progress of flavonoids in calves and adult cattle was emphasized, to provide a reference for its rational application in cattle production at different growth stages. [ABSTRACT FROM AUTHOR]

Aims In this study, we evaluated the phenotypic virulence characteristics of avian pathogenic Escherichia coli (APEC) isolates from broiler breeders with colibacillosis in Mississippi. Also, the relationship between phenotypic and genotypic virulence patterns was determined. Methods and Results Twenty-eight APEC isolated from lesions of broiler breeders diagnosed with colibacillosis were used for embryo lethality assay and chick challenge study. The percentage of embryo mortality following embryo lethality assay and pathogenicity score following the chick challenge study were used to categorize the isolates based on virulence. Pearson correlation analysis was performed to determine the relationship between embryo mortality, chick pathogenicity, and the presence of virulence-associated genes in the isolates. Overall, 39.3% of the isolates were highly virulent and 3.5% were avirulent, following both assays. There existed a positive correlation between embryo mortality and chick pathogenicity (r  = 0.73, P  < .01), as well as percentage embryo mortality and pathogenicity score with the presence of some virulence genes. Conclusions Even though all the APEC were isolated from lesions of diseased breeders, the virulence potential varied from being avirulent to highly virulent. Further, we identified a positive relationship between phenotypic virulence and the frequency of virulence-associated genes. [ABSTRACT FROM AUTHOR]

Following a request from the European Commission, EFSA was asked to deliver a scientific opinion on the safety and efficacy of muramidase produced with Trichoderma reesei DSM 32338 (Balancius™) as a feed additive for laying hens. The additive is already authorised as a zootechnical additive (functional group: other zootechnical additives) for chickens, turkeys and minor poultry species for fattening or reared for breeding, and for weaned piglets. The enzyme is produced by fermentation with a genetically modified strain of Trichoderma reesei; viable cells of the production strain and its recombinant DNA were not detected in the additive. The EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) concluded that the additive does not give rise to safety concerns regarding the genetic modification of the production strain. Based on the data available from a sub‐chronic oral toxicity study, the Panel concluded that the additive is safe for laying hens at the maximum recommended level of 60,000 LSU(F) (muramidase activity units)/kg feed. The Panel also concluded that the additive is safe for the consumers and the environment. The liquid formulation of the additive is considered not irritant to the skin or eyes. The solid formulation of the additive is considered not irritant to the skin. The Panel cannot conclude on the potential of the additive (both formulations) to be a dermal sensitiser or on the potential of the solid formulation to be irritant to the eyes. Due to the proteinaceous nature, both forms of the additive should be considered respiratory sensitisers. The additive has the potential to be efficacious as a zootechnical additive for laying hens at 30,000 LSU(F)/kg feed. [ABSTRACT FROM AUTHOR]

Meat and eggs from chicken are the major source of animal protein for the human population. The cryopreservation of poultry species is needed to guarantee sustainable production. Here, we describe the existing cryopreservation technologies for avian reproductive cells using embryonic germ cells, spermatozoa and ovarian tissues. We outline strategies to reconstitute chicken breeds from their cryopreserved embryonic germ cells using surrogate hosts and discuss the perspectives for genetic conservation and reconstitution of chicken and wild avian species using surrogate host animals. [ABSTRACT FROM AUTHOR]

Background: Although multiple chicken genomes have been assembled and annotated, the numbers of protein-coding genes in chicken genomes and their variation among breeds are still uncertain due to the low quality of these genome assemblies and limited resources used in their gene annotations. To fill these gaps, we recently assembled genomes of four indigenous chicken breeds with distinct traits at chromosome-level. In this study, we annotated genes in each of these assembled genomes using a combination of RNA-seq- and homology-based approaches. Results: We identified varying numbers (17,497–17,718) of protein-coding genes in the four indigenous chicken genomes, while recovering 51 of the 274 "missing" genes in birds in general, and 36 of the 174 "missing" genes in chickens in particular. Intriguingly, based on deeply sequenced RNA-seq data collected in multiple tissues in the four breeds, we found 571 ~ 627 protein-coding genes in each genome, which were missing in the annotations of the reference chicken genomes (GRCg6a and GRCg7b/w). After removing redundancy, we ended up with a total of 1,420 newly annotated genes (NAGs). The NAGs tend to be found in subtelomeric regions of macro-chromosomes (chr1 to chr5, plus chrZ) and middle chromosomes (chr6 to chr13, plus chrW), as well as in micro-chromosomes (chr14 to chr39) and unplaced contigs, where G/C contents are high. Moreover, the NAGs have elevated quadruplexes G frequencies, while both G/C contents and quadruplexes G frequencies in their surrounding regions are also high. The NAGs showed tissue-specific expression, and we were able to verify 39 (92.9%) of 42 randomly selected ones in various tissues of the four chicken breeds using RT-qPCR experiments. Most of the NAGs were also encoded in the reference chicken genomes, thus, these genomes might harbor more genes than previously thought. Conclusion: The NAGs are widely distributed in wild, indigenous and commercial chickens, and they might play critical roles in chicken physiology. Counting these new genes, chicken genomes harbor more genes than originally thought. [ABSTRACT FROM AUTHOR]

Identifying and analysing distinct blood cells is crucial for the diagnosis and treatment of diseases in the field of biomedicine. The present study was undertaken to study the cytomorphological and cytochemical characteristics of the blood cells of Zoar, a non‐descript indigenous breed of chicken extensively reared under backyard poultry farming in Mizoram, India. For this study, 2 mL of blood samples were aseptically collected from the wings veins of 12 chickens and were processed for light microscopic study under standard protocols. The matured erythrocytes were elliptical, while the immature erythrocytes appeared oval. The heterophils were positive for SBB (SBB), Periodic Acid Schiff (PAS), acid phosphatase, alkaline phosphatase and Arylsulphatase while the eosinophils were positive for SBB, PAS, alkaline phosphatase, cytochrome oxidase and peroxidase. The basophils of were positive for toluidine blue while the thrombocytes were positive for PAS. These cytochemical and cytoenzymatic staining properties plays a very important role in diagnosis, differentiation, and classification of leukaemias. [ABSTRACT FROM AUTHOR]

Background: Although many studies have been done to reveal artificial selection signatures in commercial and indigenous chickens, a limited number of genes have been linked to specific traits. To identify more trait-related artificial selection signatures and genes, we re-sequenced a total of 85 individuals of five indigenous chicken breeds with distinct traits from Yunnan Province, China. Results: We found 30 million non-redundant single nucleotide variants and small indels (< 50 bp) in the indigenous chickens, of which 10 million were not seen in 60 broilers, 56 layers and 35 red jungle fowls (RJFs) that we compared with. The variants in each breed are enriched in non-coding regions, while those in coding regions are largely tolerant, suggesting that most variants might affect cis-regulatory sequences. Based on 27 million bi-allelic single nucleotide polymorphisms identified in the chickens, we found numerous selective sweeps and affected genes in each indigenous chicken breed and substantially larger numbers of selective sweeps and affected genes in the broilers and layers than previously reported using a rigorous statistical model. Consistent with the locations of the variants, the vast majority (~ 98.3%) of the identified selective sweeps overlap known quantitative trait loci (QTLs). Meanwhile, 74.2% known QTLs overlap our identified selective sweeps. We confirmed most of previously identified trait-related genes and identified many novel ones, some of which might be related to body size and high egg production traits. Using RT-qPCR, we validated differential expression of eight genes (GHR, GHRHR, IGF2BP1, OVALX, ELF2, MGARP, NOCT, SLC25A15) that might be related to body size and high egg production traits in relevant tissues of relevant breeds. Conclusion: We identify 30 million single nucleotide variants and small indels in the five indigenous chicken breeds, 10 million of which are novel. We predict substantially more selective sweeps and affected genes than previously reported in both indigenous and commercial breeds. These variants and affected genes are good candidates for further experimental investigations of genotype-phenotype relationships and practical applications in chicken breeding programs. [ABSTRACT FROM AUTHOR]

The policy of "changing grain to forage" is an important means to optimize the structure of farming and breeding, a powerful measure to boost the agricultural economy, and the core of promoting high-quality development of the aquaculture industry. Based on the double difference model, panel data from eight provinces implementing the "changing grain to forage" policy was selected to explore the impact of the implementation of the "changing grain to forage" policy on the scale of livestock and poultry breeding. The research results show that the implementation of the "changing grain to forage" policy has a certain driving effect on the expansion of livestock and poultry breeding scale in China. The level of intelligent breeding and fixed asset investment has a significant promoting effect on the scale of livestock and poultry breeding. The price of calves and the intensity of disease occurrence have inhibitory effects on the scale of livestock and poultry farming. Further research has found that the implementation of the "changing grain to forage" policy can significantly promote the large-scale development of livestock and poultry in breeding farms. The level of intelligent breeding has a more significant positive effect on large-scale breeding farms. Compared to medium scale farms, the intensity of disease occurrence has a relatively small adverse impact on large-scale farms. [ABSTRACT FROM AUTHOR]

With the rapid development of intensive poultry breeding in China, the demand for poultry feed raw materials is increasing rapidly. However, the shortage of cereal feed and the persistently high price make it urgent for poultry feed production industry to explore cheaper energy alternative feed. Cassava has the characteristics of high yield, rich starch and fiber, high energy value, etc. It can replace corn or other energy feed in poultry breeding. The effective use of cassava products has been proved to reduce the feed cost of poultry production. However, the utilization of cassava is limited by many factors, such as low protein and anti-nutritional factors. Using correct processing and scientific formula, the addition level of cassava in poultry diet can be improved. In this paper, the nutritional characteristics, feed utilization, and application of cassava in poultry diet were reviewed, which provided a reference for the application of cassava in poultry diet. [ABSTRACT FROM AUTHOR]

Strain-specific probiotics can present antioxidant activity and reduce damage caused by oxidation. Streptococcus alactolyticus strain FGM (S. alactolyticus strain FGM) isolated from the chicken cecum shows potential probiotic properties which have been previously demonstrated. However, the antioxidant properties of S. alactolyticus strain FGM remain unknown. In this view, cell-free supernatant (CFS), intact cells (IC) and intracellular extracts (CFE) of strain FGM and 3 strains of Lactobacillus (LAB) were prepared, and their scavenging capacities against DPPH, hydroxyl radicals and linoleic acid peroxidation inhibitory were compared in this study. The effects of strain FGM cell-free supernatant (FCFS) on NO production, activity of SOD and GSH-Px in RAW264.7 cells and LPS-induced RAW264.7 cells were analyzed. The metabolites in the supernatant were quantitated by N300 Quantitative Metabolome. It was shown that the physicochemical characteristics of CFS to scavenge DPPH, hydroxyl radicals, and linoleic acid peroxidation inhibitory were significantly stronger than that of IC and CFE in the strain FGM (P < 0.05), respectively 87.12% ± 1.62, 45.03% ± 1.27, 15.63% ± 1.34. FCFS had a promotional effect on RAW264.7 cells, and significantly elevated SOD and GSH-Px activities in RAW264.7 cells. 25 μL FCFS significantly promoted the proliferation of RAW264.7 cells induced by LPS, increased the activities of SOD and GSH-PX, and decreased the release of NO. Furthermore, among the differential metabolites of FCFS quantified by N300, 12 metabolites were significantly up-regulated, including lactic acid, indole lactic acid, linoleic acid, pyruvic acid etc., many of which are known with antioxidant properties. In conclusion, FCFS had good antioxidant properties and activity, which can be attributed to metabolites produced from strain FGM fermentation. It was further confirmed that S. alactolyticus strain FGM and its postbiotic have potential probiotic properties and bright application prospects in livestock and poultry breeding. [ABSTRACT FROM AUTHOR]

Avian pathogenic Escherichia coli (APEC) is primarily responsible for causing septicemia, pneumonitis, peritonitis, swollen head syndrome, and salpingitis in poultry, leading to significant losses in the poultry sector, particularly within the broiler industry. The removal of the lpxL and lpxM genes led to an eightfold decrease in the endotoxin levels of wild APEC strains. In this study, mutant strains of lpxL / lpxM and their O1, O2, and O78 wild-type strains were developed for an inactivated vaccine (referred to as the mutant vaccine and the wild-type vaccine, respectively), and the safety and effectiveness of these two prototype vaccines were assessed in white Leghorn chickens. Findings indicated that chickens immunized with the mutant vaccine showed a return of appetite sooner post-immunization and experienced earlier disappearance of nodules at the injection site compared to those immunized with the wild-type vaccine. Pathological examinations revealed that lesions were still present in the liver, lung, and injection site in chickens vaccinated with the wild-type vaccine 14 days post-vaccination (dpv), whereas no lesions were found in chickens vaccinated with the mutant vaccine at 14 dpv. There were no significant differences in antibody levels on the challenge day or in mortality or lesion scores between challenged birds immunized with either the mutant vaccine or the wild-type vaccine at the same dose. In this study, the safety of a single dose or overdose of the mutant vaccine and its efficacy at one dose were evaluated in broilers, and the results showed that the mutant vaccine had no adverse effects on or protected vaccinated broilers from challenge with the APEC O1, O2, or O78 strains. These results demonstrated that the mutant polyvalent inactivated vaccine is a competitive candidate against APEC O1, O2, and O78 infection compared to the wild-type vaccine. [ABSTRACT FROM AUTHOR]

Influenza A viruses (IAVs) can overcome species barriers by adaptation of the receptor-binding site of the hemagglutinin (HA). To initiate infection, HAs bind to glycan receptors with terminal sialic acids, which are either N-acetylneuraminic acid (NeuAc) or N-glycolylneuraminic acid (NeuGc); the latter is mainly found in horses and pigs but not in birds and humans. We investigated the influence of previously ident ified equine NeuGc-adapting mutations (S128T, I130V, A135E, T189A, and K193R) in avian H7 IAVs in vitro and in vivo. We observed that these mutations negatively affected viral replication in chicken cells but not in duck cells and positively affected replication in horse cells. In vivo, the mutations reduced virus virulence and mortality in chickens. Ducks excreted high viral loads longer than chickens, although they appeared clinically healthy. To elucidate why these viruses infected chickens and ducks despite the absence of NeuGc, we re-evaluated the receptor binding of H7 HAs using glycan microarray and flow cytometry studies. This re-evaluation demonstrated that mutated avian H7 HAs also bound to a2,3-linked NeuAc and sialyl-LewisX, which have an additional fucose moiety in their terminal epitope, explaining why infection of ducks and chickens was possible. Interestingly, the a2,3-linked NeuAc and sialyl-LewisX epitopes were only bound when presented on tri-antennary N-glycans, emphasizing the importance of investigating the fine receptor specificities of IAVs. In conclusion, the binding of NeuGc-adapted H7 IAV to tri-antennary N-glycans enables viral replication and shedding by chickens and ducks, potentially facilitating interspecies transmission of equine-adapted H7 IAVs. IMPORTANCE Influenza A viruses (IAVs) cause millions of deaths and illnesses in birds and mammals each year. The viral surface protein hemagglutinin initiates infection by binding to host cell terminal sialic acids. Hemagglutinin adaptations affect the binding affinity to these sialic acids and the potential host species targeted. While avian and human IAVs tend to bind to N-acetylneuraminic acid (sialic acid), equine H7 viruses prefer binding to N-glycolylneuraminic acid (NeuGc). To better understand the function of NeuGc-specific adaptations in hemagglutinin and to elucidate interspecies transmission potential NeuGc-adapted viruses, we evaluated the effects of NeuGc-specific mutations in avian H7 viruses in chickens and ducks, important economic hosts and reservoir birds, respectively. We also examined the impact on viral replication and found a binding affinity to tri-antennary N-glycans containing different terminal epitopes. These findings are significant as they contribute to the understanding of the role of receptor binding in avian influenza infection. [ABSTRACT FROM AUTHOR]

Mortality of chicken embryos and first-week chickens was reported in a commercial incubator company in Costa Rica. Six 1-day-old Cobb chickens and twenty-four embryonated chicken eggs were examined in the Laboratory of Avian Pathology and the Laboratory of Bacteriology of the National University of Costa Rica. Twelve dead-in-shell embryos showed maceration and were immersed in a putrid, turbid, slightly thick brown liquid. Additionally, the other 12 embryonated eggs had milky yellow-orange content. The livers of those embryos had congestion, haemorrhages and multifocal cream foci of necrosis. Granulocytic infiltration was observed in the bursa of Fabricius, myocardium, liver, lung and kidney. Livers and egg yolks from six embryonated chickens and all 1-day-old chickens were aseptically collected and cultured. In addition, tissues from six better conserved embryos and all 1-day-old chickens were fixed in buffered formalin and embedded in paraffin. Biochemical and molecular tests identified Comamonas testosteroni as the cause of the early, middle and late embryo mortality. As all the eggshells from the sampled embryonated eggs were dirty with soiled a fecal matter, contamination after manipulating the eggs was considered the source of infection. C. testosteroni is an environmental microorganism that has rarely been reported to cause human disease. To our knowledge, this is the first report of C. testosteroni causing mortality in a hatchery. Cleaning and disinfection using ozone were implemented in the hatchery to eliminate the embryo mortality associated with C. testosteroni. [ABSTRACT FROM AUTHOR]

Black soldier fly larvae ( Hermetia illucens L.) is a kind of scavenging insect, which can convert organic waste such as animal feces, kitchen waste, and plant residues into its own nutrition, so as to achieve green and efficient transformation of resources. Larvae, especially defatted meal, is a good source of dietary protein. At present, most of the studies on forage fertilization of black soldier fly larvae are focused on protein nutrition, but there are few studies on black soldier fly larvae oil. The paper describes the main components of black soldier fly larvae oil, analyzes its nutritional value as feed, summarizes the main factors affecting the quality of black soldier fly larvae oil, reviews the research progress of using black soldier fly larvae oil instead of traditional feed in livestock, aquatic products, and other animal breeding at home and abroad, and puts forward some shortcomings and improvement methods of black soldier fly larvae oil as feed, to provide a reference for fully exploiting the application potential of the black soldier fly larvae oil. [ABSTRACT FROM AUTHOR]

Background: Chicken is one of the most numerous and widely distributed species around the world, and many studies support the multiple ancestral origins of domestic chickens. The research regarding the yellow skin phenotype in domestic chickens (regulated by BCO2) likely originating from the grey junglefowl serves as crucial evidence for demonstrating the multiple origins of chickens. However, beyond the BCO2 gene region, much remains unknown about the introgression from the grey junglefowl into domestic chickens. Therefore, in this study, based on whole-genome data of 149 samples including 4 species of wild junglefowls and 13 local domestic chicken breeds, we explored the introgression events from the grey junglefowl to domestic chickens. Results: We successfully detected introgression regions besides BCO2, including two associated with growth trait (IGFBP2 and TKT), one associated with angiogenesis (TIMP3) and two members of the heat shock protein family (HSPB2 and CRYAB). Our findings suggest that the introgression from the grey junglefowl may impact the growth performance of chickens. Furthermore, we revealed introgression events from grey junglefowl at the BCO2 region in multiple domestic chicken breeds, indicating a phenomenon where the yellow skin phenotype likely underwent strong selection and was retained. Additionally, our haplotype analysis shed light on BCO2 introgression event from different sources of grey junglefowl into domestic chickens, possibly suggesting multiple genetic flows between the grey junglefowl and domestic chickens. Conclusions: In summary, our findings provide evidences of the grey junglefowl contributing to the genetic diversity of domestic chickens, laying the foundation for a deeper understanding of the genetic composition within domestic chickens, and offering new perspectives on the impact of introgression on domestic chickens. [ABSTRACT FROM AUTHOR]

Zika virus (ZIKV) remains a public health concern, with epidemics in endemic regions and sporadic outbreaks in new areas posing significant threats. Several mosquito-borne flaviviruses that can cause human illness, including West Nile, Usutu, and St. Louis encephalitis, have associations with birds. However, the susceptibility of chickens to ZIKV and their role in viral epidemiology is not currently known. We investigated the susceptibility of chickens to experimental ZIKV infection using chickens ranging from 1-day-old chicks to 6-week-old birds. ZIKV caused no clinical signs in chickens of all age groups tested. Viral RNA was detected in the blood and tissues during the first 5 days post-inoculation in 1-day and 4-day-old chicks inoculated with a high viral dose, but ZIKV was undetectable in 6-week-old birds at all timepoints. Minimal antibody responses were observed in 6-week-old birds, and while present in younger chicks, they waned by 28 days post-infection. Innate immune responses varied significantly between age groups. Robust type I interferon and inflammasome responses were measured in older chickens, while limited innate immune activation was observed in younger chicks. Signal transducer and activator of transcription 2 (STAT2) is a major driver of host restriction to ZIKV, and chicken STAT2 is distinct from human STAT2, potentially contributing to the observed resistance to ZIKV infection. The rapid clearance of the virus in older chickens coincided with an effective innate immune response, highlighting age-dependent susceptibility. Our study indicates that chickens are not susceptible to productive ZIKV infection and are unlikely to play a role in the ZIKV epidemiology. [ABSTRACT FROM AUTHOR]

Over the last few decades, progress in molecular biology and genetic technologies has allowed scientists to explore the mechanisms of lipid metabolism in chickens. Through techniques like RNA sequencing and gene expression profiling, researchers can now investigate how dietary fat supplements impact the expression of particular genes related to lipid metabolism regulation. Limited research exists on the comparative impacts of fat powder and fatty acid incorporation in broiler feed on the expression of lipid metabolism-regulating genes in the liver. This study aims to identify particular genes and metabolic pathways linked to reduced abdominal fat deposition in commercial broiler chickens. The study involved 500 broiler chickens from the commercial strain Ross 308, distributed in a completely randomized layout with five different treatments and five replications. The duration of the research lasted for 42 days. Initially, the control group received no fatty acid or fat powder, whereas the other groups were supplemented with either 3% or 6% fat powder or fatty acid. The experimental period was divided into two distinct phases: the starter phase (0-21 days) and the grower phase (22-41 days). Fatty acid synthase (FASN), malic enzyme 1 (ME1), stearoyl-CoA desaturase (SCD), glycerol-3-phosphate acyltransferase 3 (GPAT3), glycerol-3-phosphate acyltransferase, mitochondrial (GPAM), CD36 molecule (CD36), carnitine palmitoyltransferase 1A (CPT1A), carnitine palmitoyltransferase 2 (CPT2), acyl-CoA oxidase 1 (ACOX1), apolipoprotein B (APOB), very low-density apolipoprotein II (apoVLDLII), peroxisome proliferator-activated receptor alpha (PPARa), peroxisome proliferator-activated receptor gamma (PPARγ) genes selected as indicators of lipid metabolism-regulation and were studied using qPCR technique. The impact of fatty acids (FA) on the regulation of genes under investigation was found to be more pronounced. However, both types of fat increased abdominal fat, with FA demonstrating a stronger effect. While the fat level was deemed significant in certain instances, the current findings and methodology suggest that a 3% fat supplement may be a more cost-effective and economical option for farm use. To further enhance the initial findings and gain a more comprehensive understanding of fat metabolism in poultry, future studies should involve comparative and correlative analyses, encompass a wider range of fat sources, and consider production traits in conjunction with genes associated with fatty acids in the liver. [ABSTRACT FROM AUTHOR]

The pre-starter diet is critical for providing adequate nutrition to newly hatched chicks, whose digestive systems are not yet fully developed to handle solid feeds. Different levels of dietary energy can impact the growth and development of broilers. Hence, providing the right energy to meet their requirements is necessary. A study was conducted to examine the effect of different levels of metabolizable energy (ME) (3025, 2904, and 2783 kcal/kg) in the pre-starter diet (1 to 10 days) of broiler chickens on their growth performance traits. The experiment involved 450 broilers of the Ross 308 breed, divided into three treatments and six replications. The results of the study showed that reducing dietary energy levels increased the feed intake (FI) and body weight (BW) of broiler chickens, although it did not affect their feed conversion factor (FCR). Based on the results of the current study, reducing the recommended energy levels by up to 5% had no negative impact on growth performance. This can be useful in reducing the feed expense in broiler production. [ABSTRACT FROM AUTHOR]

Background and Aim: Filarial nematode typically produces a larval stage (microfilariae) in the bloodstream of vertebrate hosts, where microfilariae reside in the blood or subcutaneous tissues. Filarial nematodes cause human diseases, such as river blindness and elephantiasis, which are widely studied. However, in avian species, they are overlooked because they are nonpathogenic. In Thailand, microfilaria can be found in wild birds and domestic chickens. Recently, an increase in the number of blood samples submitted to veterinary diagnostic laboratories may have increased the number of microfilariae. Therefore, knowledge about filarial species and reliable detection methods are important. Therefore, this study aimed to investigate the efficacy of buffy coat smear and polymerase chain reaction (PCR)-based methods for the detection of microfilaria in domestic chickens. In addition, parasites were identified using the sequence of the cytochrome c oxidase subunit 1 (COX1) gene. Materials and Methods: Giemsa-stained buffy coat smears from a previous study were reanalyzed. These available buffy coat smears were prepared from 55 domestic chickens raised as backyard free-ranging in Southern Thailand. Fifty-seven frozen genomic DNA extracted from chicken blood were used to detect the presence of the COX1 gene in Onchocercidae nematodes. The nested PCR protocol for amplification of the OnchoCOI_R2-OnchoCOI_R2 fragment of the COX1 gene was applied from a previous report. Sequences of COX1 were analyzed to identify Onchocercidae nematodes and if they were single or mixed infections. We constructed Bayesian phylogenetics to identify parasites and assessment of the relationship between filarial nematodes in avian species and other vertebrate hosts. Results: Buffy coat smears from 15 samples revealed microfilaria. Of these 15 samples, only eight were positive for COX1 nested-PCR amplification. The other two buffy coat-negative samples were also positive for nested-PCR. Sequencing of these 11 nested PCR-positive samples revealed that almost all of them were Onchocercidae nematodes. Bayesian phylogenetic analysis showed that chicken Onchocercidae spp. were grouped with other avian filarial nematodes. However, all chickens Onchocercidae spp. showed a double peak in the sequencing chromatogram, indicating mixed filarial infection (species or haplotypes). Therefore, no chicken Onchocercidae sequence was deposited on National Center for Biotechnology Information, GenBank. Conclusion: Giemsa-stained buffy coat smear was a reliable method for the detection of chicken microfilaria in routine veterinary diagnostic laboratories. Development of a new PCR-based method is necessary. This method may provide greater sensitivity and specificity of detection. In addition, the PCR method allowed us to access the genetic characteristics of nematodes, which helped us maximize our knowledge of nematodes. Further investigations, such as the pathogenicity of filarial nematodes in chickens and their potential vectors, are required. [ABSTRACT FROM AUTHOR]

Following a request from the European Commission, the Panel on Additives and Products or Substances used in Animal Feed (FEEDAP Panel) was asked to deliver a scientific opinion on the safety for the users of the feed additive consisting of ferric tyrosine chelate (TYFER™) when used as a zootechnical additive for chickens, turkeys and minor poultry species for fattening or reared for laying/breeding. The European Commission request follows a previous opinion of the FEEDAP Panel. In that opinion, the Panel identified several risks for the users of the additive; it was listed that it posed a risk to users by inhalation, should be considered as an irritant to skin, eyes and mucous membranes, and also that, due to its nickel content, should be considered as a dermal and respiratory sensitiser. In the current application, the applicant proposed a maximum content of nickel (50 mg/kg). No changes in the manufacturing process have been reported by the applicant. In the absence of new data, the FEEDAP Panel reiterates its previous conclusion that the additive should be as an irritant to skin, eyes and mucous membranes and as a dermal and respiratory sensitiser. [ABSTRACT FROM AUTHOR]

Following a request from the European Commission, EFSA was asked to deliver a scientific opinion on the safety and efficacy of a tincture from the dried fruit of Schisandra chinensis (Turcz.) Baill. (omicha tincture), when used as a sensory additive in feed for horses, cats, dogs, and in feed and in water for drinking for poultry. The product is a water/ethanol (55:45 v/v) solution, with a dry matter content of not more than 4% (w/w) and a content of 0.01%–0.15% (w/w) for the sum of schisandrin and deoxyschisandrin. The Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) concluded that omicha tincture is safe at the following concentrations in complete feed: 16 mg/kg for turkeys for fattening, 12 mg/kg for chickens for fattening and other poultry for fattening or reared for laying/reproduction, 18 mg/kg for laying hens and other laying/reproductive birds, 56 mg/kg for dogs and 47 mg/kg for horses and cats. The additive is considered safe for consumers when used up to the highest safe level in feed for poultry species and horses. Omicha tincture should be considered as irritants to skin and eyes, and as dermal and respiratory sensitisers. The use of omicha tincture as a flavour in feed for poultry species and horses was not considered to be a risk to the environment. Since it was recognised that the fruit of S. chinensis can influence sensory properties of feedingstuffs, no further demonstration of efficacy was considered necessary for the tincture under assessment. [ABSTRACT FROM AUTHOR]

Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZFST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits. [ABSTRACT FROM AUTHOR]

The study describes three clinical cases of infection with Avibacterium spp.. In case no. 1, respiratory clinical signs and high mortality (0.7–4.2% daily; total 21.2%) in Ross 308 broiler chickens were shown to be caused by coinfection with sequence type 9 of O. rhinotracheale presumptive serotype A and A. paragallinarum presumptive serotype B. The identical (pulsed-field gel electrophoresis) restriction pattern (pulsotype) of seven A. paragallinarum isolates indicated that infectious coryza in broilers was caused by the same clone. In cases 2 and 3, sudden increased deaths in Ross 308 broiler breeders (especially males) with lesions in the endocardium (valvular or mural endocarditis) were shown to be caused by A. endocarditis. Among nine antibiotics tested, florfenicol was the only antibiotic to which all A. paragallinarum and O. rhinotracheale isolates were susceptible. Out of the eight antibiotics tested, 11 A. endocarditis isolates from both clinical cases of infective endocarditis were susceptible to penicillin, amoxicillin, doxycycline and florfenicol. The A. endocarditis isolates tested in both clinical cases had different PFGE patterns (pulsotypes), but identical within a case. The causes of infectious coryza and infective endocarditis in the cases presented have not been determined. In the prevention of infectious diseases in large-scale livestock farming, it is very important to follow the rules of biosecurity. [ABSTRACT FROM AUTHOR]

Body weight is an economically important trait in poultry that shows sexual dimorphism (SD). In the present study, variation in SD in Mazandaran native chickens was investigated in terms of the (Co) variance components and genetic parameters of body weight between males and females. Studied traits were body weights at hatch (BW1), 8 weeks (BW8) and 12 weeks of age (BW12). Also, for weight at sexual maturity (WSM) covariance components were only estimated in females. Cross‐sex direct and maternal correlations were also estimated for studied traits except for WSM. For this purpose, a deep 21‐generation pedigree and body weight data (57,576 BW1, 72,925 BW8, 62,727 BW12 and, 42,496 WSM) were used. Evaluation of SD of body weight was performed using six bivariate animal models with and without considering the genetic and permanent maternal environmental effects under the restricted maximum likelihood method in WOMBAT software. Model with direct additive genetic effects and maternal genetic effects without covariance between them was identified as the best model for BW1 and BW8. The Model including direct additive genetic effects and permanent maternal environmental effects was the best model for BW12 and WSM. Direct heritability (h2) estimates for BW1, BW8 and, BW12 were, respectively, 0.05 ± 0.013, 0.17 ± 0.02 and, 0.25 ± 0.03 in males and, 0.05 ± 0.012, 0.15 ± 0.01 and 0.21 ± 0.01 in females. Also, the direct heritability of WSM based on univariate analysis in females was estimated to be 0.40 ± 0.01. Maternal heritability (hm2) varied from 0.39 ± 0.01 (BW1) to 0.04 ± 0.009 (BW8) in males, and 0.36 ± 0.10 (BW1) to 0.04 ± 0.006 (BW8) in females. The correlation between direct genetic effects between males and females for BW1 was not significantly different from one. The direct genetic correlation between the two sexes for BW8 and BW12 was significantly different from 1 concluding that these traits are dimorphic in terms of direct genetic effects and therefore independent selection in both sexes is possible. [ABSTRACT FROM AUTHOR]

Background: Incubation behaviour, an instinct for natural breeding in poultry, is strictly controlled by the central nervous system and multiple neuroendocrine hormones and neurotransmitters, and is closely associated with the cessation of egg laying. Therefore, it is essential for the commercial poultry industry to clarify the molecular regulation mechanism of incubation behaviour. Here, we used high-throughput sequencing technology to examine the pituitary transcriptome of Changshun green-shell laying hen, a local breed from Guizhou province, China, with strong broodiness, in two reproductive stages, including egg-laying phase (LP) and incubation phase (BP). We also analyze the differences in gene expression during the transition from egg-laying to incubation, and identify critical pathways and candidate genes involved in controlling the incubation behaviour in the pituitary. Results: In this study, we demonstrated that a total of 2089 differently expressed genes (DEGs) were identified in the pituitary, including 842 up-regulated and 1247 down-regulated genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that steroid biosynthesis pathway and neuroactive ligand-receptor interaction were significantly enriched based on DEGs commonly identified in pituitary. Further analysis revealed that SRC, ITGB4, ITGB3, PIK3R3 and DRD2 may play crucial roles in the regulation of incubation behaviour. Conclusions: We identified 2089 DEGs and the key signaling pathways which may be closely correlated with incubation in Changshun green-shell laying hens, and clarified the molecular regulation mechanism of incubation behaviour. Our results indicate the complexity and variety of differences in reproductive behaviour of different chicken breeds. [ABSTRACT FROM AUTHOR]

Background: Body weight and size are important economic traits in chickens. While many growth-related quantitative trait loci (QTLs) and candidate genes have been identified, further research is needed to confirm and characterize these findings. In this study, we investigate genetic and genomic markers associated with chicken body weight and size. This study provides new insights into potential markers for genomic selection and breeding strategies to improve meat production in chickens. Methods: We performed whole-genome resequencing of and Wenshang Barred (WB) chickens (n = 596) and three additional breeds with varying body sizes (Recessive White (RW), WB, and Luxi Mini (LM) chickens; (n = 50)). We then used selective sweeps of mutations coupled with genome-wide association study (GWAS) to identify genomic markers associated with body weight and size. Results: We identified over 9.4 million high-quality single nucleotide polymorphisms (SNPs) among three chicken breeds/lines. Among these breeds, 287 protein-coding genes exhibited positive selection in the RW and WB populations, while 241 protein-coding genes showed positive selection in the LM and WB populations. Genomic heritability estimates were calculated for 26 body weight and size traits, including body weight, chest breadth, chest depth, thoracic horn, body oblique length, keel length, pelvic width, shank length, and shank circumference in the WB breed. The estimates ranged from 0.04 to 0.67. Our analysis also identified a total of 2,522 genome-wide significant SNPs, with 2,474 SNPs clustered around two genomic regions. The first region, located on chromosome 4 (7.41-7.64 Mb), was linked to body weight after ten weeks and body size traits. LCORL, LDB2, and PPARGC1A were identified as candidate genes in this region. The other region, located on chromosome 1 (170.46-171.53 Mb), was associated with body weight from four to eighteen weeks and body size traits. This region contained CAB39L and WDFY2 as candidate genes. Notably, LCORL, LDB2, and PPARGC1A showed highly selective signatures among the three breeds of chicken with varying body sizes. Conclusion: Overall this study provides a comprehensive map of genomic variants associated with body weight and size in chickens. We propose two genomic regions, one on chromosome 1 and the other on chromosome 4, that could helpful for developing genome selection breeding strategies to enhance meat yield in chickens. [ABSTRACT FROM AUTHOR]

Climate change is a threat to sustainable livestock production and livelihoods in the tropics. It has adverse impacts on feed and water availability, disease prevalence, production, environmental temperature, and biodiversity. Unravelling the drivers of local adaptation and understanding the underlying genetic variation in random mating indigenous livestock populations informs the design of genetic improvement programmes that aim to increase productivity and resilience. In the present study, we combined environmental, genomic, and phenotypic information of Ethiopian indigenous chickens to investigate their environmental adaptability. Through a hybrid sampling strategy, we captured wide biological and ecological variabilities across the country. Our environmental dataset comprised mean values of 34 climatic, vegetation and soil variables collected over a thirty-year period for 260 geolocations. Our biological dataset included whole genome sequences and quantitative measurements (on eight traits) from 513 individuals, representing 26 chicken populations spread along 4 elevational gradients (6–7 populations per gradient). We performed signatures of selection analyses ( and XP-EHH) to detect footprints of natural selection, and redundancy analyses (RDA) to determine genotype-environment and genotype-phenotype-associations. RDA identified 1909 outlier SNPs linked with six environmental predictors, which have the highest contributions as ecological drivers of adaptive phenotypic variation. The same method detected 2430 outlier SNPs that are associated with five traits. A large overlap has been observed between signatures of selection identified by and XP-EHH showing that both methods target similar selective sweep regions. Average genetic differences measured by are low between gradients, but XP-EHH signals are the strongest between agroecologies. Genes in the calcium signalling pathway, those associated with the hypoxia-inducible factor (HIF) transcription factors, and sports performance (GALNTL6) are under selection in high-altitude populations. Our study underscores the relevance of landscape genomics as a powerful interdisciplinary approach to dissect adaptive phenotypic and genetic variation in random mating indigenous livestock populations. [ABSTRACT FROM AUTHOR]

The transmission of viral diseases is highly unstable and highly contagious. As the carrier of virus transmission, cell is an important factor to explore the mechanism of virus transmission and disease. However, there is still a lack of effective means to continuously monitor the process of viral infection in cells, and there is no rapid, highthroughput method to assess the status of viral infection. On the basis of the virus light diffraction fingerprint of cells, we applied the gray co-occurrence matrix, set the two parameters effectively to distinguish the virus status and infection time of cells, and visualized the virus infection process of cells in high throughput. We provide an effcient and nondestructive testing method for the selection of excellent livestock and poultry breeds at the cellular level. Meanwhile, our work provides detection methods for the recessive transmission of human-to-human, animal-to-animal, and zoonotic diseases and to inhibit and block their further development. [ABSTRACT FROM AUTHOR]

Disuse muscle atrophy is a disease caused by restricted activity, affecting human health and animal protein quality. While extensive research on its mechanism has been studied in mammals, comparatively little is known about this process in chickens, which are a significant source of protein for human consumption worldwide. Understanding the mechanisms underlying skeletal muscle atrophy in chickens is crucial for improving poultry health and productivity, as well as for developing strategies to mitigate muscle loss. In this study, two groups of chickens were subjected to limb immobilization for two and four weeks, respectively, in order to induce disuse muscle atrophy and uniformly sampled gastrocnemius muscle at the fourth week. A combined analysis of the transcriptome and metabolome was conducted to investigate the mechanisms of disuse-induced muscle atrophy. Through H&E staining and immunofluorescence, we found that, compared to slow-twitch muscle fibers, the fast-twitch muscle fibers showed a greater reduction in cross-sectional area in the immobilized leg, and were also the main driver of changes in cross-sectional area observed in the non-immobilized leg. Integrated analysis revealed that differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were mainly enriched in pathways related to energy metabolism, such as fatty acid metabolism, oxidative phosphorylation (OXPHOS), and glycolysis. These results provide important insights for further research on disuse muscle atrophy. [ABSTRACT FROM AUTHOR]

Simple Summary: The genetic basis underlying the development of different adipose tissues in broiler chicks requires extensive study. The molecular mechanisms and specific transcripts associated with fat development and deposition remain unknown. However, little is known about the relationship between the changes in the expression of genes and fat development and deposition in chickens. Thus, the molecular mechanisms regulating the development of different adipose tissues may differ. Hence, studying the mechanisms regulating the growth and development of different adipose tissues during the early stages of broiler development is important in poultry breeding. Therefore, in this study, RNA-seq analysis was utilized to reveal the molecular mechanisms regulating the development and deposition of different adipose tissues in broiler chicks. The results obtained showed that genes such as MYOG, S100A9, CIDEC, THRSP, CXCL13, and NMU were related to the growth and development of adipose tissue. Further, genes such as HOXC9, AGT, TMEM182, ANGPTL3, CRP, and DSG2 were identified to be associated with the distribution of adipose tissue, and MN1, ANK2, and CAP2 were related to the growth of adipocytes. Therefore, the candidate genes identified in this study could be used in chicken selection to increase or decrease specific adipose tissues in broiler chickens. In an effort to enhance growth rates, chicken breeders have undertaken intensive genetic selection. In the selection process, the primary aim is to accelerate growth, inadvertently leading to new chicken breeds having an increased capacity for rapid adipose tissue accumulation. However, little is known about the relationship between changes in gene expression and adipose tissue accumulation and deposition in chickens. Therefore, in this study, RNA-seq analysis was utilized, and transcriptome data were obtained from the abdominal fat, thoracic subcutaneous fat, and clavicular fat on day 1 (d1), day 4, day 7, day 11, and day 15 to reveal the molecular mechanisms regulating the development and deposition of different adipose tissues in broiler chicks. The results showed that the key period for adipocyte differentiation and proliferation was between d4 and d7 (abdominal fat development) and between d1 and d4 (chest subcutaneous fat and clavicular fat). In addition, candidate genes such as MYOG, S100A9, CIDEC, THRSP, CXCL13, and NMU related to adipose tissue growth and development were identified. Further, genes (HOXC9, AGT, TMEM182, ANGPTL3, CRP, and DSG2) associated with the distribution of adipose tissue were identified, and genes (MN1, ANK2, and CAP2) related to adipose tissue growth were also identified. Taken together, the results from this study provide the basis for future studies on the mechanisms regulating adipose tissue development in chickens. Further, the candidate genes identified could be used in the selection process. [ABSTRACT FROM AUTHOR]

Village poultry plays a vital role in providing essential nutrition and income for rural communities in Africa. In this context, poultry are often traded through live bird markets (LBMs), which serve as central trading hubs where producers connect with traders and consumers, facilitating the flow of poultry products along the value chain. While they serve as important trading hubs, these markets create an environment where avian pathogens, like Newcastle disease virus (NDV) and avian influenza virus, can easily emerge and spread. Improving our understanding of the epidemiology of NDV in LBMs is important for assessing disease risks and identifying factors that contribute to its persistence. Local chickens at the Mawenzi LBM in Morogoro municipality were surveyed for NDV presence, its temporal and spatial distribution, and risk factors for NDV infection. Twenty-three percent of 659 local chickens sampled over a 1-year period were positive for NDV based on PCR. Increased odds of NDV infection were identified in chickens that had been in the market for 2 or more days prior to sampling and during the period extending from August through October. Four significant spatiotemporal clusters of NDV-positive chickens encompassing 13 villages were detected between August and October 2020, illustrating geographic hotspots of infection when NDV was most prevalent. Similar to the other LBMs, this market had enclosures with high densities of birds of mixed species, limited biosecurity, and the presence of birds with observable illness. Bird traders who source the chickens from the villages, described long transit times in mixed enclosures with limited sanitation practices and without consideration of sick birds or vaccination status prior to arriving at the LBM. This study highlights the need to invest in improvements to infrastructure and biosecurity for LBMs as well as training opportunities for increasing traders' knowledge on hygiene and sanitation practices, animal welfare, and poultry biosecurity measures. [ABSTRACT FROM AUTHOR]

In Thailand, native chickens have a deep-rooted history of cultivation driven by diverse purposes, including food production, aesthetic appeal, exhibition, and cockfighting. Their remarkable adaptability, robustness, and resistance to diseases play pivotal roles in the evolution of chicken breeds. The study of morphological characteristics in native chicken breeds assumes significance for biodiversity conservation, sustainable agriculture, and cultural preservation. These traits not only unveil genetic diversity but also provide insights into adaptation that is crucial for the survival of native chicken populations in varied environmental conditions. The primary aim of this extensive research, conducted from June 2020 to May 2023, is to elucidate the morphological traits of six indigenous chicken breeds in Thailand's Uttaradit province. The research methodology involved the purposive selection of a research group from chicken farms with a minimum of 5 individuals, followed by a random selection of 20 names meeting specific criteria. The resulting group comprised 134 individuals from Khiew Phalee, Thao Thong, Lueng Hang Khao, Chee, Pra Dhu Hang Dam, and Jae species. The study's findings highlighted significant differences in eight qualitative morphological characteristics among the distinct chicken breeds, including comb type, beak color, neck plumage color, back plumage color, wing plumage color, long curved tail color, back tail color, and shank color p < 0.01 . Moreover, a correlation between body size and sex-specific structures across breeds was discovered, with male chickens exhibiting significantly greater body weight, size, wing length, upper and lower shank length, and toe length than females p < 0.0001 . Notably, the majority of native chickens displayed the walnut (Hin) beak type, except for Jae chickens, which exhibited the single (Jak) type. Beak colors ranged from blackish-green to ivory, while each breed showcased unique plumage, tail, and shank colors, coupled with varying body sizes. This comprehensive study, covering both qualitative and quantitative parameters, emphasizes the morphological diversities among the six native chicken breeds. The derived data serve as a valuable resource for refining or developing chicken breeds in alignment with the Standard of Perfection for Thai Native Chickens, catering to the evolving needs of the market. [ABSTRACT FROM AUTHOR]

The Nagoya breed, so-called Nagoya Cochin, is a native Japanese chicken. As the mislabeling of chickens is a matter of concern, causing economic losses relating to the production of the Nagoya breed, a simple and high-accuracy assay is required to distinguish the Nagoya breed. This study successfully developed a novel screening assay to discriminate the Nagoya breed using a high-resolution melting (HRM) assay. A primer set for HRM analysis was designed to amplify the CA repetition in the ABR0417 microsatellite marker. By comparing the results of the HRM analysis with those of the DNA sequence analysis, we investigated the applicability of the HRM-based assay using four differential chickens of the Nagoya breed and twelve other breeds. In the ABR0417 marker, the sequences of all four Nagoya breed chickens were identical to the ABR0417 reference sequence of the Nagoya breed, whereas the sequences for the twelve other chickens were different from those of the Nagoya breed chickens. The HRM analysis of the 16 chickens revealed that the melting curve and peak plots of the Nagoya breed chickens were distinct from those of other chickens. These results demonstrate that this HRM-based method is a simple genetic test to identify the Nagoya breed using the ABR0417 marker. [ABSTRACT FROM AUTHOR]

Bang Troi chicken (GBT) is a local chicken that is free-gardening raised in Quang Ninh province. A 1,268 bp of mitochondrial DNA (mtDNA) D-loop of 17 Bang Troi chicken individuals was sequenced and analyzed. Comparative multiple sequence alignment revealed 17 base substitutions within 17 Bang Troi chicken individuals. Bang Troi chicken had a relatively high level of genetic diversity, expressed in the number of 13 haplotypes, haplotype diversity of 0.949. The Tajima's test indicated that the analysed population in balancing selection with a D-value of 2.39. A phylogenetic tree based on 455 bp of hypervariable mtDloop sequence classified 17 Bang Troi chicken individuals into three clades A, B, and E, which are common groups of Vietnamese and Asia indigenous chickens. This result provides the first genetic information and maternal lineages of Bang Troi chickens and it can support for registration of local chicken breeds. [ABSTRACT FROM AUTHOR]