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Chicken coccidiosis causes annual losses exceeding GBP 10 billion globally. The most pathogenic species for domestic fowls including Eimeria tenella, E. acervulina, and E. maxima, can lead to gastrointestinal issues ranging from mild to fatal. In this study, stages of E. tenella and freshly isolated chicken heterophils were co-cultured for 180 min. These interactions were analyzed using live 3D holotomographic and confocal microscopy. We observed that E. tenella stages were entrapped by heterophils and heterophil extracellular traps (HETs). Notably, different HET phenotypes, specifically sprHETs and aggHETs, were induced regardless of the stage. Furthermore, the quantification of extracellular DNA release from co-cultures of heterophils and sporozoites (ratio 1:1) for 180 min demonstrated a significantly higher release (p = 0.04) compared to negative controls. In conclusion, research on the chicken innate immune system, particularly fowl-derived HETs, remains limited. More detailed investigations are needed, such as exploring the time-dependent triggering of HETs, to establish a standard incubation time for this pathogen defense mechanism. This will enhance our understanding of its role in parasite survival or death during HET confrontation. [ABSTRACT FROM AUTHOR]

Two experiments were conducted to assess the efficiency of including the novel protein ingredient Arthrospira platensis or improved soybean meal in a broiler diet. The first experiment aimed to determine the feeding value of soybean meal produced from varieties of soybeans bred for increased amino acid content (SBAA) and improved oil content (SBO) compared to a conventional soybean variety in an ANOVA design fed to Cobb 500 female broilers for 28–42 d. The SBAA and SBO soybeans contained overall higher amino acid content and lower oligosaccharide content compared to the conventional soybean variety in addition to improved oil quality. The second experiment assessed the novel protein ingredient microalgae, Arthrospira platensis (algae), and was conducted to evaluate algae and corn distillers' grain (DDGS) inclusion on broiler performance for a 28–42 d feeding period in Cobb CF05 male broilers with a 2 × 2 factorial treatment array. Prior to the experimental period, all birds were reared on common feeds. In Experiment 1, birds were fed a diet containing 20% inclusion of an experimental soybean source in the form of full-fat soybean meal. In Experiment 2, the four dietary treatments consisted of diets containing algae at inclusion levels of either 0 or 2% and DDGS at inclusion levels of 0% and 8%. Diets were fed to 288 female broilers (Experiment 1) and 384 male broilers (Experiment 2), placed in eight replicate pens of twelve birds, and live performance was assessed from d 28 to 42. At d 42, six birds from each pen were randomly selected and processed for evaluation of carcass traits and incidence of woody breast. For Experiment 1, all performance data were analyzed using a one-way ANOVA using JMP Pro 16 software with diet as the fixed effect and block as a random effect. Statistical significance was considered at p ≤ 0.05. No significant responses were observed for any recorded measurement for live performance, carcass traits, or woody breast. All data in Experiment 2 were analyzed as a full factorial with a mixed model using JMP software with algae, DDGS, and algae × DDGS as fixed effects and block as a random effect. The F-protected Fisher's LSD test was used to separate means when p ≤ 0.05. No significant responses were observed for the algae, DDGS, and algae × DDGS influences on BWG, FI, and FCR or processing characteristics; the ingredient source did not affect bird performance. Experimental soybean lines developed at the University of Arkansas were able to be incorporated into broiler diets without decreasing performance. Algae has the potential to be a protein-contributing ingredient for broilers. [ABSTRACT FROM AUTHOR]

The production of backyard chickens is an activity of great importance in the economy of rural families in Paraguay. The Rustipollos population was created through directed crosses between a commercial meat line and a local population belonging to non-specific breeds but phenotypically assimilated to Creole breeds. The aim of this study was to evaluate the genetic diversity, relationship, and structure of Rustipollos using 29 microsatellite markers. Analysis was performed on 50 Rustipollos animals and 926 other individuals as reference breeds/populations from Europe, Africa, South, and North America. A total of 318 alleles were detected, with a mean of 10.97 per locus. The polymorphic information content indicated that 80% of all loci were highly to moderately informative. Only two breeds/populations showed loci that did not deviate from the Hardy–Weinberg equilibrium. The results of genetic diversity indexes suggested moderate levels of genetic variability in Rustipollos population and low inbreeding level. The genetic differentiation index indicates a high genetic differentiation between populations. The results of the Neighbor-Net tree and STRUCTURE analyses indicate the existence of distinct gene pools, with some genetic relationships between Rustipollos, the commercial chicken strain, and south Spanish breeds. The Discriminant Analysis of Principal Components confirmed the observed genetic distances between breeds/populations. The results will be useful for sustainable use and official recognition of this population. [ABSTRACT FROM AUTHOR]

Small-scale poultry production in Africa plays a significant role in alleviating malnutrition and poverty in rural communities. Global climate change and infectious poultry disease such as Newcastle disease (ND) have had tremendous negative impact on poultry production and health due to limited biosecurity, cold chain, and inadequate extension service. Genetic selection for enhanced resistance to ND virus (NDV) offers a promising complementary approach to vaccination and biosecurity in addressing constraints in village production systems. The Feed the Future Innovation Lab for Genomics to Improve Poultry (GIP IL) has led an effort on the identification of genetic markers, genes and signalling pathways associated with enhanced resistance to NDV by conducting NDV challenging experiments in diverse inbred, commercial, and African indigenous chickens. The GIP IL developed a comprehensive genetic selection platform focusing on improved survival time and reduced virus shedding in the face of NDV infection and on enhanced growth rate and egg production. The programme applied the platform for genetic selection and breeding of indigenous chickens through velogenic NDV natural exposure trials. To improve our understanding of the epidemiology of NDV in Africa, we characterised circulating strains of the virus in Ghana and Tanzania and identified NDV risk factors among local chickens. These data contribute to a body of knowledge useful for guiding disease control efforts, informing vaccine strategies, enhancing biosecurity, and contributing to our overall understanding of NDV dynamics. To gauge the demand for genetically improved indigenous poultry lines, we undertook assessments of the poultry value chain and conducted choice experiments in Ghana and Tanzania, and the findings suggest that both ND enhanced resistance attribute and other productivity attributes of chicken such as egg production and body weight gain are important for a breeding programme. [ABSTRACT FROM AUTHOR]

Indigenous chickens reared in South and East Asian region have been assessed for their carcass and meat quality traits over the past years. This review provides the overview of findings on the carcass and meat quality traits of indigenous chickens. Ancestry analysis revealed that these chickens have evolved from the Red jungle fowl (Gallus gallus). These indigenous breeds/ecotypes are named based on their unique phenotypic characteristics. In most Asian countries, indigenous chicken populations are sustained due to the cross-breeding programmes between different lines of local and exotic breeds. The production systems for these chicken breeds/ecotypes are mainly semi-intensive of the backyard and free-range systems. The carcass and meat quality parameters of these chickens are primarily influenced by genotype, age, body weight, feed, and several other environmental conditions. At present, consumer preference for indigenous chicken meat has increased due to its superior quality compared to broiler meat, particularly in terms of unique taste, texture, and nutritional value. Indigenous chicken meat exhibits favourable fatty acid profiles including n-3 and n-6 fatty acids, and desirable physiochemical and sensory attributes compared to commercial broiler meat. However, further research is needed to explore the carcass and meat quality parameters, and histological traits of the meat from different indigenous chicken breeds/ecotypes in the South and East Asian regions. [ABSTRACT FROM AUTHOR]

Native chickens are the backbone of backyard poultry farming in India. Native chicken production is a valuable asset for rural and tribal poor as it is a source of nutritional and livelihood security to them. Native chickens have minimal input requirements, are well adapted to hard scavenging environments, inadequate nutrition, parasite and disease obstacles, and have significant genetic variation for numerous traits, making them excellent genetic resources for current and subsequent generations. The performance and genetic parameters are evaluated to understand the inheritance patterns of several economically viable traits in native chickens in order to allow the development of appropriate breeding strategies for improved performance. The production levels of hens will rise as a result of breeding native hens for economic traits, which will also encourage traditional producers to use native hens. The estimation of performance and genetic characteristics pertaining to economic traits in chickens might be beneficial in comprehending and enhancing their genetic diversity. Furthermore, the development of any breeding programme requires an understanding of the performance and genetic characteristics of traits. Additionally, indirect selection for any of the significantly correlated traits has the potential to genetically improve other traits due to the pleiotropic effect of genes. The current review discusses the estimates of performance and genetic parameters like means, heritability and correlation coefficients for body weights, morphometric traits, production and reproduction traits, egg quality parameters and semen attributes of native chickens in India. [ABSTRACT FROM AUTHOR]

Newcastle disease (ND) is one of the most devastating illnesses in the chicken industry. The World Organization for Animal Health (WOAH) requires notification of ND as soon as it is discovered due to its enormous economic impact and the potential for rapid spread to naive birds in the region. This is attributed to ND's tremendous socioeconomic value and its propensity to spread quickly to naive birds in the surrounding area. ND vaccinations have stood the test of time when it comes to disease prevention and control, having established a proven track record for 60 years. Even though these vaccinations protect against replication and infection to some degree, most of the highly pathogenic and phylogenetically different NDV isolates that are now going around can't be stopped. To overcome these problems with immunisation, it's essential to use 'genotype-matched vaccines', or vaccines that are made to target the most common genotypes (genotype VII and genotype XIII). Reverse genetic vaccines are the most promising new way to make vaccines that match a person's genotype. There was no ambiguity in this observation. This study examines the target virus proteins and the safety of new vaccines for Newcastle disease (NDV). Researchers evaluate global strategies to ensure safe, effective, and easy-to-control vaccines. They consider established practices and new trends to evaluate the effectiveness and feasibility of different vaccine strategies. The study aims to make informed decisions about the most suitable approach for developing safe, effective, and easy-to-control NDV vaccines. [ABSTRACT FROM AUTHOR]

Demand towards healthy, high-quality animal products is growing, and at the same time, more ethical animal husbandry methods which consider animal welfare and sustainability are under a high social spotlight. Culling of day-old male layer chicks is one of the main animal welfare concerns in the poultry sector, along with cage use, also in relation to changes in social demands. Political and societal disapproval towards this practice led to consider alternatives to day-old male layer chicks culling such as the rearing of male chicks, the use of dual-purpose strains and in ovo sex determination of embryos. This review summarised the available literature sources about the alternatives to the culling method and the public perspective on these approaches. Regarding in ovo sex determination several techniques were released in the last decades employing genetic, optical, biological, physicochemical, and biotechnological approaches. Animal welfare, costs, and ethical aspects, along with customers' acceptance, are the main aspects to be considered in the choice of alternative methods. Although rearing dual-propose chicken or layer-type cockerels produced very socially acceptable alternatives, their production costs are excessively expensive to be appropriate for mass markets. Based on the literature, in ovo sex determination seems to be the main potential alternative method to male chicks culling and the most preferred by consumers especially if performed during the first days of incubation. However, all the commercially available technologies are applicable only in the late stage of embryo development and are not yet ready to be used on large scales. Therefore, the development of an early, non-invasive, rapid, economical, and ethically acceptable in ovo sexing technique remains the main challenge as well as a priority. Moreover, the potential benefit or risk balance of the use of genetic methodologies needs to be discussed more globally. [ABSTRACT FROM AUTHOR]

The production and reproductive capacity of geese depend on a number of non-genetic factors in addition to genetic factors. The production and reproductive performance of a flock often depends on the influence of non-genetic factors present in the rearing of the flock, such as: applied breeding technology, period of exploitation, age of the flock, body weight of the birds, nutrition, fertility of the males, weight and quality of hatching eggs, and technological procedures during the incubation of the eggs. Productive and reproductive characteristics of geese can be significantly improved by appropriate application of egg production and incubation technology. The application of appropriate breeding technology should be in accordance with the genotype being bred and specific regional growth conditions that allow maximum expression of genetic potential. [ABSTRACT FROM AUTHOR]

This article presents a review of the productive and reproductive performances, egg-laying capability, egg quality, and carcass characteristics of indigenous, exotic, and crossbred chicken genotypes in Ethiopia. Indigenous chickens can reach sexual maturity in 193.5–238 days when raised under scavenging management systems, laying eggs that average 43.9 g. However, those reared intensively can attain sexual maturity in 156 days. Those chickens kept in scavenging management systems produced 49.4–54.6 eggs per hen per year. Fertility rates for indigenous chicken eggs range from 74.5% to 78.2%, while hatchability ranges from 84.1% to 91.5% under scavenging management, while under improved management, the fertility and hatchability percentages could be increased to 80% and 91.7%, respectively. The male exotic Novo colour chicken genotypes have the highest body weight (2934.4 g) and the lowest (better) feed conversion ratio (2.36) compared to the other. Several crosses, such as Dominant Red Bared crosses with Horro ecotype in the dam line, resulted in higher growth rates than purebred lines. The exotic chicken genotype had significantly superior egg weight, egg length and width, albumen weight, and huge unit compared to the indigenous and crossbred genotypes. Novo-colour chicken genotypes had the highest slaughter weight, while Kuroiler chickens had the highest dressing percentage (81%) compared to the other genotypes. The Sasso crossbred chicken had the highest slaughter weight (2403 g) compared to the indigenous chickens (1605 g) under scavenging management. Generally, this review presented that crossbreeding indigenous chicken with exotic breeds resulted in better performance traits than the indigenous chicken genotypes. Thus, for the crossbreeding programme selecting an appropriate exotic chicken genotype that performs better under various agroecological settings is crucial for sustainable utilisation and maintaining food security in Ethiopia. [ABSTRACT FROM AUTHOR]

Among the genus Avipoxvirus (APV) of the family Poxviridae, Fowlpox virus (FWPV) is of the highest economic importance associated with a severe drop in egg production, retarded growth of younger birds, and sometimes heavy mortality. Despite its worldwide prevalence, the status of fowlpox infection varies in different geographical regions due to differences in climate, vector population, vaccination status, management, and employed hygienic practices. The disease is frequently seen in all production systems, ranging from backyard to commercial poultry flocks due to insufficient vaccination coverage, strain differences or the emergence of novel variants. FWPV can either produce cutaneous lesions (hypertrophy/hyperplasia of epidermal cells) or can affect mucous membranes of the upper respiratory tract or digestive system (diphtheritic form). The host specificity has been considered broader than previously thought: (a) 'fowlpox-like viruses' being mainly isolated from Galliformes, (b) 'canarypox-like viruses' from Passeriformes and (c) viruses of Psittaciformes. Currently, fowlpox is considered an evolving disease in the poultry industry with several incidences documented in vaccinated chicken flocks worldwide. Limited reports are available on the antigenic, genetic, and biological characterisation of FWPV and other APVs. Complete genome sequencing of different APVs is necessary to understand its molecular epidemiology which would help to solve the complex paradigm of its host range. In the recent past, FWPV has been used as a vector to produce recombinant veterinary vaccines. This review has briefed the aetiology, epidemiology, pathogenesis, clinical signs, prevention, and control strategies related to fowlpox infection. [ABSTRACT FROM AUTHOR]

This review aims to suggest sustainable and conservation-based genetic improvement approaches by analysing the genetic diversity erosion in Ethiopia's local chicken gene pool. Ethiopia has ample chicken genetic resources with 10 different chicken ecotypes. Indigenous chickens are excellent in adaptive traits and are highly variable in performance and morphological characteristics. They have comparable and promising potential for production if they are given improved nutrition, housing and health care. They are the primary protein sources for rural and urban societies and play a significant role in food security. However, the genetic diversities of the chicken have now been seriously threatened in the past six decades by indiscriminate crossbreeding, production-derived breed reference, changes in the production system and an unbalanced extension system. About 20 different improved exotic chicken breeds were imported to Ethiopia via government and non-government organisations from 1953 onwards. No previous efforts have been made to conserve and improve the local chickens, but successful selective breeding has been carried out in indigenous Tilili, Horro and Debre Zeit White chickens. Selective breeding resulted in significant improvement in egg number, body weight, egg weight, age at first and survival in all chicken populations, particularly in Horro chicken. These situations call for conservation-based genetic improvement, focusing on the utilisation of within-breed selection and the unique features of the chicken. Community-based selective breeding complemented with an improved chicken management package may be the primary strategy to preserve and improve the local chickens. The government and other bodies should plan important activities encouraging farmers to keep and improve indigenous chickens. The review could also serve as baseline information for policymakers, researchers, agricultural offices and students to take necessary actions on chicken genetic improvement, conservation and management and undertake further studies. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Animal Production & Processing Technology / JurnalIlmu Produksi dan Teknologi Hasil Peternakan is the property of IPB University and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

A total of 16, 18-weeks old chickens with mean weight 1.99±0.12 kg (1.85-2.30kg) were used to compare the serum biochemical characteristics of four chicken genotypes (breeds/strains) from south-eastern part of Nigeria. The chickens were grouped based on their genotypes (breeds/strain) in a Completely Randomized Design for the four-week study. The genotypes (breeds) considered were Black Australorp (BA), Isa Brown (IB), Noiler (NOI) and Local chicken (LC) at 4 chickens per genotype. At the end of the experiment, four (4) birds per genotype were drawn and their blood samples analysed for serum biochemical studies. The mean total cholesterol (TC), triaceylglycerol (TAG) and very low density lipoprotein cholesterol (VLDL-C) concentrations of local chicken (LC) were significantly (P < 0.05) higher than the Isa brown (IB) values. Similarly, the mean blood urea nitrogen (BUN) concentrations of LC was significantly (P < 0.05) higher than the Noiler value. The mean high density lipoprotein cholesterol (HDL-C) of black Australorp (BA) was significantly (P < 0.05) higher than the value of Noiler but showed no significant (p > 0.05) difference when compared to the values of IB and LC. There were however no significant (p > 0.05) variations in the mean low density lipoprotein cholesterol (LDL-C), total bilirubin, direct bilirubin, indirect bilirubin and creatinine concentrations among all the breeds investigated. In conclusion, the results obtained in this study will be helpful in creating a baseline data on biochemical profiles of indigenous and exotic chicken breeds in Nigeria which in turn can be used for assessing the health status of these birds, improving desirable breeds/traits and designing appropriate breeding strategies for indigenous poultry birds in the country. [ABSTRACT FROM AUTHOR]

Copyright of Journal of the Chinese Society of Animal Science is the property of Chinese Society of Animal Science and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Summary: The genetic improvement of economic traits suggests that chicken is an excellent model for exploring the genetic changes and molecular mechanisms underlying phenotypic diversity and artificial selection. Here, the sequencing data including 477 samples from 25 breeds worldwide were used to reveal the genomic patterns of chicken domestication. We analyzed 7.4 Tb clean data with 14.8× per individual to identify 23,504,766 SNPs, 3,289,782 InDels, and 27,027 SVs. The diversity analysis indicates that high-intensity artificial selection would accelerate population differentiation. We also found that the human-driven traits are controlled by polygenes and major genes, such as the primary candidates SOX5 and IGF1 for body size, and NEDD4 for sperm storage capacity. Our findings provide an important reference for understanding how genomic patterns shape phenotypes in livestock.

Solid phase DNA isolation kit was used to isolate genomic DNA (gDNA) from duck blood samples. The manufacturer’s protocol was modified by reducing the quantity of blood from 200 µL to 10 µL. Normal saline was used to extend the volume to 200 µL. DNA was isolated with the modified protocol and was used for amplifying a segment of exon 2 of duck growth hormone gene. [ABSTRACT FROM AUTHOR]

In recent years, single-cell RNA sequencing (scRNA-seq) has marked significant strides in livestock and poultry research, especially when integrated with multi-omics approaches. These advancements provide a nuanced view into complex regulatory networks and cellular dynamics. This review outlines the application of scRNA-seq in key species, including poultry, swine, and ruminants, with a focus on outcomes related to cellular heterogeneity, developmental biology, and reproductive mechanisms. We emphasize the synergistic power of combining scRNA-seq with epigenomic, proteomic, and spatial transcriptomic data, enhancing molecular breeding precision, optimizing health management strategies, and refining production traits in livestock and poultry. The integration of these technologies offers a multidimensional approach that not only broadens the scope of data analysis but also provides actionable insights for improving animal health and productivity.

Despite the significant threat of heat stress to livestock animals, only a few studies have considered the potential relationship between broiler chickens and their microbiota. Therefore, this study examined microbial modifications, transcriptional changes and host-microbiome interactions using a predicted metabolome data-based approach to understand the impact of heat stress on poultry. After the analysis, the host functional enrichment analysis revealed that pathways related to lipid and protein metabolism were elevated under heat stress conditions. In contrast, pathways related to the cell cycle were suppressed under normal environmental temperatures. In line with the transcriptome analysis, the microbial analysis results indicate that taxonomic changes affect lipid degradation. Heat stress engendered statistically significant difference in the abundance of 11 microorganisms, including Bacteroides and Peptostreptococcacea . Together, integrative approach analysis suggests that microbiota-induced metabolites affect host fatty acid peroxidation metabolism, which is correlated with the gene families of Acyl-CoA dehydrogenase long chain ( ACADL ), Acyl-CoA Oxidase ( ACOX ) and Acetyl-CoA Acyltransferase ( ACAA ). This integrated approach provides novel insights into heat stress problems and identifies potential biomarkers associated with heat stress.

The general objective of this study is to comparatively assess the climate-resilient potential of four different poultry genotypes-Giriraja (n = 8), Country chicken (n = 8), Naked neck (n = 8), and Kadaknath (n = 8)-reared in a hot-humid tropical environment. Birds from all genotypes had ad libitum access to feed and water and were exposed to identical environmental temperatures in the experimental shed. Diurnal meteorological data were recorded inside and outside the shed daily. Blood biochemical, hormonal, and endocrine variables were monitored monthly until the birds reached 12 weeks of age. Significant variations (P < 0.01) were observed at different intervals in variables, including total protein, albumin, globulin, triglycerides, and cholesterol. Genotype-specific differences were noted in triglycerides (P < 0.01), albumin (P < 0.01), total protein (P < 0.05), and cholesterol (P < 0.05). Inter-genotype variations (P < 0.05) were also observed in serum cortisol, T 3 , and T 4 levels. Distinct variations (P < 0.05) were also observed during specific intervals, particularly in cortisol and T 3 levels. The study of hepatic mRNA expression of HSPs and HSF-1 revealed a significant breed difference (P < 0.05) in the expression pattern of HSP60, HSP70, HSP90, and HSP110, while no difference was observed between genotypes for HSP40 and HSF-1. The study highlights the Naked Neck breed as an exemplar of resilience, showcasing its distinctive ability to maintain homeostasis under heat stress compared to other genotypes. The genetic and physiological insights gained from this investigation offer prospective pathways for aligning sustainable poultry farming with environmental exigencies., (© 2024. The Author(s) under exclusive licence to International Society of Biometeorology.)

Heat stress is becoming a major problem because it limits growth in poultry production, especially in tropical areas. The development of genetic lines of Thai native chickens (TNC) which can tolerate the tropical climate with the least compromise on growth performance is therefore necessary. This research aims to analyze the appropriate growth curve function and to estimate the effect of heat stress on the genetic absolute growth rate (AGR) in TNC and Thai synthetic chickens (TSC). The data comprised 35,355 records for body weight from hatching to slaughtering weight of 7241 TNC and 10,220 records of 2022 TSC. The best-fitting growth curve was investigated from three nonlinear regression models (von Bertalanffy, Gompertz, and logistic) and used to analyze the individual AGR. In addition, a repeatability test-day model on the temperature-humidity index (THI) function was used to estimate the genetic parameters for heat stress. The Gompertz function produced the lowest mean squared error (MSE) and Akaike information criterion (AIC) and highest the pseudo-coefficient of determination (Pseudo-R²) in both chicken breeds. The growth rates in TSC were higher than TNC; the growth rates of males were greater than females, but the age at inflection point in females was lower than in males in both chicken breeds. The THI threshold started at 76. The heritability of the AGR was 0.23 and 0.18 in TNC and TSC, respectively. The additive variance and permanent environmental variance of the heat stress effect increased sharply after the THI of 76. The growth rate decreased more severely in TSC than TNC. In conclusion, the Gompertz function can be applied with the THI to evaluate genetic performance for heat tolerance and increase growth performance in slow-growing chicken. [ABSTRACT FROM AUTHOR]

The Chantecler chicken, a unique Canadian indigenous breed, is well adapted to extremely cold environments. However, its genetic characteristics have not been well studied. Here, we analyzed the whole genomes of 10 Chantecler chickens and 121 worldwide chickens, which indicated that Chantecler chickens were derived from commercial chickens and exhibit a high level of inbreeding. Based on a genome-wide scan, we identified two vital candidate regions containing ME3 and ZNF536, which are related to fat metabolism and nervous system in cold adaptation, respectively. We also found that the genetic mechanism of cold adaptation in Chantecler chickens differed from that of chickens from other cold regions, such as northern China. Our study indicated that specialized commercial chickens in the early 20th century contained sufficient genetic diversity to adapt to extreme cold environments over a very short time. These findings enrich our understanding of the adaptive potential of commercial species. [ABSTRACT FROM AUTHOR]

Domestication and breeding have reshaped the genomic architecture of chicken, but the retention and loss of genomic elements during these evolutionary processes remain unclear. We present the first chicken pan-genome constructed using 664 individuals, which identified an additional approximately 66.5-Mb sequences that are absent from the reference genome (GRCg6a). The constructed pan-genome encoded 20,491 predicated protein-coding genes, of which higher expression levels are observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated that gene PAV in chicken was shaped by selection, genetic drift, and hybridization. PAV-based genome-wide association studies identified numerous candidate mutations related to growth, carcass composition, meat quality, or physiological traits. Among them, a deletion in the promoter region of IGF2BP1 affecting chicken body size is reported, which is supported by functional studies and extra samples. This is the first time to report the causal variant of chicken body size quantitative trait locus located at chromosome 27 which was repeatedly reported. Therefore, the chicken pan-genome is a useful resource for biological discovery and breeding. It improves our understanding of chicken genome diversity and provides materials to unveil the evolution history of chicken domestication. [ABSTRACT FROM AUTHOR]

Pseudomonas aeruginosa (P. aeruginosa) is an ESKAPE pathogen that can quickly develop resistance to most antibiotics. This bacterium is a zoonotic pathogen that can be found in humans, animals, foods, and environmental samples, making it a One-Health concern. P. aeruginosa threatens the poultry industry in Egypt, leading to significant economic losses. However, the investigation of this bacterium using NGS technology is nearly non-existent in Egypt. In this study, 38 isolates obtained from broiler farms of the Delta region were phenotypically investigated, and their genomes were characterized using whole genome sequencing (WGS). The study found that 100% of the isolates were resistant to fosfomycin and harbored the fosA gene. They were also resistant to trimethoprim/sulfamethoxazole, although only one isolate harbored the sul1 gene. Non-susceptibility (resistant, susceptible with increased dose) of colistin was observed in all isolates. WGS analysis revealed a high level of diversity between isolates, and MLST analysis allocated the 38 P. aeruginosa isolates into 11 distinct sequence types. The most predominant sequence type was ST267, found in 13 isolates, followed by ST1395 in 8 isolates. The isolates were susceptible to almost all tested antibiotics carrying only few different antimicrobial resistance (AMR) genes. Various AMR genes that confer resistance mainly to ß-lactam, aminoglycoside, sulfonamide, and phenicol compounds were identified. Additionally, several virulence associated genes were found without any significant differences in number and distribution among isolates. The majority of the virulence genes was identified in almost all isolates. The fact that P. aeruginosa, which harbors several AMR and virulence-associated factors, is present in poultry farms is alarming and threatens public health. The misuse of antimicrobial compounds in poultry farms plays a significant role in resistance development. Thus, increasing awareness and implementing strict veterinary regulations to guide the use of veterinary antibiotics is required to reduce health and environmental risks. Further studies from a One-Health perspective using WGS are necessary to trace the potential transmission routes of resistance between animals and humans and clarify resistance mechanisms., Competing Interests: Declaration of Competing Interest All authors declare that the research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

CRISPR/Cas9 gene editing technology, as a highly efficient genome editing method, has been extensively employed in the realm of animal husbandry for genetic improvement. With its remarkable efficiency and precision, this technology has revolutionized the field of animal husbandry. Currently, CRISPR/Cas9-based gene knockout, gene knock-in and gene modification techniques are widely employed to achieve precise enhancements in crucial production traits of livestock and poultry species. In this review, we summarize the operational principle and development history of CRISPR/Cas9 technology. Additionally, we highlight the research advancements utilizing this technology in muscle growth and development, fiber growth, milk quality composition, disease resistance breeding, and animal welfare within the livestock and poultry sectors. Our aim is to provide a more comprehensive understanding of the application of CRISPR/Cas9 technology in gene editing for livestock and poultry.

Background: Pathogenic and non-pathogenic strains of Escherichia coli harbouring antibiotic resistance genes (ARGs) from any source (clinical samples, animal settings, or environment) might be transmitted and contribute to the spread and increase of antibiotic resistance in the biosphere. The goal of this study was to investigate the genome to decipher the repertoire of ARGs, virulence genes carried by E. coli strains isolated from livestock, poultry, and their handlers (humans), and then unveil the genetic relatedness between the strains., Methods: Whole genome sequencing was done to investigate the genetic makeup of E. coli isolates (n = 20) [swine (n = 2), cattle (n = 2), sheep (n = 4), poultry (n = 7), and animal handlers (n = 5)] from southern India. The detection of resistome, virulome, biofilm forming genes, mobile genetic elements (MGE), followed by multilocus sequence typing (MLST) and phylogenetic analyses, were performed., Results: E. coli strains were found to be multi drug resistant, with a resistome encompassing > 20 ARGs, the virulome-17-22 genes, and > 20 key biofilm genes. MGE analysis showed four E. coli isolates (host: poultry, swine and cattle) harbouring composite transposons with ARGs/virulence genes (bla TEM , dfr, qnr/nleB, tir, eae,and esp) with the potential for horizontal transfer. MLST analyses revealed the presence of ST937 and ST3107 in both livestock/poultry and their handlers. Phylogenomic analyses with global E. coli isolates (human/livestock/poultry hosts) showed close relatedness with strains originating from different parts of the world (the United States, China, etc.)., Conclusion: The current study emphasizes the circulation of strains of pathogenic sequence types of clinical importance, carrying a diverse repertoire of genes associated with antibiotic resistance, biofilm formation and virulence properties in animal settings, necessitating immediate mitigation measures to reduce the risk of spread across the biosphere., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Gallibacterium anatis is a Gram-negative bacterium found in the respiratory and genital tracts of various animals, primarily poultry. Its association with septicemia and high mortality in poultry, along with the rise in multidrug-resistant strains, has amplified concerns. Recent research uncovered significant variability in antibiotic resistance profiles among G. anatis isolates from different Austrian flocks, and even between different organs within the same bird. In response, in the present study 60 of these isolates were sequenced and a combination of comparative genomics and genome-wide association study (GWAS) analysis was applied to understand the genetic variability of G. anatis across flocks and organs and to identify genes related to antibiotic resistance. The results showed that each flock harbored one or two strains of G. anatis with only a few strains shared between flocks, demonstrating a great variability among flocks. We identified genes associated with resistance to nalidixic acid, trimethoprim, cefoxitin, tetracycline, ampicillin and sulfamethoxazole. Our findings revealed that G. anatis may develop antibiotic resistance through two mechanisms: single-nucleotide mutations and the presence of specific genes that confer resistance. Unexpectedly, some tetracycline-resistant isolates lacked all known tetracycline-associated genes, suggesting the involvement of novel mechanisms of tetracycline resistance that require additional exploration. Furthermore, our functional annotation of resistance genes highlighted the citric acid cycle pathway as a potential key modulator of antibiotic resistance in G. anatis. In summary, this study describes the first application of GWAS analysis to G. anatis and provides new insights into the acquisition of multidrug resistance in this important avian pathogen., Competing Interests: Declaration of Competing Interest The authors of this study declare that they have no conflicts of interest, financial or otherwise, that could influence the results or interpretation of the research presented. All authors have contributed to the work and approved the final manuscript for submission., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

The present research was designed to investigate the impact of dwgene on fertility, hatchability and eggs traits in dwarf and normal local hens.300eggs gathered from normal local and dwarf hen to evaluate the weights of egg and chicks, egg shape index,percentages of egg contents, hatchability from setting and fertilized eggs, and to determine the correlation among egg weight with fertility characters. The statistical analysis reporteda significant (P<0.05) raising in a percentages of hatchability of setting and fertilized eggs from normal local hens when compared with that from dwarf hen.Also, weights of egg and chick reported a significant (P<0.05) reducing in dwarf egg when comparing with local egg. The yolk percentage and shell thickness recorded a significant raising in dwarf egg in comparing with normal local egg. In conclusion, the dwarf gene influenced on eggs features subsequently affected on the fertility of dwarf hen. [ABSTRACT FROM AUTHOR]

The article examines the effects of domestication and artificial selection on the genome of domesticated chickens. It explores the corroboration between prediction algorithms of deleteriousness and the population frequency of deleterious alleles. The domestication and selection continuum of commercial chickens are discussed, as well as the effect size of mutations derived from sequence data.

Escherichia coli ST117 is a pandemic extraintestinal pathogenic E. coli (ExPEC) causing significant morbidity globally. Poultry are a known reservoir of this pathogen, but the characteristics of ST117 strains from other animal sources have not been adequately investigated. Here we characterize the genomes of 36 ST117 strains recovered primarily from preweaned dairy calves, but also from older postweaned calves and lactating cows, in the context of other bovine-associated strains and strains from poultry, swine, and humans. Results of this study demonstrate that bovine-associated ST117 genomes encode virulence factors (VFs) known to be involved in extraintestinal infections, but also occasionally encode the Shiga toxin, a virulence factor (VF) involved in severe gastrointestinal infections and more frequently identified in E. coli from ruminants than other animals. Bovine-associated ST117 genomes were also more likely to encode afa-VIII (adhesins), pap (P-fimbriae), cdt (cytolethal distending toxin), and stx (Shiga toxins) than were poultry and swine-associated genomes. All of the ST117 genomes were grouped into seven virulence clusters, with bovine-associated genomes grouping into Clusters 1, 2, 4, 5, but not 3, 6, or 7. Major differences in the presence of virulence factors between clusters were observed as well. Antimicrobial resistance genes were detected in 112 of 122 (91%) bovine-associated genomes, with 103 of these being multidrug-resistant (MDR). Inclusion of genomes that differed from ST117 by one multi-locus sequence type (MLST) allele identified 31 STs, four of these among the bovine-associated genomes. These non-ST117 genomes clustered with the ST117 genomes suggesting that they may cause similar disease as ST117. Results of this study identify cattle as a reservoir of ST117 strains, some of which are highly similar to those isolated from other food animals and some of which have unique bovine-specific characteristics., Competing Interests: The authors have declared that no competing interests exist. Mention of trade names or commercial products in this article is solely for providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. This does not alter our adherence to PLOS ONE policies on sharing data and materials., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)

This article aimed to detect the existence of barley-specific Nikita and Sukkula retrotransposons in domestic geese samples and to evaluate the evolutionary relationships between these and other transposons belonging to the family Anatidae. Inter-retrotransposonamplified polymorphism-polymerase chain reaction (IRAP-PCR) method was performed for these retrotransposons movements in three diverse domestic goose populations (Chinese x Embden crossbred, Turkish White, and Turkish Multicolor). Polymorphism ratios were between 0 and 33% in all samples for Nikita and 0-73% in all samples for Sukkula . In addition, intrapopulation genetic polymorphism rates were also 0-15% in Chinese x Embden crossbred, 0-25% in Turkish White, 0-25% in Turkish Multicolor for Nikita ; while 0-27% in Chinese x Embden, and 0-50% in Turkish Multicolor for Sukkula . There was no polymorphism for Sukkula among Turkish White samples. Moreover, the neighbour-joining method was used for phylogenetic tree construction using 38 sequences of different ducks, geese, and swans. In silico analyses supported the transitions of retrotransposons in the family Anatidae. It is concluded that transposon mobility among the phylogenetically distant species may lead to understanding evolutionary relationships. This report is one of the first studies investigating retrotransposon movements in domestic geese, revealing a new perspective on the goose genome regarding mobile genetic elements.

The novel mosquito-borne Tembusu virus (TMUV, family Flaviviridae) was discovered as the cause of a severe outbreak of egg-drop syndrome affecting ducks in Southeast Asia in 2010. TMUV infection can also lead to high mortality in various additional avian species such as geese, pigeons, and chickens. This study describes the construction of an infectious cDNA clone of a contemporary duck-isolate (TMUV WU2016). The virus recovered after transfection of BHK-21 cells shows enhanced virus replication compared to the mosquito-derived MM1775 strain. Next, the WU2016 cDNA clone was modified to create a SP6 promoter-driven, self-amplifying mRNA (replicon) capable of expressing a range of different reporter genes (Renilla luciferase, mScarlet, mCherry, and GFP) and viral (glyco)proteins of avian influenza virus (AIV; family Orthomyxoviridae), infectious bursal disease virus (IDBV; family Bunyaviridae) and infectious bronchitis virus (IBV; family Coronaviridae). The current study demonstrates the flexibility of the TMUV replicon system, to produce different heterologous proteins over an extended period of time and its potential use as a platform technology for novel poultry vaccines., (© 2023 The Authors. Biotechnology Journal published by Wiley-VCH GmbH.)

Gene chip is a high-throughput technique for detecting specific DNA sequences by DNA or DNA-RNA complementary hybridization, among which SNP genotyping chips have been widely employed in the animal genetics and breeding, and have made great achievements in cattle (Bos taurus), pigs (Sus scrofa), sheep (Caprinae), chickens (Gallus gallus) and other livestock. However, genomic selection applied in production merely uses genomic information and cannot fully explain the molecular mechanism of complex traits genetics, which limits the accuracy of genomic selection. With the continuous progresses in epigenetic research, the development of commercial methylation chips and the application of the epigenome-wide association study (EWAS), DNA methylation has been extensively used to draw the causal connections between genetics and phenotypes. In the future, it is hopefully expected to develop methylation chips customized for livestock and poultry and explore methylation sites significantly related to economic traits of livestock and poultry through EWAS thereby extending the understanding of causal variation of complex traits. Combining methylation chips and SNP chips, we can capture the epigenomic and genomic information of livestock and poultry, interpret genetic variation more precisely, improve the accuracy of genome selection, and promote the fine evolution of molecular genetic breeding of livestock and poultry. In this review, we summarize the application of SNP chips and depict the prospects of the application of methylation chips in livestock and poultry. This review will provide valuable insights for further application of gene chips in farm animal breeding.

Animal husbandry is increasing yearly due to the growing demand for meat and livestock products, among other reasons. To meet these demands, prophylactic antibiotics are used in the livestock industry (i.e., poultry farming) to promote health and stimulate animal growth. However, antibiotics are not fully metabolized by animals, and they are evacuated to the environment with excreta. Animal manure is used as fertilizer to reduce the volume of waste generated in the livestock sector. However, manure often contains microorganisms harboring antibiotic resistance genes (ARGs). Then, the microbiome of manure applicate to the soil may contribute to the spread of antibiotic resistance in the environment, including autochthonous soil-dwelling microorganisms. The present study was conducted during the crops growing season in Poland (May to September 2019) to determine the influence of poultry manure as well as poultry manure supplemented with selected antibiotics on the diversity of the soil microbiome in treatments that had not been previously fertilized with manure and the ability of antibiotic-resistant bacteria to transfer ARGs to other soil bacteria. Antibiotic concentrations were elevated at the beginning of the study and decreased over time. Poultry manure induced significant changes in the structure of microbial communities in soil; the diversity of the soil microbiome decreased, and the abundance of bacterial genera Bradyrhizobium, Streptomyces, and Pseudomonas, which are characteristic of the analyzed manure, increased. Over time, soil microbial diversity was restored to the state observed before the application of manure. Genes conferring resistance to multiple drugs as well as genes encoding resistance to bacitracin and aminoglycosides were the most frequently identified ARGs in the analyzed bacteria, including on mobile genetic elements. Multidrug resistance was observed in 17 bacterial taxa, whereas ARGs were identified in 32 bacterial taxa identified in the soil microbiome. The results of the study conclude that the application of poultry manure supplemented with antibiotics initially affects soil microbiome and resistome diversity but finally, the soil shows resilience and returns to its original state after time, with most antibiotic resistance genes disappearing. This phenomenon is of great importance in sustainable soil health after manure application., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The objective of this study was to identify Eimeria spp. in alternative poultry production systems (APPS) in the State of São Paulo, Brazil. Fecal samples (168) and DNA extracted from fecal samples obtained in APPS located in different Municipalities in the State of São Paulo (93) were examined by microscopy or genera-specific PCR (ITS-1 locus). Samples positive for Eimeria spp. were examined using Eimeria lata, Eimeria nagambie, and Eimeria zaria species-specific PCR protocols (ITS-2 locus) and another E. lata-specific PCR (candidate IMP1 genomic locus) followed by molecular cloning (E. lata and E. zaria ITS-2 amplicons) and genetic sequencing. All positive DNA samples were also submitted to genera-specific nested PCR (18S rRNA gene) followed by next-generation sequencing to identify Eimeria spp. Eimeria nagambie, E. zaria, and Eimeria sp. were identified by ITS2-targeted species-specific PCRs and genetic sequencing. Next-generation sequencing identified, in order of prevalence: E. nagambie; Eimeria acervulina; Eimeria mivati; Eimeria praecox; Eimeria brunetti; Eimeria mitis; Eimeria sp.; Eimeria maxima; E. zaria, and Eimeria necatrix/tenella. Our results confirmed, for the first time in Brazil, the identification of E. nagambie, E. zaria, and Eimeria spp. ITS-2 and 18S rRNA gene sequences not yet described in Brazil.

The jungle fowl ( Gallus gallus ) is a tropical bird with important hereditary and phenotypical traits like disease resistance and resistance to harsh conditions and can often survive with scanty diet. However, as commercial chicken breeds replace them, their population is dwindling, which poses a significant threat to fowl genetic resources. There is minimal information on the variety of Indian poultry, mainly native chicken from Northeast India. As a result, the record of the fowl's genetic diversity is essential for its preservation and formulation of conservation strategies. The current study sought to identify indigenous chicken, Kaunayen ( Gallus gallus domesticus ), from Manipur using barcoding based on DNA sequences. A total of 5 CO1 DNA barcodes from several indigenous chickens were sequenced and compared to the previous data of diverse taxa of Phasianidae using the conventional methodology and were recognized as Gallus gallus. The Phasianid birds that were researched were accurately classified into their appropriate species. There is a minuscule genomic difference between G. gallus and G. varius (1.2%) and the highest between Arborophila rufipectus and Tympanuchus pallidicinctus (22.5%). The phylogenetic relationship established on the NJ tree revealed a coherent gathering of indigenous fowl with G. gallus and unique to all other species studied, showing their taxonomic classification. Nonetheless, the investigation offered a genetic identity tag for indigenous chicken for the first time. It will be a potential guide for identifying distinctive and genetically unique poultry sequences for later requirements.

In poultry production, there has been a trend of continuous increase in cost of feed ingredients which represents the major proportion of the production costs. Feed costs can be reduced by improving feed efficiency traits which increase the possibility of using various indigestible feed sources and decrease the environmental impact of the enhanced poultry production. Therefore, feed efficiency has been used as one of the most important economic traits of selection in the breeding program of chickens. Recently, many OMICs experimental studies have been designed to characterize biological differences between the high and low feed efficiency chicken phenotypes. Biological complexity cannot be fully captured by main individual OMICs such as genomics, transcriptomics, proteomics and metabolomics. Therefore, researchers have combined multiple assays from the same set of samples to create multi-OMICs datasets. OMICs findings are crucial in improving existing approaches to poultry breeding. The current review aimed to highlight the components of feed efficiency and general OMICs approaches and technologies. Besides, individual and multi-OMICs based understanding of chicken feed efficiency traits and the application of the acquired knowledge in the chicken breeding program were addressed.

Background: Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease caused by Dabie bandavirus , which belongs to the genus Bandavirus , family Phenuiviridae , and order Bunyavirales. It has been found in tick species, various animals, and humans. The aim of this study was to detect RNA of antigens and antibodies against SFTS virus (SFTSV) among poultry such as chickens, ducks, and wild geese from five provinces in the Republic of Korea (ROK). Materials and Methods: A one-step reverse transcriptase (RT)-PCR and nested PCR were performed after viral RNA extraction. The phylogenetic tree was constructed after sequencing data were analyzed and aligned. An indirect enzyme-linked immunosorbent assay (ELISA) and a neutralization test (NT) were performed to test for IgG antibodies of SFTSV. Results: Of a total of 606 poultry serum samples collected, 568 and 539 serum samples were used to perform ELISA and NT, respectively. Of a total of 606 serum samples tested by RT-PCR targeting the S segment, 15 (2.5%) were positive for SFTSV. From the 15 positive serum samples for the SFTSV antigen, three from chickens, three from ducks, and one from wild geese were classified as genotype B-2; one from chickens was classified as genotype B-3; and three from chickens and four from wild geese were classified as genotype D. Of the 568 serum samples tested by ELISA, 83 (28.0%) from chickens, 81 (32.9%) from ducks, and 8 (30.8%) from wild geese were seropositive. Of the 539 serum samples for which an NT was performed, 113 (38.6%) from chickens and 75 (30.5%) from ducks were positive for SFTSV antibodies. Conclusions: The results of this study provide useful information regarding detection of SFTSV RNA and antibodies among poultry and the possibility of SFTSV transmission in various types of poultry, including chickens, ducks, and wild geese, in the ROK.

The purebred-crossbred genetic correlation (r pc ) is a key parameter to determine whether the optimal selection of purebred animals to improve crossbred performance should rely on crossbred phenotypes, purebred phenotypes, or both. We reviewed published estimates of the r pc in poultry. In total, 19 studies were included, of which four were on broilers and 15 on laying hens, with 150 r pc estimates for nine different trait categories. Average reported r pc estimates were highest for egg weight, egg quality and egg colour (0.74-0.82), intermediate for BW, maturity and mortality (0.61-0.70) and egg number (0.58), and low for resilience (0.40) and body conformation (0.14). Most studies were based on measuring purebred and crossbred phenotypes in the same environment and thus did not capture the contribution of genotype by environment interactions to the r pc , suggesting that the presented average estimates may be higher than values that apply in practice. Nearly all studies were based on two-way crossbred animals. We hypothesised that r pc values for a two-way cross are good proxies for r pc of a four-way cross. Only eight out of 19 studies were published in the last 25 years, and only two of those used genomic data. We expect that more studies using genomic data may be published in the coming years, as the required data may be generated when implementing genomic selection for crossbred performance, which will lead to more accurate r pc estimates. Future studies that aim to estimate r pc are encouraged to capture the genotype by environment interaction component by housing purebred and crossbred animals differently as is done in practice. Moreover, there is a need for further studies that enable to explicitly estimate the magnitude of genotype by environment versus genotype by genotype interactions for multiple trait categories. Further, studies are advised to report: the specific housing conditions of the animals, any differences between measurements of purebred versus crossbred performance, and the heritabilities of purebred and crossbred performance., (Copyright © 2023 The Author(s). Published by Elsevier B.V. All rights reserved.)

The eggshell blueness is an interesting object for chicken genetic studies and blue-shelled chicken industry, especially after the discovery of the causative mutation of chicken blue eggshell. In the present study, genome wide association study (GWAS) was conducted in Chinese Dongxiang blue-shelled chicken underlying four traits of blue eggshell pigments: quantity of biliverdin (QB), quantity of protoporphyrin (QP), quantity of total pigment (QT), and color density trait (CD). A total of 139 individuals were randomly collected for GWAS. We detected two SNPs in genome-wise significance and 35 in suggestive significance, 24 out of the 37 SNP were located either within intron/exon or near 15 genes in a range of ~1.17 Mb on GGA21. For further confirmation of the identified SNP loci by GWAS, the follow-up replication studies were performed in two populations. A total of 146 individuals of the second generation derived from the former GWAS population, as well as 280 individuals from an alternative independent population were employed for genotyping by MALDI-TOF MS in a genotype-phenotype association study. Eighteen SNPs evenly distributed on the GGA21 significant region were successfully genotyped in the two populations, of which 4 and 6 SNP loci were shown significantly associated with QB, QT and QP in the two repeat populations, respectively. Further, the SNPs were narrowed down to a region of ~ 653.819 Kb on GGA21 that harbors five candidate genes: AJAP1, TNFRSF9, C1ORF174, CAMTA1, and CEP104. Shell gland of chickens laying dark and light blue eggshell was chosen for detection of mRNA expression of the five candidate genes. The results showed differential expression levels of these genes in the two groups. The specific function of these genes has not yet been defined clearly in chickens and further in-depth studies are needed to explore the new functional role in chicken eggshell blueness. [ABSTRACT FROM AUTHOR]

1. The genetic diversity and population structure were studied for eight local chicken breeds, including Anjiyan (AN), Hetian Black (HH), Hetian Ma (HM), Aheqi (AH), Baicheng You (BC), Hejing (HJ), Tashkurghan (TS) and Ruoqiang (RQ), in the Southern Xinjiang region of China, using 20 microsatellite markers. 2. Total 336 alleles were obtained from all chicken breeds, with a mean of 16.8 alleles per locus. The polymorphism information content ranged from 0.444 to 0.911, with a mean of 0.729 and almost all of the loci showed significant deviation from Hardy-Weinberg standards. The observed and expected heterozygosity of the eight breeds ranged from 0.5 to 0.677 and from 0.656 to 0.774, with the lowest observed in the AN and the highest in BC breed. The average breed genetic diversity was 0.655 for AN and 0.766 for BC chickens. 3. According to the neighbour-joining (NJ) method, three main clusters were identified in the NJ phylogenetic tree with AN and RQ breeds in one clade, HH and HM breeds in the second clade and TS, HJ, AH and BC breeds in the third clade. 4. Based on STRUCTURE analysis, the most likely cluster number of all breeds was K = 4, whereby HH and HM breeds formed one cluster and AH, BC, HJ and TS formed another, and RQ, AN chicken formed their own distinct cluster. These results indicated that HH and HM breeds had similar genetic background, as did the breeds of AH, BC, HJ and TS. RQ, AN breed had unique genetic backgrounds, distinct from the other breeds. Genetic introgression was detected from AN to HH and HM. 5. The results of the current study can be used as baseline genetic information to implement effective conservation programs and to make better use of these local chicken breeds, especially for the AN, RQ and TS breeds. [ABSTRACT FROM AUTHOR]

1. The objectives of the current study were to investigate the mitochondrial genome and molecular phylogeny of Lueyang black-bone chicken, and  provide  molecule base to preserve and explore the specific chicken strain. 2. Based on sequencing and clustering, the complete mitochondrial DNA map and sequences of Lueyang black-bone chicken were revealed, and two phylogenetic trees of Lueyang black-bone chickens based on D-loop sequences and the mitochondrial genome were constructed. 3. The results showed that the complete mitochondrial genome of Lueyang black-bone chickens is 16,784bp in size, consisting of 22 transfer RNA genes, two ribosomal RNA genes, 13 protein-coding genes, and one non-coding control region. The base composition of the complete mtDNA sequence is 30.28% for A, 23.78% for T, 32.42% for C, 13.52% for G. Additionally, 10 haplotypes of D-loop sequences in 32 Lueyang black-bone chickens were detected, which were distributed into 4 clades (A, B, C and E). 4. It was concluded that genetic diversity is wide in Lueyang black-bone chickens, and this strain has multiple maternal origins from different regions in China and neighbouring regions. [ABSTRACT FROM AUTHOR]

Objective: To investigate the genotype and diversity of Pasteurella multocida present in pig herds and to determine the extent of overlap with isolates from poultry flocks in Australia. Methods: A total of 43 isolates from pigs from different farms and regions of Australia were used in this study. A diverse collection of 41 poultry isolates, with 31 being previously characterised, was also used. The pig isolates and 10 poultry isolates were identified by species‐specific PCR assay, serotyped by the Heddleston scheme and genotyped by a multiplex PCR based on the lipopolysaccharide (LPS) outer core biosynthesis locus, repetitive element PCR fingerprinting (rep‐PCR) and multilocus sequence typing (MLST), with the latter being used on a subset of the isolates based on the rep‐PCR results. Results: Only 4 out of 8 recognised LPS genotypes were found in the pig isolates, with each isolate assigned to an LPS genotype. In contrast, 77% of the isolates were non‐typable or cross‐reacting in the Heddleston serotyping scheme. The rep‐PCR analysis recognised 20 patterns, yet only 16 sequence types (STs) were found and 4 were new STs. There were 5 STs (STs 7, 11, 20, 24 and 58) shared among the pig and poultry isolates. Conclusions: Although only limited numbers of isolates have been examined, there is evidence of a sharing of genotypes between Australian pigs and chickens. These findings have major implication for biosecurity measures with regard to minimising both direct (e.g. animal to animal) and in‐direct (e.g. shared staff or cross‐visitors) contact between poultry and pigs. [ABSTRACT FROM AUTHOR]

Abstract H5 and H7 subtypes of low pathogenicity avian influenza viruses (LPAIVs) have the potential to evolve into highly pathogenic avian influenza viruses (HPAIVs), causing high mortality in galliforme poultry with substantial economic losses for the poultry industry. This study provides direct evidence of H7N7 LPAIV mutation to HPAIV on a single poultry premises during an outbreak that occurred in June 2008 in free range laying hens in Oxfordshire, UK. We report the first detection of a rare di-basic cleavage site (CS) motif (PEIPKKRGLF), unique to galliformes, that has previously been associated with a LPAIV phenotype. Three distinct HPAIV CS sequences (PEIPKRKKRGLF, PEIPKKKKRGLF and PEIPKKKKKKRGLF) were identified in the infected sheds suggesting molecular evolution at the outbreak premises. Further evidence for H7N7 LPAIV preceding mutation to HPAIV was derived by examining clinical signs, epidemiological descriptions and analysing laboratory results on the timing and proportions of seroconversion and virus shedding at each infected shed on the premises. In addition to describing how the outbreak was diagnosed and managed via statutory laboratory testing, phylogenetic analysis revealed reassortant events during 2006–2008 that suggested likely incursion of a wild bird origin LPAIV precursor to the H7N7 HPAIV outbreak. Identifying a precursor LPAIV is important for understanding the molecular changes and mechanisms involved in the emergence of HPAIV. This information can lead to understanding how and why only some H7 LPAIVs appear to readily mutate to HPAIV. Highlights • Direct evidence of influenza virus evolution on a single poultry outbreak premises • First detection of a rare di-basic cleavage site motif unique to galliformes • Reassortment events suggested likely incursion of a wild bird origin precursor. [ABSTRACT FROM AUTHOR]

1. There has been substantial research focused on the roles of microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs) derived from mammalian spermatozoa; however, comparatively little is known about the role of spermatozoa-derived miRNAs and piRNAs within breeding cockerels’ spermatozoa. 2. A small RNA library of cockerels’ spermatozoa was constructed using Illumina high-throughput sequencing technology. Unique sequences with lengths of 18-26 nucleotides were mapped to miRBase 21.0 and unique sequences with lengths of 25-37 nucleotides were mapped to a piRNA database. A total of 1311 miRNAs and 2448 potential piRNAs were identified. Based on stem-loop qRT-PCR, 8 miRNAs were validated. 3. Potential target genes of the abundant miRNAs were predicted, and further Kyoto Encyclopedia of Genes and Genomes database (KEGG) and Gene Ontology (GO) analyses were performed, which revealed that some candidate miRNAs were involved in the spermatogenesis process, spermatozoa epigenetic programming and further embryonic development. 5. GO and KEGG analyses based on mapping genes of expressed piRNAs were performed, which revealed that spermatozoal piRNAs could play important regulatory roles in embryonic development of offspring. 6. The search for endogenous spermatozoa miRNAs and piRNAs will contribute to a preliminary database for functional and molecular mechanistic studies in embryonic development and spermatozoa epigenetic programming. [ABSTRACT FROM AUTHOR]

The present study was conducted to investigate the polymorphisms of prolactin receptor (PRLR5) gene and its association with egg production in Kadaknath hens. Egg production is a polygenic inheritance trait. Study was conducted on twenty female birds of Kadaknath kept for laying. Egg production performances were recorded as age at first laying (AFE), Body Weight at First Egg (WFE), Mean Egg Weight (MEW) and Total No. of Eggs at 90 days of laying (TEN). Genomic DNA isolated from 2-3 of blood collected from wing vein of each bird was amplified for prolactin receptor (PRLR5) gene with specific primer by standardizing and optimising the PCR protocols. PCR was performed in a final volume of 20 µl. The amplified PCR products were resolved on the gels to generate polymorphisms. PRLR5 was digested with BamHI. Retriction digested products were run on 2% agarose gel electrophoresis. PRLR5 showed two alleles & two genotypes. The frequency of AA genotype at this locus was 0.75 & BB genotype was 0.25. The AFE (d), WFE (Kg), MEW (g) and TEN of Kadaknath hens in the present study were found to be 188.00±0.71, 1.26±0.03, 42.83±0.21 & 37.75±0.59 respectively. Birds with AA genotype of PRLR5 had a significantly (P<0.05) better WFE & AFE than BB genotype. Prolactin receptor (PRLR5) genes produced polymorphism in Kadaknath and were associated with egg production traits. [ABSTRACT FROM AUTHOR]