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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]

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: 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]

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]

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]

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]

Background: Over many centuries, the conventional methods of poultry breeding is based on the phenotypic selection of the birds with superior trait in a particular population. Prolactin is a physiological candidate gene that has significant effects on production traits in poultry. The objective of this study was to investigate 24 bp insertion (I) polymorphism of prolactin gene and its association with quantitative traits in Tellicherry native chicken. Methods: A total of 200 blood samples were collected from the randomly selected birds of All India Co-ordinated Research Project (AICRP) on Poultry Breeding, Mannuthy. The isolated DNA samples were subjected to polymerase chain reaction (PCR) by using specific set of primers to amplify the 24 bp insertion polymorphism. PCR amplicons were sequenced to study the polymorphism at nucleotide level. Result: PCR amplification revealed the presence of a specific DNA fragment with 130/154 bp contained 24 bp insertion polymorphism. Based on the polymorphic patterns birds were designated with three genotypes as II, ID and DD. The frequency of I (0.6975) allele was found higher than D (0.3025) allele. Our experimental results revealed that 24 bp insertion polymorphism of prolactin did not have a significant association with production traits viz, age at sexual maturity, egg weight and egg number in Tellicherry native chicken. [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]

Chicken primordial germ cells (PGCs) are important cells with significant implications in preserving genetic resources, chicken breeding and production, and basic research on genetics and development. Currently, chicken PGCs can be cultured long-term in vitro to produce single-cell clones. However, systematic exploration of the cellular characteristics of these single-cell clonal lines has yet to be conducted. In this study, single-cell clonal lines were established from male and female PGCs of Rugao Yellow Chicken and Shouguang Black Chicken, respectively, using a micropipette-based method for single-cell isolation and culture. Analysis of glycogen granule staining, mRNA expression of pluripotency marker genes (POUV , SOX2 , NANOG), germ cell marker genes (DAZL , CVH), and SSEA-1, EMA-1, SOX2, C -KIT, and CVH protein expression showed positive results, indicating that PGCs maintain normal cellular properties after single-cell cloning. Furthermore, tests on proliferation ability and gene expression levels in PGC single-cell clonal lines showed high expression of the pluripotency-related genes and TERT compared to control PGCs, and PGC single-cell clonal lines demonstrated higher proliferation ability. Finally, green fluorescent protein (GFP)-PGC single-cell clonal lines were established, and it was found that these single-cell clonal lines could still migrate into the gonads of recipients, suggesting their potential for germ-line transmission. This study systematically validated the normal cellular characteristics of PGC single-cell clonal lines, indicating that they could be applied in genetic modification research on chickens. • PGC single-cell clonal lines were created from two breeds of chickens. • PGCs maintain their normal cellular properties after single-cell cloning. • Single-cell clonal lines of PGCs could still migrate into the gonads of recipients. [ABSTRACT FROM AUTHOR]

Simple Summary: Weighted gene co-expression network analysis (WGCNA) was performed to investigate the gene networks and key genes involved in regulating inosine monophosphate (IMP) content in the pectoralis major muscle of the Guangde feathered-leg chicken breed. The study indicates that four genes in the purple module may be crucial in forming IMP content. This research enhances our understanding of the molecular mechanisms that contribute to IMP content. Inosine monophosphate (IMP) is a substance that enhances flavor and plays a crucial role in the umami taste of chicken muscle. It is also an influential factor in determining chicken's economic value. However, the molecular regulatory network underlying the IMP content in muscle remains unclear. To address this issue, we performed transcriptome sequencing on 20 pectoralis major muscle samples from 120-day-old Guangde feathered-leg chicken and used weighted gene co-expression network analysis (WGCNA) to identify key regulatory factors that influence IMP content. The weighted gene co-expression network was constructed using a total of 16,344 genes, leading to the identification of 20 co-expression gene modules. Among the modules that were identified, it was observed that the purple module (R = −0.51, p = 0.02) showed a significant negative correlation with the IMP content. This suggests that the genes within the purple module had the ability to regulate the IMP content. A total of 68 hub genes were identified in the purple module through gene significance (GS) > 0.2 and module membership (MM) > 0.8. The STRING database was used for a protein–protein interaction (PPI) network of hub genes. Furthermore, troponin I type 1 (TNNI1), myozenin 2 (MYOZ2), myosin light chain 2 regulatory cardiac slow (MYL2), and myosin light chain 3 regulatory cardiac slow (MYL3) involved in the "ATP-dependent activity", "cAMP signaling pathway" and "cGMP-PKG signaling pathway" were identified as central regulators that contribute to IMP content. These results offer valuable information into the gene expression and regulation that affects IMP content in muscle. [ABSTRACT FROM AUTHOR]

Simple Summary: Lindian chickens are a local chicken variety in northern China. To explore the growth and development characteristics of Lindian chickens, various statistical methods were used to analyze their body size and carcass traits. The results showed that multiple trait measurements of Lindian chickens rapidly increased before 10 weeks of age, while after 19 weeks of age they mainly developed reproductive organs and muscles. In addition, we also found that body size traits were closely related to carcass traits, providing a foundation for the breeding and management of Lindian chickens. As an excellent chicken breed found in a high-altitude zone of northern China, Lindian chickens are characterized by good egg and meat production, strong adaptability, cold tolerance, rough feeding resistance, excellent egg quality, and delicious meat quality. To facilitate the exploitation of the unique qualities of the Lindian chicken, the varying patterns and correlations of various body size and carcass traits of 3–22-week-old Lindian chickens were analyzed in this study. The optimal growth model of these traits was determined by growth curve fitting analysis. The results showed that most traits of Lindian chickens increased steadily with increasing age, and most of them increased rapidly before 10 weeks of age. In addition, the inflection point age of each trait was predicted to be between 4 and 10 weeks. Furthermore, this study revealed that body size traits were closely related to carcass traits in Lindian chickens. In summary, Lindian chickens are in a rapid growth stage before the age of 10 weeks, and better slaughter performance can be achieved through good feeding management during this stage. The reproductive traits and muscles are the main developmental focus after the age of 19 weeks, so it is important to adequately meet their energy requirements for subsequent good breeding performance. [ABSTRACT FROM AUTHOR]

Objective: Tibetan chickens, which have unique adaptations to extreme high-altitude environments, exhibit phenotypic and physiological characteristics that are distinct from those of lowland chickens. However, the mechanisms underlying hypoxic adaptation in the liver of chickens remain unknown. Methods: RNA-sequencing (RNA-Seq) technology was used to assess the differentially expressed genes (DEGs) involved in hypoxia adaptation in highland chickens (native Tibetan chicken [HT]) and lowland chickens (Langshan chicken [LS], Beijing You chicken [BJ], Qingyuan Partridge chicken [QY], and Chahua chicken [CH]). Results: A total of 352 co-DEGs were specifically screened between HT and four native lowland chicken breeds. Gene ontology and Kyoto encyclopedia of genes and genomes enrichment analyses indicated that these co-DEGs were widely involved in lipid metabolism processes, such as the peroxisome proliferator-activated receptors (PPAR) signaling pathway, fatty acid degradation, fatty acid metabolism and fatty acid biosynthesis. To further determine the relationship from the 352 co-DEGs, protein-protein interaction network was carried out and identified eight genes (ACSL1, CPT1A, ACOX1, PPARC1A, SCD, ACSBG2, ACACA, and FASN) as the potential regulating genes that are responsible for the altitude difference between the HT and other four lowland chicken breeds. Conclusion: This study provides novel insights into the molecular mechanisms regulating hypoxia adaptation via lipid metabolism in Tibetan chickens and other highland animals. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

1. Killing male one-day-old chicks, especially from layer lines, is banned in some European countries. Therefore, dual-purpose chickens, where each sex is used for meat and egg production, respectively, offer an alternative production solution. This study evaluated the British purebred breed Ixworth as a dual-purpose chicken for meat and egg production. 2. Ixworth chicks (n = 167) were hatched and reared mixed-sex in a floor housing system, with two groups receiving a commercial pullet diet (treatment 1) and two groups receiving a diet composed for males of layer lines (treatment 2). Individual chick performance data were recorded. Males were slaughtered at 12 weeks of age, and their growth rate and carcase variables were analysed. All hens were continuously reared on the pullet diet and kept in a free-range system from 20 weeks old for one laying period (52 weeks). In addition, group-based feed consumption and mortality were recorded. 3. Cockerels in treatment 1 and 2 showed significantly different [T(88) = −2.846, P = 0.003] growth rates (25.3 vs. 27.4 g/day) and average final weights (2166 g vs. 2344 g). The hens in treatment 1 (n = 41) laid an average of 193 eggs per hen housed (mean egg weight: 56.9 g), whereas those in treatment 2 (n = 35) laid 195 eggs per hen housed (mean egg weight: 56.5 g). Nest acceptance was >97.5% and feed consumption was up to 140 g/bird/day. 4. The results showed that the Ixworth may be a suitable breed for dual-purpose use and could be improved through selective breeding, offering potential for preservation of this local breed as well as general biodiversity in poultry farming. [ABSTRACT FROM AUTHOR]

Local genetic resources have an important place in poultry production in Africa. However, knowledge of these genetic resources and their breeding systems is quite often limited. This study was conducted in Seno Province/Burkina Faso and aimed to characterize the local chicken production system, the genetic resources used, and their management in this area. A survey was conducted involving 185 chicken farmers in a rural area. The snowball sampling method was used to co-opt interviewees, and face-to-face interviews were done. The questionnaire includes closed and open-ended questions. Production system characteristics showed that local chickens were bred in a free-range production system with few inputs. There were multiple production purposes, such as self-consumption (meat and eggs), saving, selling, and donating to strangers. The sale of chickens was ranked as the main purpose with 0.48 as the index, and self-consumption of chicken meat came in the second position with 0.34 as the index. According to farmers, three phenotypes of chickens ("breed or ecotypes") are encountered in the area. However, these phenotypes are raised together with uncontrolled mating practice, leading to a tendency towards uniformity of phenotypes. Almost all farmers (98.9%) stated they select breeding roosters. This selection is mainly based on growth performance (96.6%). Nevertheless, they ranked "resistance to diseases" as the characteristic they would improve primarily if they had all the possibilities (index 0.43). In general, the production system was extensive with low input, whereas the local chicken genetic resources were under poor management, which can lead to genetic erosion. [ABSTRACT FROM AUTHOR]

The poultry population in Africa is mostly composed of local or indigenous chickens appreciated for the unique taste and texture of their meat. However, with the ever-increasing population growth, the free-range or backyard poultry farming system is no longer adapted to supply people with protein requirements. Crossbreeding local hens with an improved rooster weakens the thermotolerance and disease resistance of the offspring in African areas. In this context, the available breeds need to be preserved. The improvement of their productivity should be actualized through the implementation of a sustainable production programme that is simple and less expensive for the farmer, taking into account: feeding, habitat and chicken care. Scientific research should invest more time on the identification and characterization of all available breeds or chicken ecotypes allowing us to know production performances and their nutritional needs. Feeding with locally available resources, vaccination and use of indigenous medicine requiring training of farmers are essential perspectives. This paper focused on the productivity and resilience of indigenous chicken ecotypes in various African tropical environments and some essential factors to improve the birds. For this, a critical analysis was made based on the available data on the birds from research databases. [ABSTRACT FROM AUTHOR]

Infectious bronchitis virus (IBV) is an avian coronavirus that causes a disease in chickens known as infectious bronchitis (IB). The pathogenesis of IBV and the host immune responses against it depend on multiple factors such as the IBV variant, breed and age of the chicken, and the environment provided by the management. Since there is limited knowledge about the influence of the sex of chickens in the pathogenesis of IBV, in this study we aim to compare IBV pathogenesis and host immune responses in young male and female chickens. One-week-old specific pathogen-free (SPF) White Leghorn male and female chickens were infected with Canadian Delmarva (DMV)/1639 IBV variant at a dose of 1 × 106 embryo infectious dose (EID)50 by the oculo-nasal route while maintaining uninfected controls, and these chickens were euthanized and sampled 4- and 11-days post-infection (dpi). No significant difference was observed between the infected male and female chickens in IBV shedding, IBV genome load in the trachea, lung, kidney, bursa of Fabricius (BF), thymus, spleen, and cecal tonsils (CT), and IBV-induced lesion in all the examined tissues at both 4 and 11 dpi. In addition, there was no significant difference in the percentage of IBV immune-positive area observed between the infected male and female chickens in all tissues except for the kidney, which expressed an increased level of IBV antigen in infected males compared with females at both 4 and 11 dpi. The percentage of B lymphocytes was not significantly different between infected male and female chickens in all the examined tissues. The percentage of CD8+ T cells was not significantly different between infected male and female chickens in all the examined tissues except in the trachea at 11 dpi, where female chickens had higher recruitment when compared with male chickens. Overall, although most of the findings of this study suggest that the sex of chickens does not play a significant role in the pathogenesis of IBV and the host immune response in young chickens, marginal differences in viral replication and host responses could be observed to indicate that IBV-induced infection in male chickens is more severe. [ABSTRACT FROM AUTHOR]

Background: Understanding of breeding practices and traits preferences of the communal farmers is the bottom-up approach where livestock specialists assist farmers to identify and understand their production challenges before designing an improvement program. This study was conducted to identify the socio-economic status, breeding practices, production systems and trait preferences of chicken keepers at Madiga village, Limpopo province. Methods: A total of 38 chicken farmers out of 62 were administered a well-structured questionnaire. Descriptive statistics and Chisquare test were used to analyse and test the significance among the gender respectively. Result: The results showed that the breeding practices were not significantly affected by gender (p>0.05). Almost all the farmers in Madiga village were keeping indigenous breeds. The results indicated that the majority of the farmers were improving their indigenous chickens mainly by pure breeding. The most common trait preferences of farmers in breeding cocks were body size, mating ability and growth rate while in breeding hens they were mothering ability, hatchability and growth rate. This study indicated that pure breeding, culling and both controlled and uncontrolled mating system were the most common breeding practices in Madiga village. This study might help to attract animal scientists to develop a multipurpose chicken breed that will express the traits preferred by farmers under village production environment and promote chicken production and food security as a result. [ABSTRACT FROM AUTHOR]

Background: The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single-nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome. Methods: We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines. Results: We demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K feathering locus using short reads, which would not be possible using a linear reference. Conclusions: We expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats. [ABSTRACT FROM AUTHOR]

Simple Summary: The onset of egg laying for hens is affected by genotype, nutritional body status and environmental conditions. Local breeds (white eggshell breeds—Padovana and Polverara; tinted eggshell breeds—Pepoi, Ermellinata di Rovigo, Robusta Maculata and Robusta Lionata) from the Veneto region, in Northern Italy, were reared outdoors from spring (6 weeks of age; 6 WA) to autumn and winter. The onset of laying varied according to the breed (22–28 WA): only the tinted eggshell breeds started laying at the end of summer/beginning of autumn, in the presence of a decreasing natural photoperiod, and the egg production lasted for some weeks. At 38 WA, artificial light was gradually added to the photoperiod to obtain 14L:10D, and at 42 WA, all six breeds were laying. For hens reared outdoors, interactions among environment, body energy and nutritional requirements should be considered. The data on the productive yield and egg quality of the local breed hens are useful for the management of the birds and for an adequate supply of eggs, both for market and for brooding throughout the year. The month of hatching and the rearing management, especially temperature and photoperiod, are important factors for pullets and hens reared outdoors. The yield performance and egg quality of dual-purpose chicken breeds from the Veneto region (Italy), Pepoi (PP), Ermellinata di Rovigo (ER), Robusta Maculata (RM) and Robusta Lionata (RL), with different adult body weights (ABW, kg, PP = 1.3; ER = 2.3, RM and RL = 3.1), were studied, using a factorial model (4 × 2), considering breed and age (26–33 weeks, first age, summer–autumn, under decreasing natural photoperiod—on average, 12L:12D, and 42–53 weeks, second age, winter, under implemented photoperiod-14L:10D) as the main effects and interaction. The chicks hatched in spring, and they started laying at the end of summer/beginning of autumn. Significant (p < 0.05) results were shown for many traits. ER showed higher hen–day egg production than that of PP, and RM and RL were the lowest; ER, RM and RL showed medium-size eggs and PP showed small-size eggs. RM produced the most spherical eggs and ER the most ovoid, and they showed the highest and the lowest eggshell thickness, respectively. RM showed the highest yolk to albumen ratio, and RL showed the lowest. The age increased the laying rate and the egg weight in all the groups. At 26–33 weeks, ER and PP showed higher hen–day egg production (on average 24%) than RM and RL (on average, less than 10%). The onset of laying (at least 10% laying rate) was shown, at different ages, according to the % ABW the breeds had reached: PP was the first, followed by ER, then RM, and RL was the last. At 42–53 weeks, the hen–day egg production ranged, on average, from 38 to 52%, according to the breeds; orthogonal contrasts on two-weekly data showed, at first age, increasing linear (ER) and quadratic (other groups) trends, and at second age, positive linear (ER, RM) and cubic (PP, RL) trends. Age (32 vs. 53 weeks) affected almost all the eggshell traits in PP and ER, whereas in RL, and especially RM, fewer traits changed. The age increased the yolk to albumen ratio (unchanged in PP). These results may be useful for the effective management of local purebred chickens, with the purpose to ensure the wellbeing of the hens and for supplying eggs of different quality throughout the year. [ABSTRACT FROM AUTHOR]

Simple Summary: Native chickens generally have the characteristics of low growth performance, which has also become a limiting factor for the breeding of yellow feather broilers. More and more studies have shown that gut microbiota plays an important role in the growth of livestock farming. The Guizhou yellow chicken is a breed of yellow-feathered broiler chicken with excellent meat quality and good flavor currently being cultivated in Guizhou Province, China. In order to explore the role of gut microbiota on the growth performance of native chickens, the Guizhou yellow chicken was taken as a representative, and high-market-weight and low-market-weight chicken groups were established according to their market weights. By integrating microbial 16S rRNA gene sequencing and non-targeted serum metabolome data, five key cecal microbes associated with high body weight in chickens and one key microbe associated with low body weight were identified. In addition, the results also showed that specific gut microbes might positively affect the growth rate of chickens by regulating vitamin and other metabolic pathways. These findings might improve understanding of the role of gut microbiota in chicken growth traits and their underlying metabolic mechanisms. The gut microbiota plays an important role in the physiological activities of the host and affects the formation of important economic traits in livestock farming. The effects of cecal microbiota on chicken weights were investigated using the Guizhou yellow chicken as a model. Experimental cohorts from chickens with high- (HC, n = 16) and low-market-weights (LC, n = 16) were collected. Microbial 16S rRNA gene sequencing and non-targeted serum metabolome data were integrated to explore the effect and metabolic mechanism of cecal microbiota on market weight. The genera Lachnoclostridium, Alistipes, Negativibacillus, Sellimonas, and Ruminococcus torques were enriched in the HC group, while Phascolarctobacterium was enriched in the LC group (p < 0.05). Metabolomic analysis determined that pantothenic acid (vitamin B5), luvangetin (2H-1-benzopyran-6-acrylic acid), and menadione (vitamin K3) were significantly higher in HC serum, while beclomethasone dipropionate (a glucocorticoid) and chlorophene (2-benzyl-4-chlorophenol) were present at higher levels in the LC group. The microbes enriched in HC were significantly positively correlated with metabolites, including pantothenic acid and menadione, and negatively correlated with beclomethasone dipropionate and chlorophene. These results indicated that specific cecal bacteria in Guizhou yellow chickens alter the host metabolism and growth performance. This study provides a reference for revealing the mechanism of cecal microbe actions that affect chicken body weight. [ABSTRACT FROM AUTHOR]

The evolutionary history of vertebrates is replete with emergence of novel brain morphologies, including the origin of the human brain. Existing model organisms and toolkits for investigating drivers of neuroanatomical innovations have largely proceeded on mammals. As such, a compelling non‐mammalian model system would facilitate our understanding of how unique brain morphologies evolve across vertebrates. Here, we present the domestic chicken breed, white crested Polish chickens, as an avian model for investigating how novel brain morphologies originate. Most notably, these crested chickens exhibit cerebral herniation from anterodorsal displacement of the telencephalon, which results in a prominent protuberance on the dorsal aspect of the skull. We use a high‐density geometric morphometric approach on cephalic endocasts to characterize their brain morphology. Compared with standard white Leghorn chickens (WLCs) and modern avian diversity, the results demonstrate that crested chickens possess a highly variable and unique overall brain configuration. Proportional sizes of neuroanatomical regions are within the observed range of extant birds sampled in this study, but Polish chickens differ from WLCs in possessing a relatively larger cerebrum and smaller cerebellum and medulla. Given their accessibility, phylogenetic proximity, and unique neuroanatomy, we propose that crested breeds, combined with standard chickens, form a promising comparative system for investigating the emergence of novel brain morphologies. [ABSTRACT FROM AUTHOR]

The CD4 gene plays an important role in the immune process by producing CD4 molecules that aid in producing antibodies. IPB-D2 chickens are selected from IPB-D2 chickens based on IgY concentration and ND antibody titer. This study aimed to analyze the polymorphism of the CD4 gene, unravel the mRNA expression of CD4 gene in IPB-D2 chicken related to the immunocompetence index, and detect the CD4 gene pathway. The total samples used were 100 IPB-D2 G2 chickens aged 21 weeks. Blood samples were collected for ELISA test, HI test, sequencing test, and seca tonsil tissue for relative mRNA expression. Polymorphism and association data were analyzed using MEGAX, FinchTV, SNPstat, and DNAsp. The relative mRNA expression analysis was conducted using qRT-PCR. The pathway analysis of the CD4 gene was performed using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway analysis. The result showed there were 4 SNPs of the CD4 gene in IPB-D2 chicken, i.e., g.7526 C>T, g.7825 C>T, g.8100 C>A, and g.8157 T>A. All CD4 SNPSs showed no association with IgY concentration and ND antibody titers. Relative mRNA expression shows that IPB-D2 chickens with high ND antibody titers have a higher level of expression when compared to IPB-D2 chickens with low ND antibody titers. Furthermore, pathway analysis showed the CD4 gene involved in the T cell receptor (TcR) signaling process. This study concludes that the CD4 gene is polymorphic and involved in the T cell receptor signaling process. This study demonstrated that polymorphisms of the CD4 gene in IPB-D2 chicken might not contribute to the IgY concentration and ND antibody titer but can serve as a reference in the study of CD4 genes in the other chicken breeds related to the other immunocompetence index. [ABSTRACT FROM AUTHOR]

Local chicken breeds play vital roles in rural development and sustainability; therefore, the preservation of local breeds’ genetic diversity is crucial, also, assessing and advancing local breeds is crucial considering the impact of climate change on chicken production. The current study evaluated the differences between a fully feathered local chicken line (CE2) and a naked-neck local chicken line (CE4) at the microsatellite loci level. For this purpose, nine microsatellite primers were used to scan the genomes of both lines. The results generated by different loci between the two lines showed that the lowest allele numbers were 0 and 4 alleles detected at loci LEI0094 and MCW217, respectively, and the highest allele number was 10 detected at MCW328 and ADL299 loci, with an overall mean of 6.69 alleles/locus. The levels of heterozygosity were relatively high and were higher for line CE4 than for line CE2. The genetic distance between males and females of line CE2 was shorter (0.018) than that between males and females of line CE4 (0.104), and the opposite was observed for genetic identity. Also, ΦPT values were 0.088 (P<0.001), and 0.080 (P<0.01) for line CE2 and line CE4, respectively. The association between alleles and body weights revealed different alleles of microsatellites MCW217, MCW328, MCW193, ADL299, and MCW064 contributed significantly to body weight variance at different ages. The study provided an outlook on the genetic diversity of two chicken lines and indicated substantial room for improvement within Egyptian native breeds. [ABSTRACT FROM AUTHOR]

Simple Summary: The intrinsic differences of skin histology between the feather calamus and the surrounding outer follicle sheath and neighboring cutaneous tissues reflect their resistance to thermal denaturation and account for the defeathering effect by scalding in various breeds and ages of chickens. This study aimed to delineate the fundamental skin histology and its association with feathers in broilers and native Red-Feather (RF) chickens and further elucidate their thermal alterations in respect to the defeathering effect by scalding. Comparisons of skin thickness between fresh samples and those after dehydration and fixation, as well as their collagen contents and histological differences, suggested that RF chickens had a thicker dermal layer with more collagen deposition and compact architecture, particularly in the neck and abdominal skin, but a thinner hypodermal layer in the back, chest, and abdomen skin. Despite an adolescent age, RF chickens showed a shorter calamus depth of tail feathers but a larger calamus diameter of wing feathers. Within the feather follicle punch, a very intense follicle sheath layer with compact collagenous matrixes to fulfill the space next to the inner feather root sheath was observed in RF chickens. Under both soft and hard scalding, RF chickens showed a lower degree of denaturation on hip skins and were more resistant to structural disintegration, primarily within the epidermal and dermal layer. Accordingly, a much narrower gap space between the feather sheath and surrounding follicle sheath was observed, and the gap expansion was also resistant to thermal changes. These results suggest that the defeathering effect by scalding follows the intrinsic skin histologies in chickens of various breeds and ages, primarily depending on the interaction of the feather calamus with the surrounding follicle sheath and neighboring cutaneous tissues, reflecting their resistance to thermal denaturation, but is irrelevant to the feathers per se. [ABSTRACT FROM AUTHOR]

Simple Summary: A collection of native farm animal breeds can be considered as a gene pool and a national heritage. Long-term artificial selection in domesticated animals has certain effects on their genomes, which can be investigated using genome-wide screens for DNA sequence variation, that is, so-called single nucleotide polymorphism (SNP) screens. Here, we looked at the genomes of 19 Russian chicken gene pool breeds, both native and imported, evaluating the contrasting egg, meat and dual-purpose types. Based on genetic diversity statistics, we identified differences between the breeds using many DNA markers (SNPs) that may represent genomic regions that are being selected for, either within a specific breed or shared between breeds. Our research will be helpful for further understanding the genomic diversity and demographic history of Russian domestic chickens. This would be essential for their successful breeding. A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th–19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool. [ABSTRACT FROM AUTHOR]

Simple Summary: Avian orthoreoviruses cause significant losses to the poultry industry worldwide. Reovirus-associated diseases in chickens are frequently reported even in vaccinated flocks due to the emergence and spread of novel strains. Herein we studied the genetic features of reovirus strains originating from parts of East-Central Europe. The isolated strains from the study area displayed large genetic variability and shared low genetic similarity with vaccine strains. These findings highlight the importance of immune pressure from vaccination in the epizootiology of reovirus infection in chickens. The concern that the vaccines currently used against Avian orthoreovirus (ARV) infections are less efficient in the field justifies the need for the close monitoring of circulating ARV strains. In this study, we collected necropsy samples from various chicken breeds and tested for ARV by virus isolation, RT-PCR assay and sequence analysis. ARVs were isolated from birds showing runting-stunting syndrome, uneven growth, lameness or increased mortality, with relative detection rates of 38%, 35%, 6% and 25%, respectively. Partial σC gene sequences were determined for nearly 90% of ARV isolates. The isolates could be classified into one of the major genetic clusters. Interestingly, cluster 2 and cluster 5 were isolated from vaccinated broiler breeders, while clusters 1 to 4 were isolated from unvaccinated broilers. The isolates shared less than 75% amino acid identities with the vaccine strains (range, 44.3–74.6%). This study reaffirms the global distribution of the major genetic clusters of ARVs in chicken. The diversity of ARV strains isolated from unvaccinated broilers was greater than those detected from vaccinated animals, however, the relative importance of passive and active immunity on the selection of novel strains in different chicken breeds needs to be better understood. [ABSTRACT FROM AUTHOR]

Background: Tibetan chickens (Gallus gallus; TBCs), an indigenous breed distributed in the Qinghai-Tibet Plateau, are well adapted to the hypoxic environment. Currently, the molecular genetic basis of hypoxia adaptation in TBCs remains unclear. This study investigated hypoxia adaptation patterns of embryonic brain at different development stages by integrating analysis of the transcriptome with our previously published metabolome data in TBCs and Dwarf Laying Chickens (DLCs), a lowland chicken breed. Results: During hypoxia, the results revealed that 1334, 578, and 417 differentially expressed genes (DEGs) (|log2 fold change|>1, p-value < 0.05) on days 8, 12, and 18 of development, respectively between TBCs and DLCs. Gene Ontology (GO) and pathway analyses revealed that DEGs are mainly related to metabolic pathways, vessel development, and immune response under hypoxia. This is consistent with our metabolome data that TBCs have higher energy metabolism than DLCs during hypoxia. Some vital DEGs between TBCs and DLCs, such as EPAS1, VEGFD, FBP1, FBLN5, LDHA, and IL-6 which are involved in the HIF pathway and hypoxia regulation. Conclusion: These results suggest varied adaptation patterns between TBCs and DLCs under hypoxia. Our study provides a basis for uncovering the molecular regulation mechanism of hypoxia adaptation in TBCs and a potential application of hypoxia adaptation research for other animals living on the Qinghai-Tibet Plateau, and may even contribute to the study of brain diseases caused by hypoxia. [ABSTRACT FROM AUTHOR]

An important aspect that determines the productivity of native chickens is the genetic factor. Improving the genetic quality of chickens can be done through a breeding program which involves the selection and arrangement of mating lines. The objective of the research project is to find basic information on the ancestor's qualitative and quantitative traits to produce a new Indonesian native chicken laying-hens strain. The ancestors used as the genetic source are four native chicken lines: White, Lurik, Wareng, and Ranupane (male and female). Qualitative traits were analyzed using descriptive statistics, and quantitative data were analyzed with ANOVA of a two-level Nested Classification followed by the Least Significant Difference test. The results showed differences in plumage and shank color in each chicken line. In cocks, there were differences (P < 0.05) in body weight, wing length, tail length, head circumference, and front-body width. The height, body circumference, shank length, and beak length differed (P < 0.05) between hen lines. Qualitative characteristics (plumage and shank colors) can be used as a marker for native chicken lines. They can be used as a reference for selection according to the objectives of the breeding program. Body conformation (weight and height) can be used as selection criteria for ancestors (male and female) to produce new strains of laying native hens. [ABSTRACT FROM AUTHOR]

Kadaknath is an important chicken breed of India. It is also known as Kalamashi due to its black-colored meat. The present study was planned to investigate the effect of different bedding material and dietary supplements on heamato-biochemical parameters of Kadaknath. The experiment was carried out at the Poultry unit, Livestock Farm Complex, College of Veterinary and Animal Science, Bikaner, Rajasthan University of Veterinary and Animal Sciences, Bikaner, from March to august, 2021. Day old 288 chicks reared under electrical brooder up to 7 days of age were randomly distributed in equal number into different bedding material (sand, saw dust and wheat straw) where they kept for 24 weeks. There was significantly (P<0.05) effect was recorded in haemoglobin, PCV, serum cholesterol, serum creatinine and higher significant (P<0.01) effect was recorded in serum glucose, serum albumin, serum cholesterol in immune response of birds. The mean value of SGOT (IU/L), SGPT (IU/L) and H:L ratio was non-significantly effect was recorded. All these variations in hemato-biochemical parameters in Kadaknath birds may be due to the effect of different bedding material and their feed habits. [ABSTRACT FROM AUTHOR]

Noi chicken is one of the indigenous fighting-cock breeds of Vietnam with many valuable properties. In chicken, the Golgin subfamily B member 1 (GOLGB1) gene, which locates on chromosome 1, encodes the coat protein 1 vesicle inhibiting factor. A previous study showed that the 65-bp insertion/deletion in the GOLGB1 gene was significantly associated with chicken body weight, neck weight, abdominal fat weight, abdominal fat percentage and the yellow index b of the breast in Chinese indigenous chicken (N409-breed). In this study, 65-bp indel polymorphism in the GOLGB1gene was evaluated in association with body weight in Noi chickens. The live body weight of 170 chickens (90 females, 80 males) at continuous ages of 7-day intervals (from 28 to 84 days) was recorded. A 65-bp indel polymorphism in the GOLGB1 gene was analyzed using the PCR method. The results of PCR and sequencing revealed two alleles (I and D) corresponding to three genotypes: II, ID, DD, in which, the I allele appears with the highest frequency (0.79) in the studied population. An association study using Minitab software showed that genotype was significantly associated with body weight in Noi chickens at days 35 to 84 (P < 0.05). Individuals with more allele “I” have higher live body weight than others. Both factors (sex and genotype) simultaneously affected the body weight of Noi chickens. The results of this study suggested that the 65-bp indel in the GOLGB1 gene could be considered a potential marker for Noi chicken breeding. [ABSTRACT FROM AUTHOR]

Wenchang (WC) chicken, the only indigenous chicken breed listed in Chinese genetic resources in Hainan province, is well known for its excellent meat quality and is sold all over southeast Asia. In recent years, the number of WC has decreased sharply with considerable variability in the quality at market. To explore the genetic diversity and population structure of WC chickens, the whole‐genome data of 235 WC individuals from three conservation farms were obtained using the Illumina 150 bp paired‐end platform and used in conjunction with the sequencing data from 123 individuals from other chicken breeds (including eight Chinese indigenous chicken breeds and three foreign or commercial breeds) downloaded from a public database. A total of 12 111 532 SNPs were identified, of which 11 541 878 SNPs were identified in WC. The results of gene enrichment analyses revealed that the SNPs harbored in WC genomes are mainly related to environmental adaptation, disease resistance and meat quality traits. Genetic diversity statistics, quantified by expected heterozygosity, observed heterozygosity, linkage disequilibrium, nucleotide diversity and fixation statistics, indicated that WC displays high genetic diversity compared with other Chinese indigenous chicken breeds. Genetic structure analyses showed that each population displayed great differentiation between WC and the other breeds, indicating the uniqueness of WC. In conclusion, the results of our study provide the first genomic overview of genetic variants, genetic diversity and population structure of WC from three conservation farms. This information will be valuable for the future breeding and conservation of WC and other surveyed populations. [ABSTRACT FROM AUTHOR]

Simple Summary: Wenchang chickens are the only chicken breed listed in the 'animal genetic resources in China (poultry)' in Hainan Province and are famous for their excellent meat quality. Protection of this genetic resource may ensure poultry husbandry's sustainable and successful development. For more effective conservation, development, and utilization of this genetic resource, we investigated the diversity, degree of inbreeding, and runs of homozygosity (ROH) patterns for Wenchang chickens using whole-genome sequencing data. Our analysis showed that the genetic diversity of Wenchang chickens was relatively high. Selection signal analysis of Wenchang chickens based on ROH found some candidate genes that were putatively associated with meat quality traits and stress resistance traits, such as disease resistance and heat tolerance. Wenchang chickens, a native breed in the Hainan province of China, are famous for their meat quality and adaptability to tropical conditions. For effective management and conservation, in the present study, we systematically investigated the characteristics of genetic variations and runs of homozygosity (ROH) along the genome using re-sequenced whole-genome sequencing data from 235 Wenchang chickens. A total of 16,511,769 single nucleotide polymorphisms (SNPs) and 53,506 ROH segments were identified in all individuals, and the ROH of Wenchang chicken were mainly composed of short segments (0–1 megabases (Mb)). On average, 5.664% of the genome was located in ROH segments across the Wenchang chicken samples. According to several parameters, the genetic diversity of the Wenchang chicken was relatively high. The average inbreeding coefficient of Wenchang chickens based on FHOM, FGRM, and FROH was 0.060 ± 0.014, 0.561 ± 0.020, and 0.0566 ± 0.01, respectively. A total of 19 ROH islands containing 393 genes were detected on 9 different autosomes. Some of these genes were putatively associated with growth performance (AMY1a), stress resistance (THEMIS2, PIK3C2B), meat traits (MBTPS1, DLK1, and EPS8L2), and fat deposition (LANCL2, PPARγ). These findings provide a better understanding of the degree of inbreeding in Wenchang chickens and the hereditary basis of the characteristics shaped under selection. These results are valuable for the future breeding, conservation, and utilization of Wenchang and other chicken breeds. [ABSTRACT FROM AUTHOR]

Background: Chickens provide globally important livestock products. Understanding the genetic and molecular mechanisms underpinning chicken economic traits is crucial for improving their selective breeding. Influenced by a combination of genetic and environmental factors, metabolites are the ultimate expression of physiological processes and can provide key insights into livestock economic traits. However, the serum metabolite profile and genetic architecture of the metabolome in chickens have not been well studied. Results: Here, comprehensive metabolome detection was performed using non-targeted LC–MS/MS on serum from a chicken advanced intercross line (AIL). In total, 7,191 metabolites were used to construct a chicken serum metabolomics dataset and to comprehensively characterize the serum metabolism of the chicken AIL population. Regulatory loci affecting metabolites were identified in a metabolome genome-wide association study (mGWAS). There were 10,061 significant SNPs associated with 253 metabolites that were widely distributed across the entire chicken genome. Many functional genes affect metabolite synthesis, metabolism, and regulation. We highlight the key roles of TDH and AASS in amino acids, and ABCB1 and CD36 in lipids. Conclusions: We constructed a chicken serum metabolite dataset containing 7,191 metabolites to provide a reference for future chicken metabolome characterization work. Meanwhile, we used mGWAS to analyze the genetic basis of chicken metabolic traits and metabolites and to improve chicken breeding. [ABSTRACT FROM AUTHOR]

Soil physical and chemical properties are important indicators to measure soil quality, and soil microorganisms can sensitively reflect changes in the soil environment. The impact of raising chickens under the forest on the soil environment under the forest can be fed back through the changes in both. However, previous studies on the effects of chicken breeding in Masson pine forests on soil physical and chemical properties and the diversity of soil microbial communities are rare. Thus, the design of this study was centered on the chicken coop, within 50 m, and every 10 m is a sample point. A five-point sampling method was used to study the impact of chicken flock activities on soil physical and chemical properties and microbial communities at different distances. The results showed that soil pH and nutrient content presented a decreasing trend with increasing distance, with significant differences among groups. Soil bulk density, water content and organic carbon content had opposite trends. The diversity of the soil microbial community showed a decreasing trend with increasing distance, in which bacterial diversity was higher than fungal diversity; Proteobacteria, Acidobacteria and Actinobacteria were the dominant bacteria; and Arthropoda and Ascomycota were the dominant phyla. This study shows that raising chickens under the forest has improved the forest environment, and a certain frequency of chicken activity or breeding density may be the key factor affecting the forest environment. When applying and promoting raising chickens under the forest, we should pay attention to the appropriate breeding density. [ABSTRACT FROM AUTHOR]

Transplantation of the gonadal tissue of male and female avian species, such as chicken, onto suitable surrogates and production of live offspring has been successfully demonstrated as a strategy for the conservation and re-constitution of valuable chicken germplasm. The main objective of this study was to establish and develop the male gonadal tissue transplantation technology for the conservation of the indigenous chicken germplasm. The male gonads of the Indian native chicken breed, Kadaknath (KN), were transplanted from a day-old donor to a recipient white leghorn (WL) chicken, and Khaki Campbell (KC) ducks, as surrogates. All the surgical interventions were performed under permitted general anaesthesia, and the chicks, upon recovery, were reared with and without immunosuppressant. The recipient surrogates for the donor KN gonads were housed and reared for 10–14 weeks, and post-sacrifice, developed gonadal tissues were harvested to squeeze out the fluid to perform artificial insemination (AI). The AI-entailed fertility test using the recovered seminal extract from the transplanted KN testes from both surrogate species (KC ducks and WL males), used against KN purebred females, remained very close to the percent fertility realised from purebred KN chickens (controls). These initial results revealed from this trial study suggest definitively that, Kadaknath male gonads were readily accepted and grown inside the intra- and inter-species surrogate host, WL chicken and KC ducks, demonstrating a suitable intra- and inter-species donor-host system. Furthermore, the developed transplanted male gonads of KN chicken into the surrogates were found to have the potential to fertilise the egg and give rise to pure-line KN chicks. [ABSTRACT FROM AUTHOR]

Indigenous chicken breeds have both cultural significance and economic value since they possess unique genetic characteristics that enable them to adapt to the local environment and contribute to biodiversity, food security, and sustainable agriculture in Vietnam. To (Tò in Vietnamese) chicken, a Vietnamese indigenous chicken breed, is popularly raised in Thai Binh province; however, little known is about the genetic diversity of this breed. In this study, we sequenced the complete mitochondrial genome of To chicken for a better understanding of the diversity and origin of the breed. The results of sequencing showed that the mitochondrial genome of To chicken spans a total length of 16,784 base pairs and comprises one non-coding control region (known as the displacement-loop (D-loop) region), two ribosomal RNA genes, 13 protein-coding genes, and 22 transfer RNA genes. The phylogenetic tree analyses and estimated genetic distances based on 31 complete mitochondrial genome sequences indicated that To chicken has a close genetic distance with the Laotian native chicken breed, Lv'erwu breed in China, and Nicobari black and Kadaknath breeds in India. The result of the current study might be important for conservation, breeding, and further genetic studies of To chicken. [ABSTRACT FROM AUTHOR]

The Mountainous Meihua chicken is a unique regional germplasm resource from Tongjiang County, Bazhong City, China, but its genetic structure and evolutionary relationships with other native chicken breeds in the Sichuan region remain unclear. Here, we analyzed a total of 469 sequences, including 199 Mountainous Meihua chicken sequences generated in this study, together with 30 sequences representing 13 clades and 240 sequences from seven different Sichuan local chicken breeds downloaded from NCBI. These sequences were further used to analyze genetic diversity, patterns of population differentiation, and phylogenetic relationships between groups. We show that Mountainous Meihua chicken mtDNA sequences have high haplotypic and nucleotide diversity (0.876 and 0.012, respectively) and with a T bias that is suggestive of good breeding potential. Phylogenetic analysis showed that Mountainous Meihua chickens belong to clades A, B, E, and G and have a low affinity to other chicken breeds, with a moderate degree of differentiation. A non-significant Tajima's D indicates that no demographic expansions occurred in the past. Finally, the four maternal lineages identified in Mountainous Meihua chicken showed unique genetic characteristics. [ABSTRACT FROM AUTHOR]

The experiment was designed to test the suitability of sugarcane extract (SE) as a local extender for the cryopreservation of the Banaba native chicken semen by comparing the effects of different cryoprotective agent concentrations [i.e. glycerol and dimethyl sulfoxide (DMSO)] and thawing temperatures on the post-thaw semen quality. Twelve (12) 29-month-old Banaba native roosters served as semen donors. Only samples that passed the preliminary semen quality assessment of > 70% motility and morphology were further processed and analyzed using a computerassisted semen analyzer (CASA). Pooled ejaculate samples were cryopreserved with SE extender containing 3, 5, 7, or 9% (T3%, T5%, T7%, and T9%) glycerol or DMSO concentration levels. The results showed that the inclusion level of cryoprotectants and thawing temperatures have no significant effect on the percent motile sperm, percent progressive sperm, percent normal morphology, and percent viability. The type of cryoprotectant used in cryopreservation of the semen had a significant effect on all the semen quality parameters. Semen cryopreserved with glycerol had significantly higher values compared to DMSO in all semen quality variables. [ABSTRACT FROM AUTHOR]

The purpose of the current study was to examine transcriptomic-based profiling of differentially expressed innate immune genes between indigenous and commercial chickens. In order to compare the transcriptome profiles of the different chicken breeds, we extracted RNA from blood samples of the Isfahan indigenous chicken (as indigenous) and Ross broiler chicken (as commercial) breeds. RNA-Seq yielded totals of 36,763,939 and 31,545,002 reads for the indigenous and commercial breeds, respectively, with clean reads then aligned to the chicken reference genome (Galgal5). Overall, 1327 genes were significantly differentially expressed, of which 1013 genes were upregulated in the commercial versus the indigenous breed, while 314 were more highly expressed in the indigenous birds. Furthermore, our results demonstrated that the SPARC, ATP6V0D2, IL4I1, SMPDL3A, ADAM7, TMCC3, ULK2, MYO6, THG1L and IRG1 genes were the most significantly expressed genes in the commercial birds and the PAPPA, DUSP1, PSMD12, LHX8, IL8, TRPM2, GDAP1L1, FAM161A, ABCC2 and ASAH2 genes were the most significant in the indigenous chickens. Of notable finding in this study was that the high-level gene expressions of heat-shock proteins (HSPs) in the indigenous breeds could serve as a guideline for future genetic improvement. This study identified genes with breed-specific expression, and comparative transcriptome analysis helped understanding of the differences in underlying genetic mechanisms between commercial and local breeds. Therefore, the current results can be used to identify candidate genes for further breed improvement. [ABSTRACT FROM AUTHOR]

【Objective】 The study was carried out to evaluate genetic diversity level of Qilin chicken inferred from complete mitochondrial DNA (mtDNA) D-loop sequences in order to clarify the bread formation of Qilin chicken. 【Method】 Three populations (yellow, white and black-feathered Qilin chickens) and eight indigenous chicken breeds were used for direct sequencing with PCR products of complete mtDNA D-loop region, and these sequences were then used to calculate the genetic variation and neutral test, to construct median networks of haplotypes and to investigate the breeding history of Qilin chickens. 【Result】 The length of mtDNA D-loop complete sequence ranged from 1 231 to 1 232 bp. The content of C+G (39.8%) was lower than that of T+A (60.2%). The total nucleotide diversity of Qilin chickens was 0.00630±0.00054, which was significantly higher than that of each of the eight indigenous chicken breeds. The haptype diversity and nucleotide diversity in yellow, white and black-feathered Qilin chickens were 0.777±0.076, 0.816±0.060, 0.710±0.057 and 0.00699±0.00115, 0.00662±0.00090, 0.00546±0.00062, respectively. The level of genetic diversity was positively correlated with population size. The K2P genetic distance and net genetic distance between Qilin chickens and eight indigenous chicken breeds ranged from 0.008 to 0.009 and 0.003 to 0.005, respectively, which were greater than those between the eight indigenous chicken breeds. A total of 45 mutation sites were detected in 90 samples of Qilin chickens. Seventeen haplotypes were defined in Qilin chickens, with eight exclusive haplotypes and haplotype diversity of 0.773±0.039. The numbers of haptypes of yellow, white and black-feathered Qilin chickens were 12, 7 and 5, respectively. Nineteen haplotypes were defined in eight adjacent indigenous chicken breeds, and no haplotype was shared with Qilin chickens. The number of haptypes of Hetian chicken (8) was greater than that of other chickens, and Ningdu yellow chicken only had three haptypes. The neutral test indicated that all chickens used in this study did not show obvious population expansion at the breed level, with the exception of black-feathered Qilin chickens. The haplotypes of Qilin chickens were distributed in clades A, B, C and E, and the dominated haplogroups were B (30.0%) and E (64.4%). The haplotypes of the eight indigenous chicken breeds were mainly distributed in clades A and B. 【Conclusion】 Unique haptypes indicated that Qilin chickens had an independent breed formation history, and the relatively higher level of genetic diversity of this breed will facilitate its protection and utilization. [ABSTRACT FROM AUTHOR]

Simple Summary: Vision is highly developed in fowl. Light not only provides ambient illumination, but also influences their physiological responses. Therefore, proper lighting management practices are crucial for improving the efficiency and welfare of commercial poultry operations. Light spectrum is the combination of different wavelengths of electromagnetic radiation produced by a lighting source. With a ban of traditional incandescent bulbs globally, the poultry industry is currently undergoing a shift to alternative lighting sources, such as light emitting diode (LED) bulbs, which permit the design of different and complex light spectrums output as required. The present study investigated the effects of three LED lights and one compact fluorescent lamp (CFL) with different spectrum characteristics on the performance during the pullet rearing and subsequent laying phase of Beijing-You chickens, a typical indigenous chicken breed in China. Results showed that the four lights did not show differences in feed efficiency before 17 week of age; the LED light with more balanced light spectrums (27% green light, 30% blue light, 22% yellow light, and 21% red light) promotes the prepubertal growth; and the LED light of more blue and green light (35% green light, 35% blue light, 18% yellow light, and 12% red light) provides proper sexual maturation age and better egg-laying persistence. These results inspire better design of LED lights for the indigenous chicken industry. Light presents an important exogenous factor for poultry. This study examined effects of LED lights with different defined spectrums on growth and reproduction of indigenous Beijing-You chickens. A total of 576 one-day old female chicks were divided into 16 rooms, and each were exposed to four different lights: LED A (21% green light, 30% blue light, 24% yellow light, and 25% red light), B (35%, 35%, 18%, and 12%), C (27%, 30%, 22%, and 21%), or compact fluorescent lamps (CFL, 15%, 28%, 41%, and 16%). Results showed that feed intake and feed conversion ratio were comparable among treatments throughout the 17 week rearing period (p > 0.05). LED C showed similar body weight gain with CFL, but higher than LED A and B. The CFL birds start to lay on 132.25 d, while LED B did not lay until 148.25 d. The age at 50% egg production did not vary among groups (p = 0.12). Total egg number until 43 week of LED B was higher than others (p < 0.05). Therefore, LED lights with defined spectral proportion have different effects on chickens' growth and reproduction. The LED C promotes the prepubertal growth, and the LED B provides proper sexual maturation age and better egg-laying persistence. [ABSTRACT FROM AUTHOR]

Identifying the genes responsible for quantitative traits remains a major challenge. We previously found a major QTL on chromosome 4 affecting several innate fear behavioral traits obtained by an open-field test in an F2 population between White Leghorn and Nagoya breeds of chickens (Gallus gallus). Here, an integrated approach of transcriptome, haplotype frequency, and association analyses was used to identify candidate genes for the QTL in phenotypically extreme individuals selected from the same segregating F2 population as that used in the initial QTL analysis. QTL mapping for the first principal component, which summarizes the variances of all affected behavioral traits in the F2 population, revealed the behavioral QTL located at 14-35 Mb on chromosome 4 with 333 genes. After RNA-seq analysis using two pooled RNAs from extreme F2 individuals, real-time qPCR analysis in the two parental breeds and their F1 individuals greatly reduced the number of candidate genes in the QTL interval from 333 to 16 genes. Haplotype frequency analysis in the two extreme F2 groups further reduced the number of candidate genes from 16 to 11. After comparing gene expression in the two extreme groups, a conditional correlation analysis of diplotypes between gene expression and phenotype of extreme individuals revealed that NPY5R and LOC101749214 genes were strong candidate genes for innate fear behavior. This study illustrates how the integrated approach can identify candidate genes more rapidly than fine mapping of the initial QTL interval and provides new information for studying the genetic basis of innate fear behavior in chickens. [ABSTRACT FROM AUTHOR]

Simple Summary: From birth to adulthood, the large number of microbes that in-habit the gut play an important role in many aspects of the host's normal physiological activities. Research on the development of gut microbiota and its metabolites in local chickens remains unclear. In this study, the cecal microbiota and metabolites in different developmental stages of Hainan Wenchang chickens (a native breed of Bantam) were investigated using 16S rRNA sequencing and untargeted metabolomics. With the increase of age, the gut microbiota tended to be more stable. Gut microbiota and their metabolites may have structural and functional changes in response to nutrient metabolism and immune requirements in different physiological states. The bacteria that form networks with their significant related metabolites were different in different developmental stages. These findings could potentially provide new insights into the physiological and molecular mechanisms of developmental changes of local chicken breed, as well as resources for microbial and metabolic biomarkers identification to improve the growth efficiency. Gut microbiota and their metabolites play important roles in animal growth by influencing the host's intake, storage, absorption, and utilization of nutrients. In addition to environmental factors, mainly diet, chicken breed and growth stage also affect changes in the gut microbiota. However, little research has been conducted on the development of gut microbiota and its metabolites in local chickens. In this study, the cecal microbiota and metabolites in different developmental stages of Hainan Wenchang chickens (a native breed of Bantam) were investigated using 16S rRNA sequencing and untargeted metabolomics. With aging, the structure of gut microbiota tended to be more stable. The relative proportions of dominant bacteria phyla Firmicutes, Bacteroidetes, and Proteobacteria showed stage changes with the development. With aging, gut microbiota and their metabolites may have structural and functional changes in response to nutrient metabolism and immune requirements in different physiological states. Several microbial and metabolic biomarkers with statistical differences were detected in different development stages. The bacteria that form networks with their significant related metabolites were different in various growth stages, including uncultured_bacterium_f_Ruminococcaceae, Ruminococcaceae_UCG-014, Faecalibacterium, uncultured_bacterium_o_Bacteroidales, and uncultured_bacterium_f_Lachnospiraceae. Partially differential bacteria were significantly correlated with short-chain fatty acids such as butyric acid. These findings may provide new insights into the physiological and molecular mechanisms of developmental changes of local chicken breeds, as well as resources for microbial and metabolic biomarker identification to improve growth efficiency. [ABSTRACT FROM AUTHOR]

Major advances in pathogen identification, treatment, vaccine development, and avian immunology have enabled the enormous expansion in global poultry production over the last 50 years. Looking forward, climate change, reduced feed, reduced water access, new avian pathogens and restrictions on the use of antimicrobials threaten to hamper further gains in poultry productivity and health. The development of novel in vitro cell culture systems, coupled with new genetic tools to investigate gene function, will aid in developing novel interventions for existing and newly emerging poultry pathogens. Our growing capacity to cryopreserve and generate genome-edited chicken lines will also be useful for developing improved chicken breeds for poultry farmers and conserving chicken genetic resources. [ABSTRACT FROM AUTHOR]

Darag chicken is one of the Philippine native chicken strains originating from the Western Visayas region. It is common for poultry farmers to raise native chicken breeds due to their adaptability and resistance to diseases, thus most are produced through free-management systems. The majority of Darag chicken farmers use layer diets that are available on the market and are designed to meet the nutritional needs of commercial layer chickens. This study characterized the nutrient transporters in the small intestines of the Philippine Darag chicken and commercial layer chicken (CLC). Specifically, the experiment compared the mRNA expression levels of EAAT3 and B0AT between Darag chicken and commercial layer chicken fed with commercial ration. Tissue samples were collected from the three main intestinal segments of the Darag and CLC. Total RNA extraction from the intestinal tissue samples was done followed by cDNA synthesis and real-time quantitative polymerase chain reaction to determine the relative expression levels of EAAT3 and B0AT in the two bird groups. Philippine Darag chicken displayed an increase in relative mRNA expression levels of both genes, EAAT3 and B0AT, in the three (3) intestinal segments. The observed expression levels of both genes in Darag were statistically comparable with CLC. [ABSTRACT FROM AUTHOR]

Simple Summary: this study aimed to investigate the growth of chickens by comparing their microbiota, histological characteristics, and gene expression in a local chicken breed. Four hundred and eighty Golden Montazah chickens, an Egyptian breed, were reared until they were 49 days old, and the forty-eight birds with the heaviest body weight (HW) and the lightest body weight (LW) were chosen. The positive histological changes increased significantly in the HW chickens compared to the LW chickens. The growth of the chickens may be affected by intestinal microbiota, and it has a role in feed conversion efficiency. Our findings showed that there is a difference in the microbial community colonized in the gut between the high-weight and low-weight birds which may improve the intestinal functions. this study aimed to investigate the growth mechanism in a local breed of chickens by comparing the highest weight (HW) and the lowest weight in their microbiota, histological characteristics, and gene expression. Golden Montazah chickens, an Egyptian breed, were reared until they were 49 days old. All of the birds were fed ad libitum by a starter diet from day 1 until day 21, followed by a grower diet from day 21 to the end of the study. At 49 days old, the forty-eight birds with the heaviest body weight (HW) and the lightest body weight (LW) were chosen. Blood biochemical and histological morphometric parameters, electron microscopy, and intestinal nutrient transporter gene expression were studied in the sampled jejunum. The microbial composition and functions of the content and mucosa in HW and LW chickens were studied using 16S rRNA gene sequencing. The histological morphometric parameters were all more significantly (p < 0.05) increased in the HW chickens than in the LW chickens. Total protein, albumin, and triglycerides in serum were significantly higher (p < 0.05) in the HW chickens than in the LW chickens. The microbiome profile in the gut showed that Microbacterium and Sphingomonas were positively correlated with the body weights. In the local breed, there were significant differences in the intestinal microstructure which could enhance the growth mechanism and body weight. Our findings showed that some microbial components were significantly associated with body weight and their interactions with the host could be inferred to explain why these interactions might alter the host's metabolic responses. Further investigation into combining bioinformatics with lab experiments in chickens will help us to understand how gut bacteria can change the host's metabolism by special metabolic features in the gastrointestinal system. [ABSTRACT FROM AUTHOR]