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

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

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

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

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]

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

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

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

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

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

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

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

The study was carried out to characterize native chickens of North Gujarat recently registered as "Aravali" breed of chicken for phenotypic and performance traits from field and farm levels. Observations were recorded as per the format of National Bureau of Animal Genetic Resources (NBAGR). Data collected at farm level and from field level, by survey work were analyzed. The proportion of black breasted silver-red plumage colour was highest for male and the buff-brown plumage colour in females at both field and farm level. Plumage pattern in males and females was birchen and shafty, respectively. Pre-dominantly red ear lobe was observed in males and white ear lobe in females. Body weight of adult male and female field birds was 1990.56 g and 1618.05 g, respectively while at the end of 40th week, male and female body weight was found to be 2001.80 g and 1593.57 g, respectively on farm. Age at first egg was found to be 6.25 and 5.67 months at field and farm level, respectively. Annual egg production recorded was 72.36 at field level and 95.04 at farm level upto 56 weeks of age. Clutch size and clutch intervals were 18.11 and 92.03 days, respectively, at field level. Egg weight and shell thickness were higher and intensity of the yolk colour was lower at farm level as compared to field level. Dressing percentage was higher in males as compared to the females. Fertility and hatchability were higher at field level as compared to farm level for Aravali breed of chicken. [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]

Simple Summary: This study assesses the risk of ammonia exposure in broiler chicken production and correlates these risks with health issues, utilizing machine learning techniques. Two broiler breeds, fast-growing (Ross®, 42 days) and slow growing (Hubbard®, 63 days), were studied at different densities. Slow-growing birds had a fixed density of 32 kg/m2, while fast-growing ones were housed at low (16 kg/m2) and high (32 kg/m2) densities. The high concentration of atmospheric ammonia has been associated with a greater occurrence of bird health problems, such as pododermatitis, visual impairment and mucosal lesions compared to birds stocked in controlled environments with low concentrations of atmospheric ammonia. A total of 1250 birds were used, and classification algorithms (decision tree, SMO, Naive Bayes, and Multilayer Perceptron) were applied to predict ammonia risk levels. The analysis involved data selection, pre-processing, transformation, mining, and interpretation of results. The Multilayer Perceptron proved the most effective in predicting exposure risk. The Spearman's correlation coefficient indicated a strong correlation between high ammonia concentrations and higher incidences of injuries in the birds that were evaluated. This research highlights the importance of managing ammonia levels in broiler production to mitigate health risks for both fast- and slow-growing breeds. The study aimed to forecast ammonia exposure risk in broiler chicken production, correlating it with health injuries using machine learning. Two chicken breeds, fast-growing (Ross®) and slow-growing (Hubbard®), were compared at different densities. Slow-growing birds had a constant density of 32 kg m−2, while fast-growing birds had low (16 kg m−2) and high (32 kg m−2) densities. Initial feeding was uniform, but nutritional demands led to varied diets later. Environmental data underwent selection, pre-processing, transformation, mining, analysis, and interpretation. Classification algorithms (decision tree, SMO, Naive Bayes, and Multilayer Perceptron) were employed for predicting ammonia risk (10–14 pmm, Moderate risk). Cross-validation was used for model parameterization. The Spearman correlation coefficient assessed the link between predicted ammonia risk and health injuries, such as pododermatitis, vision/affected, and mucosal injuries. These injuries encompassed trachea, bronchi, lungs, eyes, paws, and other issues. The Multilayer Perceptron model emerged as the best predictor, exceeding 98% accuracy in forecasting injuries caused by ammonia. The correlation coefficient demonstrated a strong association between elevated ammonia risks and chicken injuries. Birds exposed to higher ammonia concentrations exhibited a more robust correlation. In conclusion, the study effectively used machine learning to predict ammonia exposure risk and correlated it with health injuries in broiler chickens. The Multilayer Perceptron model demonstrated superior accuracy in forecasting injuries related to ammonia (10–14 pmm, Moderate risk). The findings underscored the significant association between increased ammonia exposure risks and the incidence of health injuries in broiler chicken production, shedding light on the importance of managing ammonia levels for bird welfare. [ABSTRACT FROM AUTHOR]

Chickens were domesticated >4,000 years ago, probably first for fighting them and only later as a source of food. Fighting chickens, commonly known as gamecocks, continue to be bred throughout the world, but the genetic relationships among geographically diverse gamecocks and with nongame chickens are not known. Here, we sequenced the genomes of 44 geographically diverse gamecocks and 62 nongame chickens representing a variety of breeds. We combined these sequences with published genomes to generate the most diverse chicken genomes dataset yet assembled, with 307 samples. We found that gamecocks do not form a homogeneous group, yet they share genetic similarities that distinguish them from nongame chickens. Such similarities are likely the result of a common origin before their local diversification into, or mixing with nongame chickens. Particularly noteworthy is a variant in an intron of the isoprenoid synthase domain containing gene (ISPD), an extreme outlier present at a frequency of 89% in gamecocks but only 4% in nongame chickens. The ISPD locus has the strongest signal of selection in gamecocks, suggesting it is important for fighting performance. Because ISPD variants that are highly prevalent in gamecocks are still segregating in nongame chickens, selective breeding may help reduce its frequency in farm conditions in which aggression is not a desired trait. Altogether, our work provides genomic resources for agricultural genetics, uncovers a common origin for gamecocks from around the world and what distinguishes them genetically from chickens bred for purposes other than fighting, and points to ISPD as the most important locus related to fighting performance. [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]

In commercial laying hens, keel bone damage (KBD) is a severe health and welfare problem leading to pain, reduced mobility and decreased laying performance. Flocks of all production systems and hybrid lines can be affected. KBD is a multifactorial welfare issue and, among other factors, associated with a high laying performance which negatively affects the calcium deposit in the medullary bones. Therefore, mature hens of local breeds with much lower egg production than commercial hybrids may be expected to show less or even no keel bone damage. This study evaluates (i) the prevalence of KBD in local breeds, (ii) the difference in type and level of damages, and (iii) if roosters and pullets are also affected. In total, we palpated 343 mature hens, 40 pullets, and 18 roosters of 13 different local breeds and one commercial hybrid. The animals were kept on eight different farms in free-range or floor-housing systems. Our results showed that on average 44.2% of mature hens per local breed were affected by KBD (range: 11.1%-84.7%). We found deviation of less than 1 cm in 26.9%, deviations of more than 1 cm in 6.4% and palpable fractures in 23.8% of the mature hens of local breeds. The tip was damaged in 23.6% of the mature hens. Also, pullets and roosters were affected by KBD. Finally, we found that KBD also occurs in local breeds. Therefore, we conclude that even the low laying performance of local breeds does not prevent them from the occurrence of KBD.KBD in local breeds may rather be associated with genetics (breed) as well as management and housing. Thus, breeders of local breeds should include bone health as a selection trait. Owners of local breeds should also pay attention to the condition of the keel and ought to be trained about preventive measures. [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]

The study was to identify the reproductive performance of Vietnamese local chickens, named Noi chickens from 36 - 46 weeks of age. The study aimed to determine the effect of breeds and rearing system on laying performance and egg quality of local chickens. The study was a factorial design with 2x2 factors and involved with 120 layers. The first factor was 2 rearing systems (experimental free-range farming system in Tra Vinh province and local free-range farming system in Ben Tre province). The second factor was 2 breeds (egg and broiler purpose). The results showed that egg production rate, laying egg per week were significantly different between breeds and rearing systems (P<0.05) while feed intake was not different. The highest egg production rate recorded at week 44 with 38.42%. For egg quality, yolk diameter, yolk color and yolk index were different breeds and rearing system. It can be recommended that rearing system in Ben Tre province and egg purpose breed was better for egg production and quality. [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]

Simple Summary: To study the molecular mechanism of chicken feather follicle density, weighted gene co-expression network analysis (WGCNA) and transcriptome analysis were established based on skin transcriptome data from Wannan male chickens. The results showed that FOXM1, GTSE1, MELK, CDK1, ECT2, and NEK2 may be involved in regulating the development of feather follicle density. This study promotes our understanding of the molecular mechanism of feather follicle density. Feather follicle density plays an important role in appealing to consumers' first impressions when making purchasing decisions. However, the molecular network that contributes to this trait remains largely unknown. The aim of this study was to perform transcriptome and weighted gene co-expression network analyses to determine the candidate genes relating to feather follicle density in Wannan male chickens. In total, five hundred one-day-old Wannan male chickens were kept in a conventional cage system. Feather follicle density was recorded for each bird at 12 weeks of age. At 12 weeks, fifteen skin tissue samples were selected for weighted gene co-expression network analysis, of which six skin tissue samples (three birds in the H group and three birds in the L group) were selected for transcriptome analysis. The results showed that, in total, 95 DEGs were identified, and 56 genes were upregulated and 39 genes were downregulated in the high-feather-follicle-density group when compared with the low-feather-follicle-density group. Thirteen co-expression gene modules were identified. The red module was highly significantly negatively correlated with feather follicle density (p < 0.01), with a significant negative correlation coefficient of −0.72. In total, 103 hub genes from the red module were screened. Upon comparing the 103 hub genes with differentially expressed genes (DEGs), it was observed that 13 genes were common to both sets, including MELK, GTSE1, CDK1, HMMR, and CENPE. From the red module, FOXM1, GTSE1, MELK, CDK1, ECT2, and NEK2 were selected as the most important genes. These genes were enriched in the DNA binding pathway, the heterocyclic compound binding pathway, the cell cycle pathway, and the oocyte meiosis pathway. This study suggests that FOXM1, GTSE1, MELK, CDK1, ECT2, and NEK2 may be involved in regulating the development of feather follicle density in Wannan male chickens. The results of this study reveal the genetic structure and molecular regulatory network of feather follicle density in Wannan male chickens, and provide a basis for further elucidating the genetic regulatory mechanism and identifying molecular markers with breeding value. [ABSTRACT FROM AUTHOR]

Simple Summary: In recent decades, the correlation between gut microbiota and the performance of animals has been widely examined. However, there is still a lack of research about the influence of different host breeds. We used five local Chinese chicken breeds as experiment materials to establish the relationship between the characteristics of hosts and the composition of microorganisms. In this study, metagenomic sequencing was used to explore the differences in the intestinal microbial composition of different breeds. Then, the functions of differentially expressed microorganisms were analyzed. Combined with previous research, we discussed the links between microorganisms and different breeds. Our study explains the relationship between the gut microbiome and the host breeds of local chickens, and reveals the specific flora in the gut of each breed of local chicken, which lays a foundation for the exploration of high-quality traits and the improvement of feeding conditions in the future. Intestinal microorganisms are closely related to the health, development, and production performance of animals and can also provide basic information for us to fully understand and explore the germplasm characteristics and traits of local chicken breeds. In this experiment, we used five local Chinese chicken breeds as research materials; metagenomic sequencing technology was used to explore the differences in the composition of intestinal microorganisms in different breeds, and it was found that each local chicken breed had unique unigenes, of which Silkies had the most, with a total of 12,948. GO and KEGG analyses found that the biological processes most enriched by differential functional genes include genetic coding, macromolecular transport, protein synthesis, and molecular functions such as glycoprotein binding, protein hydrolysis, etc. Each breed is enriched with specific pathways, such as Anyi tile-like gray chickens, which are enriched with pathways related to disease resistance, while Gamecocks' enrichment is related to amino acid metabolism. Random Forest and LEfSe analyses revealed specific species of intestinal microorganisms in the cecum of different breeds, such as Exiguobacterium, which is associated with melanin deposition in Silkies. Therefore, we infer that gut microorganisms are closely related to the formation of chicken breed characteristics, and the results of this experiment can provide a theoretical basis for the discovery of high-quality traits and the improvement of feeding conditions in the future. [ABSTRACT FROM AUTHOR]

Background: Copy number variants (CNV) hold significant functional and evolutionary importance. Numerous ongoing CNV studies aim to elucidate the etiology of human diseases and gain insights into the population structure of livestock. High-density chips have enabled the detection of CNV with increased resolution, leading to the identification of even small CNV. This study aimed to identify CNV in local Italian chicken breeds and investigate their distribution across the genome. Results: Copy number variants were mainly distributed across the first six chromosomes and primarily associated with loss type CNV. The majority of CNV in the investigated breeds were of types 0 and 1, and the minimum length of CNV was significantly larger than that reported in previous studies. Interestingly, a high proportion of the length of chromosome 16 was covered by copy number variation regions (CNVR), with the major histocompatibility complex being the likely cause. Among the genes identified within CNVR, only those present in at least five animals across breeds (n = 95) were discussed to reduce the focus on redundant CNV. Some of these genes have been associated to functional traits in chickens. Notably, several CNVR on different chromosomes harbor genes related to muscle development, tissue-specific biological processes, heat stress resistance, and immune response. Quantitative trait loci (QTL) were also analyzed to investigate potential overlapping with the identified CNVR: 54 out of the 95 gene-containing regions overlapped with 428 QTL associated to body weight and size, carcass characteristics, egg production, egg components, fat deposition, and feed intake. Conclusions: The genomic phenomena reported in this study that can cause changes in the distribution of CNV within the genome over time and the comparison of these differences in CNVR of the local chicken breeds could help in preserving these genetic resources. [ABSTRACT FROM AUTHOR]

[Display omitted] • The genomes of modern purebred broilers carried fewer deleterious mutations compared to local chickens and wild ancestors. • 163 protein-coding genes were selected positively in purebred broilers during long term selection. • The MYH1 gene family harbored the top significant selective sweep windows and displays muscle-specific expression in purebred broilers. • SOX6 gene provided key regulatory function to breast muscle traits and adaptation to artificial selection. • A haplotype within SOX6 appeared differential pattern in gene expression, breast muscle traits, and haplotype frequency. Investigating the genetic markers and genomic signatures related to chicken meat production by combing multi-omics methods could provide new insights into modern chicken breeding technology systems. Chicken is one of the most efficient and environmentally friendly livestock, especially the fast-growing white-feathered chicken (broiler), which is well known for high meat yield, but the underlying genetic basis is poorly understood. We generated whole-genome resequencing of three purebred broilers (n = 748) and six local breeds/lines (n = 114), and sequencing data of twelve chicken breeds (n = 199) were obtained from the NCBI database. Additionally, transcriptome sequencing of six tissues from two chicken breeds (n = 129) at two developmental stages was performed. A genome-wide association study combined with cis -eQTL mapping and the Mendelian randomization was applied. We identified > 17 million high-quality SNPs, of which 21.74% were newly identified, based on 21 chicken breeds/lines. A total of 163 protein-coding genes underwent positive selection in purebred broilers, and 83 genes were differentially expressed between purebred broilers and local chickens. Notably, muscle development was proven to be the major difference between purebred broilers and local chickens, or ancestors, based on genomic and transcriptomic evidence from multiple tissues and stages. The MYH1 gene family showed the top selection signatures and muscle-specific expression in purebred broilers. Furthermore, we found that the causal gene SOX6 influenced breast muscle yield and also related to myopathy occurrences. A refined haplotype was provided, which had a significant effect on SOX6 expression and phenotypic changes. Our study provides a comprehensive atlas comprising the typical genomic variants and transcriptional characteristics for muscle development and suggests a new regulatory target (SOX6 – MYH1s axis) for breast muscle yield and myopathy, which could aid in the development of genome-scale selective breeding aimed at high meat yield in broiler chickens. [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]

The experiment was conducted to investigate the effect of dietary hydroxy-methionine (MHA) chelate supplementation on the production performance, antioxidation performance, immune and reproductive hormone indexes of Xuefeng black bone breeding chickens. A total of 324 healthy 32-week-old Xuefeng black bone chickens with similar body weight were randomly divided into three groups, with six replicates per group and 18 chickens per replicate. The prefeeding period lasted for two weeks and the trial period lasted for eight weeks. The chickens in the control group were fed a basal diet. The experimental groups added 30 mg/kg MHA-Zn (MZ group, calculated by zinc), 25 mg/kg MHA-Mn (MM group, calculated by manganese) and 30 mg/kg MHA-Zn + 25 mg/kg MHA-Mn (MZM group) in the basal diet, respectively. The results showed that compared with the control group, the laying rate and healthy chick rate of the experimental groups were significantly increased (P<0.05). The hatching rate of the MZM group was significantly higher than that of the control group and MM group (P<0.05). The death rate of embryos in the MZ group and MZM group was significantly lower than that in the control group and MM group (P<0.05). The serum content of progesterone, folliclestimulating hormone, estradiol and parathyroid hormone in the MZM group was significantly higher than those in the other groups ( P<0.05). The activity of total superoxide dismutase and catalase in the serum of MZM group was significantly higher than those of the control group and MZ group (P<0.05). The serum activity of manganese superoxide dismutase and glutathione peroxidase in the MZM group was significantly higher than those in the control group and MM group (P<0.05). The serum malondialdehyde content in the MM group and MZM group was significantly lower than that in the control group (P<0.05). Compared with the control group, the content of immunoglobulin A, immunoglobulin M and interleukin-2 in the serum of the MZM group was significantly increased ( P<0.05). The study indicates that adding of MHA chelate in the diet can improve the production performance of Xuefeng black bone chickens by increasing antioxidation performance, immune and reproductive hormone levels. [ABSTRACT FROM AUTHOR]

Banat Naked Neck is the most important indigenous breed of chickens in Serbia. Marginalized until recently, it is becoming increasingly popular due to its adaptability and good productivity in alternative production systems. However, its history and the current breeding model pose challenges for breed preservation and future improvement. This study aimed to assess the genetic diversity and structure of four subpopulations of Banat Naked Neck from different districts in Serbia (West Backa, North Banat, South Banat and Kolubara) using D-loop mitochondrial DNA sequences and a set of 30 microsatellite markers. Seven haplotypes in the phylogenetic analysis of D-loop mitochondrial DNA suggested maternal origin related to the Indian subcontinent, while haplotype and nucleotide diversity averaged 0.731 ± 0.053 and 0.0067 ± 0.0018, respectively. Microsatellite genotyping showed an average detected number of alleles per locus of 5.129 ± 0.237, while the observed and expected heterozygosity averaged 0.560 ± 0.018 and 0.631 ± 0.014, respectively. Genetic differentiation estimated through FST was 0.051 (p <.001). Two clusters in STRUCTURE analysis showed possible separation of two older subpopulations (South Banat and Kolubara) from the two more recent ones (West Backa and North Banat). This first comprehensive study of genetic diversity serves as the basis for future preservation, use and improvement of the Banat Naked Neck breed. [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 poultry industry recognizes that handling day-old chicks in commercial hatcheries can lead to long-lasting changes in their behavior. However, these hatchery-related stresses are more intense and complex than those measured by traditional behavioral tests. This study developed a new behavioral handling test for day-old chickens by incorporating concepts from behavioral tests used with both young and adult birds. In the new test, 96 two-day-old chicks from seven breeds of native Japanese and Western chickens were used to evaluate 10 behavioral traits, including vocalization frequency and responses to human interaction. The results classified chicken temperaments into three categories: bustle, aggression, and timidity. These categories were used to classify the seven breeds. This new handling test provides a valuable tool for understanding the behavior of various chicken breeds and offers insights into their complex behaviors. It is well known in the poultry industry that fear and stress experienced during the handling of day-old chicks in commercial hatcheries can have long-lasting effects on their behavior later in life. These hatchery-related stresses are more intense and complex than those encountered in traditional behavioral tests. Consequently, a single behavioral test may not be sufficient to measure hatchery stresses and chicken temperament. In this study, we developed a new behavioral handling test for day-old chickens, which incorporated concepts from established behavioral tests used with both young and adult birds. The new test assessed 10 behavioral traits, including vocalization frequency and responses to human interaction. It was conducted on 96 two-day-old chicks from seven breeds of native Japanese and Western chickens. The results of the principal component analysis classified chicken temperaments into three distinct categories: bustle, aggression, and timidity. Using these categories, the seven breeds were classified into five groups, each with distinct temperaments. This study highlights the reliability and value of the new handling test in characterizing the temperaments of various chicken breeds and provides insights into the complex behaviors of chickens. [ABSTRACT FROM AUTHOR]

Simple Summary: Most Chinese local breeds have slow growth speed and high fat deposition, while European commercial chicken strains belong to fast-growing chicken breeds with low fat deposition. In general, the word "You" in China represents excessive fat deposition, and You-chicken is considered to be a typical fatten broiler. Among more than 100 local chickens in China, Baicheng-You and Beijing-You chickens are only two kinds of You-chicken breeds. However, their special genomic characteristics have not been well studied. This study analyzed the genome changes among these chicken breeds and obtained many candidate genes related to important traits of chickens, e.g., fat deposition, immune response, and melanin production. Our data provide valuable insights for understanding the formation of germplasm characteristics of these broiler breeds, which can be used to better protect and utilize the Chinese-You chickens. As the only two You-chicken breeds in China, Baicheng-You (BCY) and Beijing-You (BJY) chickens are famous for their good meat quality. However, so far, the molecular basis of germplasm of the two You-chicken breeds is not yet clear. The genetic relationship among BCY, BJY, and European-origin broilers (BRs) was analyzed using whole genome resequencing data to contribute to this issue. A total of 18,852,372 single nucleotide polymorphisms (SNPs) were obtained in this study. After quality control, 8,207,242 SNPs were applied to subsequent analysis. The data indicated that BJY chickens possessed distant distance with BRs (genetic differentiation coefficient (FST) = 0.1681) and BCY (FST = 0.1231), respectively, while BCY and BRs had a closer relationship (FST = 0.0946). In addition, by using FST, cross-population extended haplotype homozygosity (XP-EHH), and cross-population composite likelihood ratio (XP-CLR) methods, we found 374 selected genes between BJY and BRs chickens and 279 selected genes between BCY and BJY chickens, respectively, which contained a number of important candidates or genetic variations associated with feather growth and fat deposition of BJY chickens and potential disease resistance of BCY chickens. Our study demonstrates a genome-wide view of genetic diversity and differentiation among BCY, BJY, and BRs. These results may provide useful information on a molecular basis related to the special characteristics of these broiler breeds, thus enabling us to better understand the formation mechanism of Chinese-You chickens. [ABSTRACT FROM AUTHOR]

Simple Summary: Salmonellosis is the second most reported gastrointestinal disorder in the European Union, resulting from the consumption of Salmonella-contaminated foods. Chickens are considered reservoirs of this pathogen among food-producing animals, for which hygienic and sanitary measures mitigate the risk to humans through the food chain. However, data about the presence of this pathogen in autochthonous Portuguese chickens or their by-products is scarce. In this context, the aim of this study was to conduct a preliminary investigation on the occurrence of Salmonella spp. in autochthonous Portuguese laying hens raised in a semi-extensive system for small-scale production. The screening revealed an absence of Salmonella spp. in all cloaca, eggshell, and litter material samples collected (n = 279) from the 31 selected flocks. Considering these results and the fact that Salmonella is still the leading cause of food-borne outbreaks, the risk posed by Portuguese autochthonous chicken breeds produced through alternative and extensive farming methods can be considered low. However, this risk should not be neglected and needs to be further investigated, using a larger sample size, to validate this trend. The sustainability of agroecological systems, biodiversity protection, animal welfare, and consumer demand for higher quality products from alternative and extensive farming methods have reinforced interest in local breeds that are well adapted to low-input environments. However, food safety needs to be safeguarded to reinforce consumer confidence. The aim of this study was to conduct a preliminary investigation on the occurrence of Salmonella spp. in eggshells, hen's cloaca, and litter materials from autochthonous Portuguese laying hens raised in a semi-extensive system for small-scale production. A total of 279 samples from 31 flocks belonging to 12 farms were obtained, with 63 samples from the "Preta Lusitânica" breed, and 72 samples each from the remaining autochthonous breeds, namely, "Branca", "Amarela", and "Pedrês Portuguesa". None (0%) of the samples analyzed were positive for Salmonella spp. To the best of our knowledge, these are the first results of Salmonella evaluation from hen's cloaca, eggshells, and litter materials in autochthonous Portuguese chickens, suggesting that a semi-extensive production system can contribute to better food security and a lower risk to public health and the environment. [ABSTRACT FROM AUTHOR]

Simple Summary: n-3 PUFA, selenium and lutein cannot be synthesized in the human body, but these substances are very important for human health. Consuming functional eggs enriched with nutrients can increase the body's intake of these substances. To efficiently produce functional eggs, selecting breeds that can deposit higher levels of these nutrients is necessary. Therefore, we investigated the types, dosages, and cycles of additives used in the production of functional eggs. In Trial 1, we investigated the differences in n-3 PUFA deposition among five breeds of eggs. The results showed significant variations in the ability of different breeds to deposit n-3 PUFA in eggs, with Dwarf Layer demonstrating a significant advantage. In Trial 2, we investigated the difference of n-3 PUFA, selenium and lutein deposition in eggs from two reeds in terms of their ability to deposit selenium and lutein in eggs. Additionally, the n-3 PUFA content in eggs from the two breeds was similar to the findings in Trial 1. Therefore, this experiment provides valuable insights for selecting different breeds in the production of functional eggs, ultimately improving the quality and economic benefits of the production process. The purpose of this study was to compare the differences in the content of functional nutrients in eggs, performance parameters, and egg quality parameters of different chicken breeds. In Trial 1, 150 41-week-old hens of each breed, including the Dwarf Layer, White Leghorn, Silky fowl, Beijing-you chicken, and Shouguang chicken, were randomly assigned to the control (CON) and 2.5% flaxseed oil (FSO) groups to compare the difference in n-3 polyunsaturated fatty acid (PUFA) content in eggs. The contents of α-linolenic acid (ALA), eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and total n-3 PUFA in eggs were increased (p < 0.05) in the FSO groups. The ALA (4.28%), DHA (2.03%), and total n-3 PUFA (6.46%) contents in eggs of Dwarf Layer were the highest among the five breeds (p < 0.05). To further verify if other functional nutrients also have such differences, 600 24-week-old White Leghorn and Dwarf Layer were allocated to four groups: CON, FSO, 0.02% selenium-enriched yeast (SEY), and 0.20% marigold flower extract (MFE), in Trial 2. The content of functional nutrients in eggs was significantly increased (p < 0.05) after feeding these additions. After feeding FSO, the eggs of the Dwarf Layer had a higher n-3 PUFA content than the White Leghorn (p < 0.05). However, no significant differences were found in selenium and lutein content in different breeds. Performance and egg quality were not negatively impacted by FSO, SEY, or MFE. [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]

In 1919, the famous Dutch poultry judge Cornelis van Gink (1890–1968) was aware of the existence of crested turkeys. Was this bird a natural rarity, variation or mutation? A search through historical records and published works yielded very few references to crested turkeys. From the financial accounts of the Great Condé in 1679 to pictures in books and journals of the eighteenth and nineteenth century in England and America, from a mounted specimen in Parma to a first photograph in 1938 in Newsweek, the beauty and rareness of this bird is evident. Attempts to breed crested turkeys were unsuccessful. In the nineteenth century William Bernhardt Tegetmeier (1816–1912), editor of The Field, had a major interest in these turkeys and together with Charles Darwin (1809–1882) studied and described skull deformations associated with well-known and common crested breeds of chickens. Deformation of the skull was also observed in the mounted specimen of the crested turkey preserved in Parma, Italy. Genetic analyses of crested poultry indicate that a mutation (autosomal incompletely dominant) in the crest gene is responsible for this phenotype. The mutation for crest formation with additional skull deformation might be responsible for some in ovo lethality or poor hatching which could explain the failure or difficulty in breeding this phenotype. In conclusion, all data indicate that the crested turkey is a mutation of the domestic turkey Meleagris gallopavo gallopavo and does not justify a new species or subspecies name. [ABSTRACT FROM AUTHOR]

Background: The eight phenotypically distinguishable indigenous chicken breeds in Guizhou province of China are great resources for high-quality development of the poultry industry in China. However, their full value and potential have yet to be understood in depth. To illustrate the genetic diversity, the relationship and population structure, and the genetic variation patterns shaped by selection in Guizhou indigenous chickens, we performed a genome-wide analysis of 240 chickens from 8 phenotypically and geographically representative Guizhou chicken breeds and 60 chickens from 2 commercial chicken breeds (one broiler and one layer), together with 10 red jungle fowls (RJF) genomes available from previous studies. Results: The results obtained in this present study showed that Guizhou chicken breed populations harbored higher genetic diversity as compared to commercial chicken breeds, however unequal polymorphisms were present within Guizhou indigenous chicken breeds. The results from the population structure analysis markedly reflected the breeding history and the geographical distribution of Guizhou indigenous chickens, whereas, some breeds with complex genetic structure were ungrouped into one cluster. In addition, we confirmed mutual introgression within Guizhou indigenous chicken breeds and from commercial chicken breeds. Furthermore, selective sweep analysis revealed candidate genes which were associated with specific and common phenotypic characteristics evolved rapidly after domestication of Guizhou local chicken breeds and economic traits such as egg production performance, growth performance, and body size. Conclusion: Taken together, the results obtained from the comprehensive analysis of the genetic diversity, genetic relationships and population structures in this study showed that Guizhou indigenous chicken breeds harbor great potential for commercial utilization, however effective conservation measures are currently needed. Additionally, the present study drew a genome-wide selection signature draft for eight Guizhou indigenous chicken breeds and two commercial breeds, as well as established a resource that can be exploited in chicken breeding programs to manipulate the genes associated with desired phenotypes. Therefore, this study will provide an essential genetic basis for further research, conservation, and breeding of Guizhou indigenous chickens. [ABSTRACT FROM AUTHOR]