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

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]

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]

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

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

Simple Summary: This is a study associated with the prevalence and persistence of ceftiofur, the third-generation cephalosporin antibiotic-resistant Escherichia coli in a chicken layer breeding farm. Notably, epidemiological studies in poultry have been primarily focused on single breeding periods and may have underestimated the maintenance of the ceftiofur-resistant Escherichia coli in different breeding periods from layer hens. Our results showed that the detection rates of the ceftiofur-resistant Escherichia coli fluctuated across different breeding periods, and the ST101 ceftiofur-resistant Escherichia coli was the most prevalent and persistent sequence type across the breeding periods. This study contextualized ceftiofur resistance in different breeding periods, monitoring which can have important implications for food animals. We determined the longitudinal persistence of ceftiofur-resistant Escherichia coli from a chicken breeding farm in China. A total of 150 samples were collected from 5 breeding periods in a flock of layer hens, and the prevalence of ceftiofur-resistant E. coli fluctuated across the 5 chicken breeding stages: eggs, 3.33%; growing period, 100%; early laying period, 36.7%; peak laying period, 66.7% and late laying period, 80%. The most prevalent ceftiofur resistance genes were blaCTX-M-55, blaCMY and blaNDM, and ST101 was the most prevalent and persistent sequence type across the breeding periods. Our results indicated that this breeder flock was heavily contaminated by ST101 ceftiofur-resistant E. coli and that its presence should be intensively monitored on chicken farms. [ABSTRACT FROM AUTHOR]

Salmonella enterica serovar Enteritidis (S. Enteritidis) can colonize in the intestinal tract of chickens and transmit to humans. In order to decrypt the mechanism of avian resistance to S. Enteritidis, we utilized two China local chicken breeds to generate the reciprocal crosses (the Cross and the Reverse‐cross). The two lines of hybrids were orally inoculated with S. Enteritidis at 2‐day old and sampled at 3 days post‐inoculation. Along the analysis direction of multi‐omics, differential metabolites, functional pathways and correlated microbes, we found that 12 species of microbes thrived upon S. Enteritidis challenge and probably contributed to the intestinal stability in the Cross by enhancing the production of phenylpropanoids. Our findings can help to understand the symbiotic and resistant mechanisms derived from the intestinal microbiota. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance is a rapidly evolving and extremely complex issue, particularly due to the use of various types of antimicrobials within human, animal, and environmental sectors. Pleuromutilin antibiotics are used to prevent and control respiratory diseases in the rearing stage of hen chicks, but the current status of pleuromutilin resistance in the laying hen breeding process is unclear. ATP-binding cassette transporters encoded by lsa(A), lsa(E), lsa(C) , and vga(D) can be transferred by plasmids and transposons, thereby posing a potential dissemination risk. To investigate pleuromutilin resistance genes in the laying hen production chain in China, 95 samples from five environmental types were collected in four breeding stages to determine the abundances of the main resistance genes by qPCR, i.e. lsa(A), lsa(E), lsa(C) , and vga(D). The abundance (5.16 log10GC/g) and detection rate (100%) of lsa(E) was highest in all of the samples, thereby suggesting high contamination with the lsa(E) gene across the large-scale laying hen breeding environment and feces. The lsa(A) (6.02 log10GC/g) and lsa(E) (6.18 log10GC/g) genes were most abundant in flies, and the abundance of vga(D) (4.50 log10GC/g) was highest in dust (P  < .05). In addition to feces, flies and dust were important sources of contamination with pleuromutilin resistance along the laying hen production chain. In summary, we determined the abundances of four pleuromutilin resistance genes in the laying hen production chain and provided direct evidence of pleuromutilin resistance transmission and environmental contamination. In particular, the chicken breeding stage needs further attention. [ABSTRACT FROM AUTHOR]

Tengchong snow, which has white feathers and black meat, is one of the most important black-bone chicken breeds and a genetic treasure of black food in China. Although the black meat traits are dominant, there are some chickens with white meat traits born in the process of folk selection and breeding. The purpose of this study was to compare the differences in skeletal muscle development between Tengchong snow black meat chickens (BS) and white meat chickens (WS), as well as whether excessive melanin deposition has an effect on skeletal muscle development. The BS and WS groups were selected to determine their muscle development difference at stages of 1, 7, 14, 21, and 42 days, using histological stain methods to analyze the development and composing type of breast and leg muscle fibers, as well as the count of melanin in BS muscle fibers. Finally, we were validated key candidate genes associated with muscle development and melanin synthesis. The results showed that BS breast muscle development was inhibited at 7, 14, and 21 days, while the leg muscle was inhibited at 7, 14, 21, and 42 days, compared to WS. Melanin deposition was present in a temporal migration pattern and was greater in the leg muscles than in the breast muscles, and it focused around blood vessels, as well as the epithelium, perimysium, endomysium, and connective tissue. Additionally, melanin produced an inhibitory effect similar to MSTN during skeletal muscle fiber development, and the inhibition was strongest at the stage of melanin entry between muscle fibers, but the precise mechanisms need to be confirmed. This study revealed that melanin has an inhibitory effect on the early development of skeletal muscle, which will provide new insights into the role of melanin in the black-boned chicken and theoretical references for the future conservation and utilization of black-boned chicken. [ABSTRACT FROM AUTHOR]

Simple Summary: In China, although preslaughter stunning is commonly performed in large-scale production systems, this practice is less common in smaller-scale systems. To promote the concept of animal welfare, we selected common local chicken breeds and sampled the meat and blood of chickens with and without stunning. The experimental results verified that stunning before slaughter can improve meat quality, increase flavor and reduce the stress on chickens. It is more respectful of animal welfare and provides a theoretical basis for the promotion of animal welfare concepts in China. Electrical stunning is widely utilized prior to a neck cut to induce unconsciousness in order to improve animal welfare and slaughter efficiency in the broiler production industry. However, slaughter without stunning is still very commonly used in China, in part because there is a belief that stunning reduces meat quality. The purpose of this study was to determine whether the physical (hemorrhages, pH, drip loss, and shear force) and chemical (inosinic monophosphate concentration and reducing sugar content) properties of broiler meat differed between chickens in preslaughter stunning and nonstunned slaughter groups, and whether the groups differed in their levels of cortisol as an indicator of stress. Serum cortisol levels of the nonstunned group were nearly twice as high as those in the stunned group (p < 0.05). Several meat quality indicators were better in the stunned group than in the nonstunned group. We concluded that electrical stunning prior to slaughter significantly decreases the stress caused by slaughter, resulting in both improved animal welfare and meat quality traits. [ABSTRACT FROM AUTHOR]

Simple Summary: Wuliangshan Black-bone chickens, an indigenous chicken breed in southwestern China, have characteristics of black skin, black bones, and black meat, and are suitable for rearing at high altitudes. After six generations of selection, the bodyweights of chickens have been greatly improved: cocks and hens have reached 2.0 kg and 1.5 kg weight at 126 days of age, respectively. The breast and thigh muscles are the main meat-producing parts of chicken; assessing and documenting the morphological features of breast and thigh muscle development and meat composition in Wuliangshan Black-bone chickens is very important in terms of their genetic breeding and also consumer interest. This study was conducted to illustrate the morphological features of the breast and thigh muscles at four developmental stages (1, 42, 84, and 126 days of age) of Wuliangshan Black-bone chickens and to compare the chemical composition, fatty acid, and amino acid contents of their meat at 126 days of age (D126). In total, 80 chickens (male, n = 40 and female, n = 40) in the sixth generation from the breeding farm were used in the experiment under free-range rearing conditions. The cross-sectional areas (CSA) of muscle fibers and meat composition were compared between different sex and different muscle types. The results showed that gender did not affect the CSA of the breast muscle fibers but did affect the CSA of the thigh muscle fibers at D42, D84, and D126 (p < 0.05). Muscle types affected the CSA of muscle fibers: male chickens exhibited significantly higher values than female chickens at D42, D84, and D126 (p < 0.05). The results of moisture, crude protein, and crude fat at D126 showed that moisture contents were higher in the thigh muscles than in the breast muscles in male and female chickens (p < 0.05). Gender affected the crude protein contents and crude fat contents: the breast muscle crude protein content was significantly higher than that in the thigh muscle, both in males and females (p < 0.05), whereas the crude fat contents were significantly higher in females than in males (p < 0.05); moreover, the thigh muscle fat contents were significantly higher than those of the breast muscles both in males and females (p < 0.05). Gender and muscle types also affected the fatty acid contents: the PUFA contents of the breast and thigh muscles were significantly higher in male than in female chickens (p < 0.05). Muscle types significantly influenced the total EAA, NEAA, and flavor amino acid contents. The total EAA contents of the breast muscles were significantly higher than those of the thigh muscles in males and females (p < 0.05), whereas the total NEAA and total flavor amino acid contents of the thigh muscles were significantly higher than those of the breast muscles (p < 0.05). Our results may lead to a better understanding of the effects of gender on the breast and thigh muscle development and meat composition of Wuliangshan Black-bone chicken. [ABSTRACT FROM AUTHOR]

Conservation of natural resources is a vital and challenging task. Numerous animal genetic resources have been effectively conserved worldwide. However, the effectiveness of conservation programmes and the variation information of species have rarely been evaluated. Here, we performed whole-genome and whole-genome bisulfite sequencing of 90 Chinese indigenous chickens, which belonged to the Tibetan, Wenchang and Bian chicken breeds, and have been conserved under different conservation programmes. We observed that low genetic diversity and high DNA methylation variation occurs during ex situ in vivo conservation, while higher genetic diversity and differentiation occurs during in situ conservation. Further analyses revealed that most DNA methylation signatures are unique within ex situ in vivo conservation. Moreover, a high proportion of differentially methylated regions is found in genomic selection regions, suggesting a link between the effects of genomic variation and DNA methylation. Altogether our findings provide valuable information about genetic and DNA methylation variations during different conservation programmes, and hold practical relevance for species conservation. Comparisons of genomic and methylomic changes during the conservation of indigenous chicken breeds in China provide insight into conservation programmes for these breeds and their adaptations to unique environments. [ABSTRACT FROM AUTHOR]

Background: Beijing You-chicken with a unique flavor and rich nutrition is an excellent local chicken breed in China. Clarifying the change of volatile odor during the storage of chicken is helpful to assist in judging the freshness of chicken. Methods: The total viable count (TVC), total volatile basic nitrogen (TVB-N), lightness value L* and thiobarbituric acid reactive rubstances (TBARS) of chicken breast were measured at 4C and 25C, respectively. And the electronic nose and gas chromatography mass spectrometry (GC-MS) technology were used to determine the changes of volatile compounds during storage. Result: Significant changes of the volatile compounds were observed on first day at 25C and the 8th day at 4C of storage, which agreed with the results evaluated by detection of physicochemical indicators. The results of this study could serve as a theoretical basis for future research on detecting changes in chicken freshness by using the electronic nose and GC-MS technology. [ABSTRACT FROM AUTHOR]

Simple Summary: With public concern increasing in China for animal welfare in livestock production, the welfare and economic outcomes of different farming systems for laying hens needs to be examined. Animal welfare outcomes and initiatives are linked to the economic efficiency of the farm, which for the producer may require a balance or trade-off between these issues. This study investigated animal welfare, egg production and economic parameters in cage and free-range farms in China. Our results identified potential welfare issues that can be addressed on both farm types, and potential points of income that can be improved by enhancing hen welfare. Therefore, our results offer some directions for welfare and economic improvements on cage and free-range egg farms in China. Several countries and regions have regulations in place to provide standards for the welfare of production animals, which have implications for breeding, management and trade. In the chicken egg production industry, the welfare impacts of this are not well understood. In the past decades, free-range systems were widely used for local chicken breeds in poultry industry in China, but their use has gradually declined due to the lower competitiveness compared to commercial cage systems. However, the practices of free-range systems for hens raising have gradually increased again over the past decade, as consumer individualized demand for higher food quality and animal welfare has increased. We recruited 14 free-range farms and 45 cage farms from Beijing, Shandong, Hebei, Anhui, Yunnan, Gansu and Jiangsu provinces in China, for an evaluation of hen welfare, production and economic outcomes from farm operations. This study provides data for the welfare outcomes of laying hens in China and preliminarily explored the relationship between welfare level and economic income within farming system types. The researchers visited the farms and used Welfare Quality measures to investigate the welfare, and farm self-reported profits. Nonparametric Mann–Whitney U tests were used to compare the welfare scores between cage and free-range rearing farms. Correlation and regression are used for the analysis of the animal welfare scores, economic data, and production metrics. The general income from free-range farms was linearly correlated with red mite score and stocking density (p < 0.001 and p < 0.05, respectively). The results showed less centimeters of feeder and drinker space per animal in the free-range system than in cage systems (p < 0.05 and p < 0.01, respectively). Welfare scores for both the stocking density and beak condition were significantly better in the free-range systems than the cage systems (p < 0.001), as were qualitative behavior assessment scores (p < 0.05). The total egg production and peak egg production in cage farms were much higher than in free-range farms (p < 0.001), and egg loss rate was significantly lower (p < 0.001). While the production efficiency of free-range farms was lower than that of cage farms, general income per 10,000 hens was actually higher. Our results provide some evidence that some welfare indicators and general income (per 10,000 hens) in free-range farms in China were better than those of cage farms. The results indicate that better parasite control and lower stocking densities may result in improved hen welfare on free-range farms and potentially improve profitability. The level of welfare and economic benefits of free-range farms vary widely, and there was potential room for improvement in feeding space, drinking water space and human–animal relationship. [ABSTRACT FROM AUTHOR]

The introduction of exotic breeds and the cultivation of new lines by breeding companies have posed challenges to native chickens in South China, including loss of breed characteristics, decreased genetic diversity, and declining purity. Understanding the population genetic structure and genetic diversity of native chickens in South China is crucial for further advancements in breeding efforts. In this study, we analyzed the population genetic structure and genetic diversity of 321 individuals from 10 different breeds in South China. By comparing commercial chickens with native ones, we identified selection signatures occurring between local chickens and commercial breeds. The analysis of population genetic structure revealed that the native chicken populations in South China exhibited a considerable level of genetic diversity. Moreover, the commercial lines of Xiaobai chicken and Huangma chicken displayed even higher levels of genetic diversity, which distinguished them from other native varieties at the clustering level. However, certain individuals within these commercial varieties showed a discernible genetic relationship with the native populations. Notably, both commercial varieties also retained a significant degree of genetic similarity to their respective native counterparts. In order to investigate the genomic changes occurring during the commercialization of native chickens, we employed 4 methods (Fst, ROD, XPCLR, and XPEHH) to identify potential candidate regions displaying selective signatures in Southern Chinese native chicken population. A total of 168 (identified by Fst and ROD) and 86 (identified by XPCLR and XPEHH) overlapping genes were discovered. Functional annotation analysis revealed that these genes may be associated with reproduction and growth (SAMSN1, HYLS1, ROBO3, FGF14, PRSS23), musculoskeletal development (DNER, MYBPC1, DGKB, ORC1, KLF10), disease resistance and environmental adaptability (PUS3, CRB2, CALD1, USP15, SGCD, LTBP1), as well as egg production (ADGRB3, ACSF3). Overall, native chickens in South China harbor numerous selective sweep regions compared to commercial chickens, enriching valuable genomic resources for future genetic research and breeding conservation. [ABSTRACT FROM AUTHOR]

Meat quality traits are essential for producing high-quality broilers, but the genetic improvement has been limited by the complexity of measurement methods and the numerous traits involved. To systematically understand the meat quality characteristics of different broiler breeds, this study collected data on slaughter performance, skin color, fat deposition, and meat quality traits of 434 broilers from 12 different breeds in South China. The results showed that there was no significant difference in the live weight and slaughter weight of various broiler breeds at their respective market ages. Commercial broiler breeds such as Xiaobai and Huangma chickens had higher breast muscle and leg muscle rates. The skin and abdominal fat of Huangma chickens cultivated in the consumer market in South China exhibited significantly higher levels of yellowness compared to other varieties. Concerning fat traits, we observed that Wenchang chickens exhibited a strong ability to fat deposition, while the younger breeds showed lower fat deposition. Additionally, there were significant positive correlations found among different traits, including traits related to weight, traits related to fat, and skin color of different parts. Hierarchical clustering analysis revealed that fast-growing and large broiler Xiaobai chickens formed a distinct cluster based on carcass characteristics, skin color, and meat quality traits. Principal component analysis (PCA) was used to extract multiple principal components as substitutes for complex meat quality indicators, establishing a chicken meat quality evaluation model to differentiate between different breeds of chickens. At the same time, we identified 46, 22, and 20 SNP loci and their adjacent genes that were significantly associated with muscle mass traits, fat deposition, and skin color through genome-wide association studies (GWAS). The above results are helpful for systematically understanding the differences and characteristics of meat quality traits among different breeds. [ABSTRACT FROM AUTHOR]

As a Chinese local chicken breed, Hongshan chickens have 2 kinds of tail feather phenotypes, normal and taillessness. Our previous studies showed that taillessness was a sex-linked dominant trait. Abnormal development of the tail vertebrae could be explained this phenomenon in some chicken breeds. However, the number of caudal vertebrae in rumpless Hongshan chickens was normal, so rumplessness in Hongshan chicken was not related to the development of the caudal vertebrae. Afterwards, we found that rumplessness in Hongshan was due to abnormal development of tail feather rather than abnormal development of caudal vertebrae. In order to understand the genetic foundation of the rumplessness of Hongshan chickens, we compared and reanalyzed 2 sets of data in normal and rumpless Hongshan chickens from our previous studies. By joint analysis of genome-wide selection signature analysis and genome-wide association approach, we found that 1 overlapping gene (EDIL3) and 16 peak genes (ENSGALG00000051843, ENSGALG00000053498, ENSGALG00000054800, KIF27, PTPRD, ENSGALG00000047579, ENSGALG00000041052, ARHGEF28, CAMK4, SERINC5, ENSGALG00000050776, ERCC8, MCC, ADAMTS19, ENSGALG00000053322, CHRNA8) located on the Z chromosome was associated with the rumpless trait. The results of this study furtherly revealed the molecular mechanism of the rumpless trait in Hongshan chickens, and identified the candidate genes associated with this trait. Our results will help to improve the shape of chicken tail feathers and to rise individual economic value in some specific market in China. [ABSTRACT FROM AUTHOR]

China has about 107 local chicken breeds and is considered one of the richest countries in terms of genetic resources. This diversity is a source of richness natural resources across the globe and is regarded as an excellent material for genetic improvement of breeds or breeding new breeds around the world. The present review highlights the recent evidence and studies of chicken origin and domestication in China and Southeast Asia. The evidence of molecular genetics and archeological results supported that multiple regions and event were contributed to the creation of chicken evolution from Red Jungle fowl and the findings proposed that one of events happened in domestication of chicken 8000 BP in Southeast of Asia. Several researchers confirmed that China was declared as most important of the world as a first centers for the chicken’s domestication and these chickens have remained in many archaeological sites in China. [ABSTRACT FROM AUTHOR]

[Objectives] This study was conducted to improve the production efficience of dark-shank partridge-like plumage high-qualite broilere and ensure animat welfare, ss as to meet the development needs of China's yellow-feather broiler industr.. [Methods] Sichuan Animal Sciencc Academy and Sichuan Dahen Poultry Breeding Co., Ltd., formed a joint breeding research team. The team bred Dahen 799 broilee complete set tine with locai chicken breeds as the main material and improving production efficience, stabilizing meat quality and Oavor and achieving autosexing oO chicks as the main breeding goats by modern poulte breeding technologies, after 10 yeare and 8 generations. [Resslts] The Dahen 799 broilee complete set tine was approved by Nationai Commission of Livestock and Poulte Genetic Resources in December 2020. The 66-week-olO egg production ot the breed reached 189 egg. For the commercial generation, cocks and hens showed 10-week-old weight of 2 668 and 2 269 g respectively; the feed conversion ratio was 2. 26 - 2. 35; the survivabilito was 96.7% - 97. 2%; and the average intramuscular fat contents ot cocks and hens were 1v the range of 1. 8% -2.1%, and the inosinic vid contents were 1v the range of 2.3 -3.2 mg/g. The production performancc and meat Oavos of Dahen 799 broilere were better than Dahen 699 broilee, Sichuan mountainous bone-black chickens and two othes social breeds. Compared wit Sichuan mountainous bone-black chickens, the egg production at the age of 66 weeks increased by 47 eggs; the average weight ol cocks and hens ol the commercial generation at 10 weeks increased by 45. 21%; and the autosexing rate ol chicks of te commercial generation reached 99. 3 %. [Conclusions] Dahen 799 broilee have the adrantages of good production performancc, high feed conversion ratio and excellent meat flavor and the characteristic of autosexing which othec breeds do not have, and can fuliy meet the industWal development needs of dark shanks and partridge-like plumage broilers. [ABSTRACT FROM AUTHOR]

Summary: In poultry, HyLine (HL) Hens are known for their excellent laying performance. However, ZhenNing (ZN) Hens, a native chicken breed in China, are known for their unique flavour. The intestinal mucosa, which is the main organ for nutrient absorption, could affect livestock product quality. In ZN Hens' intestinal mucosa, we found more villus wrinkles, larger villus circumference and higher amino acid transporters mRNA abundance compared with HL Hens. Among three laying periods of ZN Hens, in the intestinal lumen, Lactobacillus salivarius (L. sa.), Lactobacillus agilis (L. ag.) and Lactobacillus aviarius were the predominant species in the laying peak period. Furthermore, multiple‐antibiotics feeding in ZN Hens and predominant Lactobacillus feeding in HL Hens suggested that these Lactobacilli could indeed increase villus wrinkles and improve intestinal absorption. In HL Hens, L. sa. + L. ag. treatment could promote organoids budding in vitro, and promote epithelial proliferation in vivo. Collectively, the unique intestinal mucosa morphology in ZN Hens was due to the high abundance of intestinal L. sa. and L. ag. Transplant these Lactobacilli to HL Hens could increase their intestinal probiotics abundance, fine adjust the intestinal stem cell function and promote the epithelial proliferation, in turn, increase villus winkles and mucosal absorption area. [ABSTRACT FROM AUTHOR]

Objective: The extensive breeding of commercial chickens has led to a sharp decrease in the resources of many indigenous chickens, especially the indigenous chickens in the southeastern coastal region, which are on the verge of extinction, and the indigenous chickens in the northwestern region of China, which are also at risk. However, there are few reports on the evaluation of genetic diversity and conservation of genetic resources of indigenous chickens in remote areas in the Northwest of China. Methods: In the present study, the genetic diversity and phylogenetic relationship of six indigenous chickens from different regions were studied based on variation in mitochondrial DNA control region (D-loop), and the degree of introgression from commercial breeds into these chickens was determined by the amount of haplotype sharing between indigenous and commercial breeds. Results: Twenty-five polymorphic sites and 25 haplotypes were detected in 206 individuals. Principal component analysis showed that the Jingning chicken had the highest genetic diversity among the six indigenous chickens. According to the degree of introgression, the six indigenous breeds may be involved in haplotype sharing with commercial breeds, and the introgression from commercial chickens into the Haidong chicken is the most serious. Conclusion: The genetic uniqueness of indigenous chickens has been eroded, so it is necessary to consider the protection of their genetic resources. Phylogenetic analysis suggests that the six indigenous chickens have two major matrilineal origins: one from Yunnan or its surrounding areas in China and the other from the Indian subcontinent. [ABSTRACT FROM AUTHOR]

Avian leukosis virus subgroup J (ALV-J) infection can cause tumors and immunosuppression, which has made huge financial loss in the poultry industry. More and more new pathogenic avian leukosis virus, which were recombined from exogenous avian leukosis virus and endogenous retrovirus viruses were isolated from China and other regions in the world. To uncover the characteristic of the potential recombinant elements, we analyzed the genomes of avian endogenous retrovirus ev/J in ten chicken breeds in China. Six of the ten chicken breeds contained two sizes of ev/J (3.8 kb and 2.2 kb) and the other only contained 3.8 kb ev/J. The ten 3.8 kb ev/J were much closer to type I, II and III ev/J prototypes, while the six 2.2 kb ev/J were close to type IV ev/J prototype in the phylogenetic trees. Moreover, three novel deletion fragments were identified in the sixteen ev/J in chicken flocks in China, which made most of the ev/J (10/16) significantly different from the four ev/J prototypes. The emergence of these novel deletions resulted in the diversity of ev/J in chicken breeds in China, which may become the source of further recombination of avian leukosis viruses (ALVs), especially the exogenous ALV subgroup J. [ABSTRACT FROM AUTHOR]

Subgroup K avian leukosis virus (ALV-K) is a new subgroup of avian leukosis virus (ALV) first identified in Chinese indigenous chickens in recent years. In this study, an ALV-K strain was isolated from Luhua chicken in Shandong province, China, and designated SD20LH01. The full-length genomic sequence of SD20LH01 was 7491 bp, which had the highest homology with ALV-K reference strains GDFX0601, GDFX0602 and GDFX0603. The nucleotide homology of env gene of SD20LH01 with reference strains of subgroup A, B, C, D, E, and J was ranged from 57.1 to 93.2%, while 94.1 to 99.4% with other ALV-K reference strains. The nucleotide difference of SD20LH01 mainly clustered with gp85 gene and U3 sequence when compared with the reference strain of ALV-K. In order to investigate the pathogenicity of SD20LH01, SPF chicken embryos were infected by yolk sac inoculation, and 1-day-old chickens were infected by intraperitoneal inoculation of SD20LH01. The results showed that yolk sac inoculation of SD20LH01 could induce persistent viremia, growth retardation and reduce the immune response to NDV and AIV-H9 vaccines. However, intraperitoneal inoculation in 1-day-old chickens could only induce a low level of viremia. In addition, no tumors were found in infected chickens during the animal experiments. This study enriched the genomic sequence data of ALV-K isolated in Chinese indigenous chickens, and laid a foundation for further study on the pathogenesis and prevention of ALV-K. [ABSTRACT FROM AUTHOR]

Pullorum disease is characterized by white diarrhea resulting from infection by S. Pullorum, but arthritis associated with S. Pullorum infection has become increasingly frequent recently, especially in Chinese native chicken flocks. In this study, we isolated and identified 4 S. Pullorum strains from the Qingjiaoma chicken breeders with arthritis symptoms. The LD 50 of the isolate 20JS04 was 1.33 × 106 CFU, which was considered as a highly virulent strain in chicks. Reproducible arthritis symptoms were observed in the experimentally chickens infected with the isolate 20JS04, and the disease occurrence was 27.78% (5/18). In addition to the characteristics of high virulence and induced-arthritis, our results confirmed that the arthritis-causing isolate 20JS04 had greater negative impact on BW, ADFI, and ADG, compared with the white diarrhea-causing S. Pullorum standard strain CVCC526 (P < 0.05). These results suggest that the pathogenic diversity of S. Pullorum in China deserves more attention and stringent measures should be taken to control salmonellosis. [ABSTRACT FROM AUTHOR]