Game Fowl Research Articles

Comprehensive sequencing of the genome and transcriptome of the Xishuangbanna game fowl

The Xishuangbanna game fowl, a local Chinese chicken breed renowned for its athleticism, is facing extinction. Despite its significance, research on its genome assembly and resequencing remains sparse, limiting our understanding of its genetic structure and function. In this study, we assembled a chromosome-level genome using second-generation sequencing and high-throughput chromosome conformation capture (Hi-C), along with transcriptome sequencing. We also resequenced 62 individuals. The resulting assembly yielded a 1.09 gigabase (Gb) high-quality genome, 994.34 Gb of resequencing data, and 141.38 Gb of transcriptome data from 15 tissues. This comprehensive dataset provides valuable insights into the artificial selection processes shaping the breed and offers a solid foundation for further genetic and population studies.

Morphometric Diversity and Genetic Relationship of “Bangkok” Chicken (Thai Game Fowl) in East Java, Indonesia

Morphometric Diversity and Genetic Relationship of “Bangkok” Chicken (Thai Game Fowl) in East Java, Indonesia

Genetic diversity and breed identification of Chinese and Vietnamese local chicken breeds based on microsatellite analysis.

South Asia and Southeast Asia are the origins of domestic chickens and are rich in poultry genetic resources, resulting in many unique local chicken breeds. However, with the rapid intensification of poultry farming worldwide, many local chicken breeds are threatened with extinction. In response to China's "One Belt, One Road" policy, it is imperative to strengthen the conservation and breeding of local chicken breeds in China and Vietnam. This study characterized 18 microsatellite molecular genetic markers to analyze the genetic diversity of 21 local chicken populations in southern China (Yunnan and Guangxi Provinces) and Vietnam, breed identification tags for microsatellite loci were constructed. The results showed that a total of 377 alleles were detected in all breeds, and the most alleles (44) and the highest polymorphic information content (0.7820) were detected at the LEI0094 locus. The average polymorphic information content (PIC) content of the whole population was 0.65, indicating moderate polymorphism. The genetic diversity of the whole population was rich, except for two loci MCW0111 and MCW0016, that showed heterozygote excess at microsatellite loci, and the population had high genetic differentiation. The Vietnamese breeds showed low pairwise fixation coefficient (FST) and Nei's standard genetic distance (DS) between them. According to the neighbor-joining dendrogram constructed by DS and the analysis of population genetic structure using the structure program, Longshengfeng chicken, Yunlong dwarf chicken, Tengchong white chicken, Xiayan chicken, and Daweishan mini chicken are similar, and Xishuangbanna game fowl, Wuding chicken, and Lanping silky chicken are similar to Yanjin black-bone chicken. In addition, excluding Dongtao chicken, other Vietnamese breeds are clustered together, indicating that the southern chicken breeds are closely related and have experienced better breeding. Overall, the whole population is rich in genetic resources, and the chicken breeds in the three regions are genetically close because of geographical factors and human activities. Dongtao chicken in Vietnamese, Chinese Yunnan local chicken breeds (Gallus gallus spadiceus), and red jungle fowl chickens (Gallus gallus) may have the same origin. We also constructed unique microsatellite molecular markers for 20 cultivars using 15 microsatellite loci. This study provides valuable insights to facilitate breed identification, improve cultivar protection, and new germplasm construction.

Collagen Content and Collagen Fiber Architecture in the Skin of Shamo Chicken, a Japanese Game Fowl.

Collagen content and collagen fiber architecture in the skin of Shamo chickens were compared between sexes and body parts. Cervical, thoracic, dorsal, femoral, and crural skin samples were collected and their collagen content was analyzed. Collagen fiber specimens were prepared for scanning electron microscopy using the cell maceration method with a NaOH solution. Sex differences in collagen content were only observed in the femoral skin of mature chickens, but not in 10-week-old chicks. The difference in collagen content between body parts was obvious; femoral and crural skin had higher collagen content than those of other parts in both sexes. Scanning electron microscopy indicated that the collagen fiber architecture was quite different between the superficial and deep layers in the dermis, with the former consisting of loosely tangled band-like collagen fibers, and the latter composed of thick and dense layers of collagen bundles in a parallel arrangement. The width of collagen fibers in the superficial layer of the dermis differed between sexes in the dorsal, femoral, and crural skin. From these results, it is likely that the difference in collagen content in the femoral skin is not due to sex hormones but other factors, such as mechanical stimulation in daily activity. Additionally, collagen fiber width in the superficial layer is likely related to the difference in collagen content between sexes and between body parts.

Population Genomic Sequencing Delineates Global Landscape of Copy Number Variations that Drive Domestication and Breed Formation of in Chicken.

Copy number variation (CNV) is an important genetic mechanism that drives evolution and generates new phenotypic variations. To explore the impact of CNV on chicken domestication and breed shaping, the whole-genome CNVs were detected via multiple methods. Using the whole-genome sequencing data from 51 individuals, corresponding to six domestic breeds and wild red jungle fowl (RJF), we determined 19,329 duplications and 98,736 deletions, which covered 11,123 copy number variation regions (CNVRs) and 2,636 protein-coding genes. The principal component analysis (PCA) showed that these individuals could be divided into four populations according to their domestication and selection purpose. Seventy-two highly duplicated CNVRs were detected across all individuals, revealing pivotal roles of nervous system (NRG3, NCAM2), sensory (OR), and follicle development (VTG2) in chicken genome. When contrasting the CNVs of domestic breeds to those of RJFs, 235 CNVRs harboring 255 protein-coding genes, which were predominantly involved in pathways of nervous, immunity, and reproductive system development, were discovered. In breed-specific CNVRs, some valuable genes were identified, including HOXB7 for beard trait in Beijing You chicken; EDN3, SLMO2, TUBB1, and GFPT1 for melanin deposition in Silkie chicken; and SORCS2 for aggressiveness in Luxi Game fowl. Moreover, CSMD1 and NTRK3 with high duplications found exclusively in White Leghorn chicken, and POLR3H, MCM9, DOCK3, and AKR1B1L found in Recessive White Rock chicken may contribute to high egg production and fast-growing traits, respectively. The candidate genes of breed characteristics are valuable resources for further studies on phenotypic variation and the artificial breeding of chickens.

Web crawling of social media and related web platforms to analyze backyard poultry owners responses to the 2018-2020 Newcastle Disease (ND) outbreak in Southern California.

As social media becomes an ever-increasing staple of everyday life and a growing percentage of people turn to community driven platforms as a primary source of information, the data created from these posts can provide a new source of information from which to better understand an event in near real time. The 2018-2020 outbreak of Newcastle Disease (ND) in Southern California is the third outbreak of ND in Southern California within a 50-year time span. These outbreaks are thought to be primarily driven by non-commercial poultry (i.e. backyard and game fowl) in the region. Here we employed a commercial 'web crawling' tool between June of 2018 and July of 2020 which encompassed the majority of the outbreak in order to collect all available online mentions of 'virulent Newcastle Disease' (vND), the terminology commonly used by the California Department of Food and Agriculture (CDFA), United States Department of Agriculture (USDA), and the general public, in relation to the outbreak. A total of 2498 posts in English and Spanish were returned using a Boolean logic-based string search. While the number of posts was relatively small, their impact as measured by the number of visitors to the website and the number of people viewing the post (where provided) was much larger. Posts with negative sentiment were found to have a larger audience relative to posts with a positive sentiment. In addition, posts with negative sentiment peaked in May of 2019 which preceded the formation of the anti-depopulation group Save Our Birds (SOB). As the usage and impact of social media grows, the ability to utilize tools to analyze social media may improve both response and outreach-based strategies for various disease outbreaks including vND in Southern California which has a large non-commercial poultry population.

Assessment of the Dermal Acute Irritation Potential of Natural Veterinary Medicine Minyak Rajas in Albino Rabbits

Aims: This study was designed to assess the potential for acute dermal irritation of natural veterinary medicine Minyak Rajas (produce by Songgolangit Persada Limited Company, Bali, Indonesia) in albino rabbits. It is a rather thick liquid which contains various medicinal herbal extracts, formulated with effective microorganism technology. This medicine is effective in the treatment of skin infections and inflammation, wounds, intestinal worms and digestive disorder. Additionally, it works for game fowl muscle strengthening.
 Place and Duration of Study: This study was conducted at the Veterinary Pharmacy and Pharmacology Laboratory, Faculty of Veterinary Medicine, Udayana University, between April 2020 and May 2020.
 Methodology: Experimental animals used were three male albino rabbits (Oryctolagus cuniculus) in healthy conditions and weighing of >2 Kg. Test procedures followed the guidelines of Organisation for Economic Cooperation and Development, and chemicals used were applied in a single dose of 0.5 ml on animal skins, with untreated skin as a control.
 Results: Very slight erythema was found after the Minyak Rajas application and the lesion was about 48 hours. Overall, no severe erythema, edema or other skin lesions were observed. According to the Amanded Draize system, the Primary Irritation Indexes of 0.16 is categorized as non-irritating.
 Conclusion: We conclude that the natural veterinary medicine of Minyak Rajasis safe to be used.

Genome scan for selection in South American chickens reveals a region under selection associated with aggressiveness

ABSTRACT Domestic chicken populations have been subjected to selection strategies to improve different production traits. Throughout history, selection coupled with diverse demographic dynamics have shaped the genome of many local populations which might harbor important genetic combinations with potential for production and survival to future unknown climate changes. South American local chickens include several well-adapted local breeds that thrive in extreme environments (e.g., tropical rain forest, high altitude and desert). In addition, there has been a long tradition of game fowl breeding in South America about which very little is known. As game fowl display distinct phenotypes compared to other types of chickens, i.e., aggressiveness, we have screened for single nucleotide polymorphisms (SNPs) localized in genes related to behavior that depart from neutrality (i.e., outliers) and therefore might be influenced by selection. Here we used restriction site-associated DNA sequencing (RADseq) to identify 122,801 SNPs distributed across the genome to scan for selection signatures in South American chicken populations. We detected 892 SNPs that were under selection. Two SNPs under positive selection localized in a genomic region harboring the Dopamine Receptor 2 (DRD2) gene and the Ankyrin Repeat and Kinase Domain Containing 1 (ANKK1) gene which have been associated with behavior. The population branch statistics analysis (PBS) on these two SNPs provided further evidence that these two variants have been under positive selection in game fowl. These findings contribute to the understanding of the genetic architecture behind the aggressiveness behavior in chickens, a trait of paramount importance in the poultry industry.

Re-emergence of a genotype VIII virulent Newcastle disease virus isolated from Chinese game fowl after 13years.

Circulation of dominant genotypes VI and VII of Newcastle disease virus (NDV) is causing significant economic losses to the poultry industry in China. However, reports of Newcastle disease (ND) outbreaks caused by genotype VIII strains of NDV are rare. In this study, a virulent genotype VIII strain of NDV, designated GXGB2011, was isolated from a vaccinated game fowl flock showing clinic signs of infection in Pinxiang county, Guangxi, China. The whole genome of the isolate was completely sequenced and was found to be comprised of 15,192 nucleotides (nt), encoding the six structural proteins in the order of 3'-NP-P-M-F-HN-L-5'. The pattern of cleavage site 112 RRQKR↓F117 in the fusion (F) protein and the intracerebral pathogenicity index (ICPI) value of 1.5 showed that the strain GXGB2011 was a velogenic NDV. The results of the challenge experiment with the 5-week-old SPF chickens showed that the strain was highly pathogenic with 100% morbidity and mortality of the challenged birds. Based on the detection of virus in different organs of the infected birds, the highest viral load in caecal tonsils was observed and viral levels in immune organs were higher than those in the respiratory organs. Bayesian reconstruction of complete genomes based on the sequences of 66 NDV reference strains showed that the strain belonged to the genotype VIII of NDV. Phylogenetic analysis showed that the strain was more closely related to the foreign strains gamefowl/U.S.(CA)/24225/98, 1ITTY94060 and IT-147/94 rather than to the first domestic strains of the emergence genotype VIII in Qinghai, China during 1979-1985. In summary, the results of the study demonstrated the re-emergence of a highly pathogenic virulent isolate of genotype VIII of NDV. These results indicate the risk that this genotype VIII of NDV may spread to commercial chickens from game fowl.

Genomic Analyses Reveal Potential Independent Adaptation to High Altitude in Tibetan Chickens.

Much like other indigenous domesticated animals, Tibetan chickens living at high altitudes (2,200-4,100 m) show specific physiological adaptations to the extreme environmental conditions of the Tibetan Plateau, but the genetic bases of these adaptations are not well characterized. Here, we assembled a de novo genome of a Tibetan chicken and resequenced whole genomes of 32 additional chickens, including Tibetan chickens, village chickens, game fowl, and Red Junglefowl, and found that the Tibetan chickens could broadly be placed into two groups. Further analyses revealed that several candidate genes in the calcium-signaling pathway are possibly involved in adaptation to the hypoxia experienced by these chickens, as these genes appear to have experienced directional selection in the two Tibetan chicken populations, suggesting a potential genetic mechanism underlying high altitude adaptation in Tibetan chickens. The candidate selected genes identified in this study, and their variants, may be useful targets for clarifying our understanding of the domestication of chickens in Tibet, and might be useful in current breeding efforts to develop improved breeds for the highlands.

Influence of Age Combination and Protein Supplementation on the Rate of Lay, Egg Quality and Chick Viability

Farm trail was conducted to determine the effect of short-term game fowl management interventions on egg production and chick viability. It involved two studies. In study 1, the experimental treatments were: a) brood cock x brood pullets, b) brood stag x brood hens, c) brood cock x brood hens, and d) brood stag x brood pullets. In Study 2, protein supplementation at different day intervals with different dosage (number of capsule) were used: a) zero supplementation, b) one capsule per week, c) two capsules per week, and d) three capsules per week. Results showed that egg production, egg shape index, hatchability and chick viability were not influenced by age combination of brood fowls. with high protein concentrate and energy utilization enhancer did not influence egg production and egg and chick viability. There were relative improvements in egg and chick viability, suggesring that those may be with long term supplementation. It is recommended that a study for longer duration of time of pairing of different combinations be conducted to further test the productive efficiency in terms of rate of lay, hatchability and chick viability, and supplementing brood fowl with energy utilization enhancer for a longer duration of time and with a bigger experimental bird population.

XXXth IUGB Congress and Perdix XIII

XXXth IUGB Congress and Perdix XIII

Sequence analysis of a pea comb locus on chicken chromosome 1

To facilitate gene identification, this study aimed to narrow the scope of the genome region affecting chicken comb type by using two bird populations. First, an F2 resource population was generated by crossing Japanese game fowl (Shamo; pea comb, P/p and P/P) with White Plymouth Rock (single comb, p/p). Comb types of the 240 F2 offspring produced by an F1 intercross between eight males and 57 females were segregated at a ratio of 3:1 (pea:single). The pea comb locus was mapped to a chromosomal region on Gallus gallus chromosome 1 that was flanked by microsatellite markers MCW0112, MCW0019 and ABR521. The second population (five-generation, n=1300 animals) was derived from a cross between Shamo and Rhode Island Red (single comb, p/p) that had been genotyped for additional polymorphic single nucleotide polymorphisms and microsatellite markers within this region through development of chicken draft sequences. To close some gaps in these draft sequences, we constructed a bacterial artificial chromosome contig and sequenced it using the shotgun sequencing technique. Chickens selected from pedigrees in these populations were grouped by inheritance of a P or p haplotype at the locus constructed by the additional markers. Finally, this locus was fine-mapped to roughly 60 kb based on the association of haplotypes and comb types. Chicken genome sequences suggest that the most likely polymorphism responsible for the pea comb locus is a duplicated sequence and that the sex determining region Y-box 5 gene, one predicted gene and one expressed sequence tag in a critical region may be associated with the duplicated sequence.

Biosecurity: Educational Programs

Multiple educational programs dealing with biosecurity were developed during and following the exotic Newcastle disease outbreak of 2002 and 2003 in California. Extension clientele involved with game fowl, fairs and expositions, poultry clubs, and poultry youth were all in need of biosecurity training. Collaborative efforts between the University of California Cooperative Extension and the California Department of Food and Agriculture resulted in the development of educational programs that addressed issues raised during the outbreak and continue to help clientele protect their birds from emerging diseases.

Serological survey of the infectious disease status of Old English Game fowl in the lower North Island, New Zealand

AIM: To investigate the serological status of Old English Game (OEG) cockerels for a range of infectious diseases of poultry. METHODS: Standard methods were used to screen serum collected from approximately 200 birds during routine dubbing operations, in 2004 and 2005. RESULTS: There was no serological evidence of infection with Newcastle disease, infectious bursal disease, or Salmonella Pullorum. Antibodies to infectious bronchitis virus, avian encephalomyelitis (AE) virus, Mycoplasma gallisepticum and Mycoplasma synoviae were detected. CONCLUSIONS AND CLINICAL RELEVANCE: The disease status of OEG birds is similar to that of commercial poultry.

Prevalence of Campylobacter, Salmonella, and Escherichia coli on the External Packaging of Raw Meat

During September and October 2002, 3,662 prepackaged raw meat samples were collected to evaluate the extent and nature of microbiological contamination on external surfaces of the packaging, which could potentially cross-contaminate ready-to-eat foods during and after purchase. Salmonella was detected on two (<1%) samples of external packaging (both from raw chicken), and Campylobacter was detected on 41 (1.1%) samples of external packaging. The external packaging of game fowl exhibited the highest Campylobacter contamination (3.6%), followed by raw chicken (3.0%), lamb (1.6%), turkey (0.8%), pork (0.2%), and beef (0.1%); Campylobacter jejuni and Campylobacter coli accounted for 59% (24 of 41) and 24% (10 of 41) of the contaminating Campylobacter species, respectively. C. coli isolates from the external packaging were more multiresistant to antimicrobial drugs, including quinolones such as ciprofloxacin, than was C. jejuni. Escherichia coli (an indicator of fecal contamination) was isolated from the external packaging on 4% of the raw meat samples at levels of 40 to 105 CFU per swab. The external packaging of raw meats is a vehicle for potential cross-contamination by Campylobacter, Salmonella, and E. coli in retail premises and consumers' homes. The external surface of heat-sealed packaging was less frequently contaminated with Campylobacter and E. coli compared with other types of packaging (e.g., overwrapping, bag, and tie tape) (P < 0.0001 to 0.01). In addition, external packaging of raw meats was contaminated less frequently with Campylobacter and E. coli when packaging was intact, packaging and display areas were visually clean, display temperatures were below 8°C, and hazard analysis systems were in place.

Antibodies for Newcastle Disease Virus and Mycoplasma gallisepticum in Sera from Domestic Chickens and Game Fowl of Kenya

Studies by one of the authors (2) present serological evidence for infection with a member or members of the group A (1) sarcoma-leukosis viruses in Kenya which indicate that they maintain themselves as endemic infections under natural conditions in a variety of game fowl as well as chickens running free in local villages in remote areas of the African bush country. Representative sera of those collected were examined for the presence of antibodies to Newcastle Disease virus (NDV) and Mycoplcsma gallisepticum (MG), using the hemagglutination-inhibition test for NDV and the agglutination test for MG in order to establish the infection with these agents in the areas studied.

The Amount of Manganese Required to Prevent Perosis in the Chick

PEROSIS has recently been recognized as a deficiency disease affecting the development of bone. Up to the present time it has been observed in several species of domesticated and game fowl but has not been observed in other animals. The most characteristic symptoms of the disease are enlargement of the tibio-metatarsal joint, bending of the distal end of the tibia and the proximal end of the metatarsus, and displacement of the Achilles tendon. Locomotion is impaired and in severe cases the animal is unable to stand. These outward manifestations of injury have given rise to the descriptive terms of “slipped tendon” and “enlarged hock” as names for the deformity. Titus (1932) first proposed the name perosis.The disease is prevalent among rapidly growing chicks confined in battery brooders. Diets high in calcium and phosphorus aggravate the condition according to Wilgus (1931). That the disease is distinct from rickets, in sensu .

Indian game fowl

Indian game fowl