• Asian-Australasian Journal of Animal Sciences
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• v.33 no.10
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• pp.1566-1572
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• 2020

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.

• Animal Bioscience
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• v.35 no.6
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• pp.826-837
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• 2022

Objective: Cambodia is located within the distribution range of the red junglefowl, the common ancestor of domestic chickens. Although a variety of indigenous chickens have been reared in Cambodia since ancient times, their genetic characteristics have yet to be sufficiently defined. Here, we conducted a large-scale population genetic study to investigate the genetic diversity and population genetic structure of Cambodian indigenous chickens and their phylogenetic relationships with other chicken breeds and native chickens worldwide. Methods: A Bayesian phylogenetic tree was constructed based on 625 mitochondrial DNA D-loop sequences, and Bayesian clustering analysis was performed for 666 individuals with 23 microsatellite markers, using samples collected from 28 indigenous chicken populations in 24 provinces and three commercial chicken breeds. Results: A total of 92 haplotypes of mitochondrial D-loop sequences belonging to haplogroups A to F and J were detected in Cambodian chickens; in the indigenous chickens, haplogroup D (44.4%) was the most common, and haplogroups A (21.0%) and B (13.2%) were also dominant. However, haplogroup J, which is rare in domestic chickens but abundant in Thai red junglefowl, was found at a high frequency (14.5%), whereas the frequency of haplogroup E was considerably lower (4.6%). Population genetic structure analysis based on microsatellite markers revealed the presence of three major genetic clusters in Cambodian indigenous chickens. Their genetic diversity was relatively high, which was similar to findings reported for indigenous chickens from other Southeast Asian countries. Conclusion: Cambodian indigenous chickens are characterized by mitochondrial D-loop haplotypes that are common to indigenous chickens throughout Southeast Asia, and may retain many of the haplotypes that originated from wild ancestral populations. These chickens exhibit high population genetic diversity, and the geographical distribution of three major clusters may be attributed to inter-regional trade and poultry transportation routes within Cambodia or international movement between Cambodia and other countries.

• Animal Bioscience
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• v.35 no.5
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• pp.778-788
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• 2022

Objective: The objective of the study was to understand and document socio-economic characteristics, production parameters, challenges and management practices used by Fijian households which keep indigenous chickens. Methods: A survey involving 200 households was carried out in coastal and inland communities of Fiji's wet and semi-dry ecoregions. Data on the influence of ecoregion and location of households relative to the sea on management practices, challenges and productivity of indigenous chickens were analyzed using logistic regression and general linear model of SAS software. Results: Irrespective of location relative to the sea and ecoregion, households indicated that they kept indigenous chickens for food and income generation. The Welsummer was the most (p>0.05) preferred breed. Households in the semi-dry inland communities had the largest (p<0.05) flocks compared to those in semi-dry coastal communities and the wet region. Chickens in the semi-dry region performed better (p<0.05) than those in the wet region in terms of number of clutches per year and mature live weight. Predators and feed shortages were the biggest challenges faced by households in all areas. The mongoose was ranked as the most (p>0.05) common predator followed by domestic dogs. Most households in the wet ecoregion's coastal communities housed their chickens at night, whereas communities in semi-dry ecoregion housed their chickens most of the time (p<0.05). In all regions, no households sold their chickens to commercial markets (p>0.05). Households in semi-dry ecoregion were more likely (p>0.05) to sell their chickens at the local market place. Conclusion: The productivity of local chickens in Fiji is low because of feed shortage, predators such as the mongoose and lack of market linkages.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.11
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• pp.1817-1823
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• 2020

Objective: The increasing consumer awareness of food, which can provide health benefits and potentially aid disease prevention, has become the driving force of the functional food market. Accordingly, the aim of this study was to investigate the effects of chicken genotype on the macronutrient content, bioactive peptide content, and antioxidant capacity within different breast meat. Methods: In this experiment, three genotypes of chicken, Thai indigenous, black-boned, and broiler (control), were reared with commercial feed under the same conditions. Thirty chickens were slaughtered at typical market age and the breasts were separated from the carcass to determine macronutrient content using the AOAC method. The antioxidant capacities of the chicken breasts were evaluated by in vitro antioxidant assays and the protein pattern was investigated using gel electrophoresis. Carnosine and anserine, which have antioxidant properties in animal tissue, were determined using high performance liquid chromatography. Results: The results showed that breast meat from Thai indigenous chickens had a greater macronutrient content and higher antioxidant capacity compared with the other genotypes (p<0.05). The protein pattern was similar between genotypes, however Thai indigenous chickens had the greatest myosin and actin content (p<0.05). In addition, carnosine and anserine values were greatest in the black-boned and Thai indigenous chickens compared with the broiler genotype (p<0.05). Conclusion: Thai indigenous chicken breast meat may be classified as a functional food as it has good nutritional value and is rich in antioxidant peptides.

• Food Science of Animal Resources
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• v.42 no.5
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• pp.833-848
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• 2022

The objective of this study was to characterize the meat quality traits that affect the texture and savory taste of Ufipa indigenous chickens by comparing the proximate composition, physical characteristics, collagen, and nucleic acid contents with those of commercial broilers. It was found that Ufipa chicken breast and thigh meat had a higher protein content (p<0.05) than broiler chicken meat, whereas the fat content was lower (p<0.01). The moisture content of thigh meat was lower in Ufipa chicken meat than in broiler chicken meat (p<0.05). Regarding meat color, broiler chickens had considerably higher L^* and b^* than Ufipa chickens in both the breast and the thigh meat, except for a^* (p<0.01). Regarding water holding capacity, Ufipa chicken breast exhibited higher drip loss but lower thawing and cooking losses than broiler chicken (p<0.01). In contrast, its thigh meat had a much lower drip and thawing losses but higher cooking losses (p<0.01). The shear force of Ufipa chickens' breasts and thighs was higher than that of broiler chickens (p<0.05), while the amount of total collagen in the thigh meat was higher than that of broiler chickens (p<0.05). Additionally, the inosine-5'-monophosphate (IMP) of Ufipa chicken breast and thigh meat was higher than that of broiler meat (p<0.05). The principal component analysis of meat quality traits provides a correlation between the proximate and physical-chemical prosperties of both breeds with some contrast. In conclusion, the present study provides information on healthy food with good-tasting Ufipa indigenous chickens, which offer a promising market due to consumers' preferences.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.6
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• pp.804-811
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• 2018

Objective: Complete mtDNA D-loop sequences of four Thai indigenous chicken varieties, including Pra-dhu-hang-dam (PD), Leung-hang-khao (LK), Chee (CH), and Dang (DA) were explored for genetic diversity and relationships with their potential ancestor and possible associates to address chicken domestication in Thailand. Methods: A total of 220 complete mtDNA D-loop sequences of the four Thai indigenous chicken varieties were obtained by Sanger direct sequencing of polymerase chain reaction amplicons of 1,231 to 1,232 base pair in size. A neighbor-joining dendrogram was constructed with reference complete mtDNA D-loop sequences of Red Junglefowl (RJF) and those different chicken breeds available on National Center for Biotechnology Information database. Genetic diversity indices and neutrality test by Tajima's D test were performed. Genetic differences both within and among populations were estimated using analysis of molecular variance (AMOVA). Pairwise fixation index ($F_{ST}$) was conducted to evaluated genetic relationships between these varieties. Results: Twenty-three identified haplotypes were classified in six haplogroups (A-E and H) with the majority clustered in haplogroup A and B. Each variety was in multiple haplogroups with haplogroups A, B, D, and E being shared by all studied varieties. The averaged haplotype and nucleotide diversities were, respectively 0.8607 and 0.00579 with non-significant Tajima's D values being observed in all populations. Haplogroup distribution was closely related to that of RJF particularly Gallus gallus gallus (G. g. gallus) and G. g. spadiceus. As denoted by AMOVA, the mean diversity was mostly due to within-population variation (90.53%) while between-population variation (9.47%) accounted for much less. By pairwise $F_{ST}$, LK was most closely related to DA ($F_{ST}=0.00879$) while DA was farthest from CH ($F_{ST}=0.24882$). Conclusion: All 4 Thai indigenous chickens are in close relationship with their potential ancestor, the RJF. A contribution of shared, multiple maternal lineages was in the nature of these varieties, which have been domesticated under neutral selection.

• Animal Bioscience
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• v.36 no.4
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• pp.570-583
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• 2023

Objective: Fibroblast growth factors (FGFs) play critical roles in embryo development, and immune responses to infectious diseases. In this study, to investigate the roles of FGFs, we performed genome-wide identification, expression, and functional analyses of FGF family members in chickens. Methods: Chicken FGFs genes were identified and analyzed by using bioinformatics approach. Expression profiles and Hierarchical cluster analysis of the FGFs genes in different chicken tissues were obtained from the genome-wide RNA-seq. Results: A total of 20 FGF genes were identified in the chicken genome, which were classified into seven distinct groups (A-F) in the phylogenetic tree. Gene structure analysis revealed that members of the same clade had the same or similar exon-intron structure. Chromosome mapping suggested that FGF genes were widely dispersed across the chicken genome and were located on chromosomes 1, 4-6, 9-10, 13, 15, 28, and Z. In addition, the interactions among FGF proteins and between FGFs and mitogen-activated protein kinase (MAPK) proteins are limited, indicating that the remaining functions of FGF proteins should be further investigated in chickens. Kyoto encyclopedia of genes and genomes pathway analysis showed that FGF gene interacts with MAPK genes and are involved in stimulating signaling pathway and regulating immune responses. Furthermore, this study identified 15 differentially expressed genes (DEG) in 21 different growth stages during early chicken embryo development. RNA-sequencing data identified the DEG of FGFs on 1- and 3-days post infection in two indigenous Ri chicken lines infected with the highly pathogenic avian influenza virus H5N1 (HPAIV). Finally, all the genes examined through quantitative real-time polymerase chain reaction and RNA-Seq analyses showed similar responses to HPAIV infection in indigenous Ri chicken lines (R² = 0.92-0.95, p<0.01). Conclusion: This study provides significant insights into the potential functions of FGFs in chickens, including the regulation of MAPK signaling pathways and the immune response of chickens to HPAIV infections.

• Korean Journal of Poultry Science
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• v.39 no.2
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• pp.105-112
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• 2012

Genetic resource conservation of indigenous species is important to conserve terrestrial, aquatic and avian species throughout the world. The native Korean Oge (KO) chickens are important and protected indigenous avian species in Korea. This KO breed is very popular in Korea because of its external appearances of blackish color. The characterization of morphology and growth performances of KO were performed since 1980s, however the information is still not sufficient for breed selection. In this study, we compared various growth performances including body growth, tibia length, shank length, chest width, chest grith and length of tail feather between male and female chickens of KO and widely known White Leghorn (WL) breeds at 1 week, 2 weeks, 5 weeks, 10 weeks, and 24 weeks. We observed differences on various growth performances at different aged groups between KO and WL chickens. This study may help for the selection of chicken breeds based on age, body growth and meat production.

• Animal Bioscience
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• v.37 no.1
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• pp.16-27
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• 2024

Objective: The objective of this study was to investigate the effect of heat stress on the growth traits and genetic parameters of Thai native chickens. Methods: A total of 16,487 records for growth traits of Thai native chickens between 2017 and 2022 were used in this study. Data included the body weight at birth, body weight at 4, 8, and 12 weeks of age (BW0, BW4, BW8, BW12), average daily gain during 0 to 4, 4 to 8, and 8 to 12 weeks of age (ADG0-4, ADG4-8, ADG8-12), absolute growth rate at birth, at 4, 8, and 12 weeks of age (AGR0, AGR4, AGR8, AGR12). The repeatability test day model used the reaction-norm procedure to analyze the threshold point of heat stress, rate of decline of growth traits, and genetic parameters. Results: At temperature and humidity index (THI) of 76, Thai native chickens began to lose their growth traits, which was the onset of heat stress in this study. The estimated heritability, genetic correlation between animal and heat stress effect, and correlations between the intercept and slope of the permanent environmental effects were 0.27, -0.85, and -0.83 for BW, 0.17, -0.81, and -0.95 for ADG, 0.25, -0.61, and -0.83 for AGR, respectively. Male chickens are more affected by heat stress than female chickens with a greater reduction of BW, ADG, and AGR, values equal to -9.30, -0.23, -15.21 (in males) and -6.04, -0.21, -10.10 (in females) gram per 1 level increase of THI from the THI of 76. Conclusion: The influence of thermal stress had a strong effect on the decline in growth traits and genetic parameters in Thai native chickens. This study indicated that genetic models used in conjunction with THI data are an effective method for the analysis and assessment of the effects of heat stress on the growth traits and genetics of native chickens.

• Journal of Animal Science and Technology
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• v.65 no.5
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• pp.912-921
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• 2023

Genetic diversity analysis is crucial for maintaining and managing genetic resources. Several studies have examined the genetic diversity of Korean domestic chicken (KDC) populations using microsatellite markers, but it is difficult to capture the characteristics of the whole genome in this manner. Hence, this study analyzed the genetic diversity of several KDC populations using high-density single nucleotide polymorphism (SNP) genotype data. We examined 935 birds from 21 KDC populations, including indigenous and adapted Korean native chicken (KNC), Hyunin and Jeju KDC, and Hanhyup commercial KDC populations. A total of 212,420 SNPs of 21 KDC populations were used for calculating genetic distances and fixation index, and for ADMIXTURE analysis. As a result of the analysis, the indigenous KNC groups were genetically closer and more fixed than the other groups. Furthermore, Hyunin and Jeju KDC were similar to the indigenous KNC. In comparison, adapted KNC and Hanhyup KDC populations derived from the same original species were genetically close to each other, but had different genetic structures from the others. In conclusion, this study suggests that continuous evaluation and management are required to prevent a loss of genetic diversity in each group. Basic genetic information is provided that can be used to improve breeds quickly by utilizing the various characteristics of native chickens.