• 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.

• 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.

• 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.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.10
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• pp.1394-1398
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• 2014

Indigenous (native) breeds of livestock have higher disease resistance and adaptation to the environment due to high genetic diversity. Even though their extinction rate is accelerated due to the increase of commercial breeds, natural disaster, and civil war, there is a lack of well-established databases for the native breeds. Thus, we constructed the native pig and chicken breed database (NPCDB) which integrates available information on the breeds from around the world. It is a nonprofit public database aimed to provide information on the genetic resources of indigenous pig and chicken breeds for their conservation. The NPCDB (http://npcdb.snu.ac.kr/) provides the phenotypic information and population size of each breed as well as its specific habitat. In addition, it provides information on the distribution of genetic resources across the country. The database will contribute to understanding of the breed's characteristics such as disease resistance and adaptation to environmental changes as well as the conservation of indigenous genetic resources.

• 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.

• 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.21 no.1
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• pp.6-10
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• 2008

Five chicken populations viz. Chittagong, Ghagus, Kalasthi, Kadaknath, Tellichery were genotyped using 25 highly polymorphic microsatellite loci. White leg horn was taken as an outgroup. To reveal the relationship and distinctiveness among five indigenous breeds various genetic distances based on molecular co-ancestry were estimated and multidimensional scaling was performed. The Ghagus and Kalasthi breeds were closely related and their separation was recent, whereas Chittagong had a remote ancestry with other indigenous chicken populations.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.3
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• pp.336-342
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• 2009

Avian embryos at high altitude are independent of maternal protection against hypoxia, which is contrary to mammals. It is well known that chronic hypoxic exposure at key points can significantly impact on avian development. Tibetan Chicken, a Chinese indigenous breed, living in Tibetan areas with an altitude of 2.2 to 4.1 thousand meters, has an adaptive mechanism to hypoxia. In the present study, fertilized eggs of Tibetan Chicken were incubated under 13% and 21% oxygen concentration. Two lowland chicken breeds, Shouguang Chicken, an indigenous chicken breed in Shandong Province of China, and Dwarf Recessive White Chicken, an imported breed in Beijing, were used as control groups. The embryo mass and some organs such as brain, heart, liver, stomach and eye weight in the three species were measured at Hamburger-Hamilton stage 39, 41, 43 and 45 under hypoxic and normal conditions. The results showed that in hypoxia Tibetan Chicken significantly differed from the two lowland chicken breeds in embryo mass at Hamburger-Hamilton stage 41, 43 and 45 (p<0.01). In particular, Dwarf Recessive White Chicken and Shouguang Chicken showed retarded growth in hypoxic incubation (p<0.01), whereas Tibetan Chicken showed no significant difference between hypoxic and normal conditions (p>0.05). In addition, heart and the other organs showed different susceptibility to hypoxia at the studied stages. In conclusion, chronic hypoxia induced a change in the embryo development of the three different species and Tibetan Chicken showed adaptation to hypoxia. Of note, the embryo developmental physiology of Tibetan Chicken in response to hypoxia will shed light on the process of physiological acclimation or evolutionary adaptation as well as the study of clinical disease.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.2
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• pp.153-159
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• 2006

A 2,656 bp fragment of chicken ghrelin gene was cloned and SNPs were detected by PCR-RFLP and Allele Specific PCR (ASP) in 12 Chinese indigenous chicken breeds and a commercial chicken population. The results showed that there were 23 base variations and an amino acid change ($Gln{\rightarrow}Arg$) in cloned chicken ghrelin gene. Three SNPs were confirmed in 13 populations and associations between this gene and growth traits of Tibetan chicken (TC) and Recessive White chicken (RW) were investigated. The results of haplotype analysis revealed that 26 haplotype genotypes were composed of eight haplotypes. The results of $x^2$ tests indicated that there were significant differences between genotypes or haplotype genotype frequencies in some of the breeds or sexes at 0.05 or 0.01 levels. The results of ANOVA revealed that there were significant differences between genotypes or haplotype genotypes on some growth traits of TC and RW chicken breeds at 0.05 or 0.01 levels. Multiple comparisons showed that there were significant associations between genotype CT at site 71 and some growth traits of two chicken breeds and between genotype AG at site 1,215 and body weight at 16 wk of two chicken breeds, and there was a significant association between haplotype genotype CAA/CAG and body weight and shank girth at 16 wk of two chicken breeds.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.11
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• pp.1732-1740
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• 2020

Objective: The objectives of this study were to investigate the genetic diversity, population structure and relatedness among the five chicken populations of Bangladesh using microsatellite markers. Methods: A total of 161 individuals representing 5 chicken populations (non-descript Deshi [ND], naked neck [NN], hilly [HI], Aseel [AS], and red jungle fowl [JF]) were included in this study to investigate genetic diversity measures, population structure, genetic distance and phylogenetic relationships. Genotyping was performed using 16 selected polymorphic microsatellite markers distributed across 10 chromosomes. Results: The average observed and expected heterozygosity, mean number of alleles and polymorphic information content were found to be 0.67±0.01, 0.70±0.01, 10.7 and 0.748, respectively in the studied populations. The estimated overall fixation index across the loci (F), heterozygote deficiency within (F_IS) and among (F_IT) chicken populations were 0.04±0.02, 0.05 and 0.16, respectively. Analysis of molecular variance analysis revealed 88.07% of the total genetic diversity was accounted for within population variation and the rest 11.93% was incurred with population differentiation (F_ST). The highest pairwise genetic distance (0.154) was found between ND and AS while the lowest distance was between JF and AS (0.084). Structure analysis depicted that the studied samples can be categorized into four distinct types or varieties (ΔK = 3.74) such as ND, NN, and HI where AS and JF clustered together as an admixed population. The Neighbor-Joining phylogenetic tree and discriminant analysis of principal component also showed close relatedness among three chicken varieties namely AS, HI, and JF. Conclusion: The results reflected that indigenous chicken of Bangladesh still possess rich genetic diversity but weak differentiation among the studied populations. This finding provides some important insight on genetic diversity measures that could support the designing and implementing of future breeding plans for indigenous chickens of Bangladesh.