• Korean Journal of Poultry Science
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• v.23 no.4
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• pp.177-183
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• 1996

This study was conducted to analyze genetic characteristics of Korean Native Chicken three lines classified on the basis of the feather color and appearance (Red, Yellow, and Black) using DNA fingerprinting method. To estimate the genetic relatedness among breeds and similarities within breeds, we collected blood samples from Korean Native Chicken (KNC), Rhode Island Red (RIR), White Leghorn (WL), and Cornish(CN) and obtained genomic DNA from the blood of 10 individuals randomly selected within the breeds and lines. The genomic DNA samples were digested with restriction enzymes (Hinf J, Hae Ill) and hybridized with various probes (Jeffreys' probes 33.15, 33.6 and M13) after Southern transfer. Genetic similarities within breeds were characterized by band sharing (BS) value, estimated by the DFP band pattern between the pair of lanes. BS values within WL, RIR, and KNC were 0.82, 0.70 and 0.56, respectively. Relative genetic diversity (BS value) of KNC was higher than those two breeds (WL, RIR). Estimation of genetic similarity between KNC lines and control breed (RIR) was 0.32, whereas similarity within KNC lines (6 groups) was 0.50. In this analysis, KNC was showed to have a highly genetic diver-sity at the DNA level, and to be closer in genetic distance to RIR (0.67) than any other breeds.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.8
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• pp.1071-1074
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• 2005

Microsatellite polymorphism and their genetic relationships were estimated using genotype information of 183 dogs from 11 microsatellite loci. The breeds include the indigenous Korean breeds Jindo dog (30), Poongsan dog (20) and Miryang dog (44) together with Chihauhau dog (31) and German Shepherd dog (58). Jindo dogs showed the highest expected heterozygosity (0.796${\pm}$0.030) and polymorphic information contents (0.755) in all populations. The phylogenetic analysis showed the existence of two distinct clusters supported by high bootstrap values: the Korean native dogs and other dogs. They clearly show that Poongsan dog and Miryang dog are closely related to each other when compared with Jindo dog. Microsatellite polymorphism data was shown to be useful for estimating the genetic relationship between Korean native dogs and other dog breeds, and also can be applied for parentage testing in those dog breeds.

• Korean Journal of Poultry Science
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• v.43 no.2
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• pp.63-76
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• 2016

The genetic diversity of Korean native chicken is important for conservation of native chicken breeds and developing economically valuable traits in Korea. In this review, various types of genetic markers using Korean native chickens were investigated, which are mtDNA variations, microsatellite markers, markers in Major Histocompatibility Complex (MHC), and single nucleotide polymorphisms (SNPs). These genetic markers are suitable for breed discrimination and diversity studies because of their high polymorphism status. Thus, the purpose of this study was to summarize the genetic markers developed in the Korean native chickens and diversity studies using these breeds. Ultimately, these markers can be used for the future studies for understanding of genetic characteristics.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.11
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• pp.1547-1554
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• 2016

To assess genetic diversity and maternal origin of Turkish and Iranian native chicken breeds, we analyzed the mtDNA D-loop sequences of 222 chickens from 2 Turkish (Denizli and Gerze) and 7 Iranian (White Marandi, Black Marandi, Naked Neck, Common Breed, Lari, West Azarbaijan, and New Hampshire) native chicken breeds, together with the available reference sequences of G. gallus gallus in GenBank. The haplotype diversity was estimated as $0.24{\pm}0.01$ and $0.36{\pm}0.02$ for Turkish and Iranian populations, respectively. In total, 19 haplotypes were observed from 24 polymorphic sites in Turkish and Iranian native chicken populations. Two different clades or haplogroups (A and E) were found in Turkish and Iranian chickens. Clade A haplotypes were found only in White Marandi, Common Breed and New Hampshire populations. Clade E haplotypes, which are quite common, were observed in Turkish and Iranian populations with 18 different haplotypes, of which Turkish and Iranian chickens, Clade E, haplotype 1 (TRIRE1) was a major haplotype with the frequency of 81.5% (181/222) across all breeds. Compared to red jungle fowl, Turkish and Iranian chicken breeds are closely related to each other. These results suggest that Turkish and Iranian chickens originated from the same region, the Indian subcontinent. Our results will provide reliable basic information for mtDNA haplotypes of Turkish and Iranian chickens and for studying the origin of domestic chickens.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.7
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• pp.903-909
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• 2004

The variability of mtDNA hypervariable segment I (HVS I) sequences was investigated in a total of 48 birds belonging to 12 Chinese native chicken breeds. Sixteen haplotypes were identified from 35 polymorphic nucleotide sites which accounted for 6.4% of a sequenced 544 bp fragment. Diversity analysis of the haplotypes showed that Tibetan, Langshan and Henan cockfight chicken had only one haplotype, while ancient haplotypes existed in Taihe silky and Chahua chicken. Phylogenetic analysis of the haplotypes suggested that Chinese native chicken breeds shared 5 maternal lineages and some breeds would share the same maternal lineage, regardless of their external features and ecological types. Both divergent and phylogenetic analysis of the haplotypes indicated the close genetic relationships between the Chinese native chicken breeds and G. g. gallus and G. g. spadiceus from different areas, which implied that G. g. gallus and G. g. spadiceus were the original ancestors of the Chinese native chicken breeds.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.9
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• pp.1263-1269
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• 2014

Comprehensive information on genetic diversity and introgression is desirable for the design of rational breed improvement and conservation programs. Despite the concerns regarding the genetic introgression of Western pig breeds into the gene pool of the Korean native pig (KNP), the level of this admixture has not yet been quantified. In the present study, we genotyped 93 animals, representing four Western pig breeds and KNP, using the porcine SNP 60K BeadChip to assess their genetic diversity and to estimate the level of admixture among the breeds. Expected heterozygosity was the lowest in Berkshire (0.31) and highest in Landrace (0.42). Population differentiation ($F_{ST}$) estimates were significantly different (p<0.000), accounting for 27% of the variability among the breeds. The evidence of inbreeding observed in KNP (0.029) and Yorkshire (0.031) may result in deficient heterozygosity. Principal components one (PC1) and two (PC2) explained approximately 35.06% and 25.20% of the variation, respectively, and placed KNP somewhat proximal to the Western pig breeds (Berkshire and Landrace). When K = 2, KNP shared a substantial proportion of ancestry with Western breeds. Similarly, when K = 3, over 86% of the KNP individuals were in the same cluster with Berkshire and Landrace. The linkage disquilbrium (LD) values at $r^2_{0.3}$, the physical distance at which LD decays below a threshold of 0.3, ranged from 72.40 kb in Landrace to 85.86 kb in Yorkshire. Based on our structure analysis, a substantial level of admixture between Western and Korean native pig breeds was observed.

• Asian-Australasian Journal of Animal Sciences
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• v.9 no.4
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• pp.405-410
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• 1996

Phylogenetic analyses were carried out using four Indonesian native chicken breeds; Kampung, Bangkok, Pelung and Kedu. Gene frequencies of four blood group (A, B, D and E) and eight electrophoretic loci (akp, Akp-2, Es-1, Amy-1, Alb, Tf, Pas and Pa-1) were examined. Geographical and breed specific trends in the gene frequencies were not found in the local population of Kampung breed or in four native breeds. The values of average heterozygosity were estimated as 0.35-0.45. Genetic distances among the local populations of Kampung breed and other native breeds were comparatively small. In a cluster analysis, the Bangkok breed and Kampung E population showed distance from another cluster. The coefficient of gene differentiation for local populations of Kampung breed was estimated as 0.099.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.10
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• pp.1369-1378
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• 2006

This is the first study in which genetic variability and relationships of a large number of Japanese chicken breeds were revealed along with those of several foreign breeds by using microsatellite DNA polymorphisms. Twenty-eight breeds (34 populations) of native Japanese chickens and seven foreign breeds or varieties were analyzed. The mean number of alleles per locus, the proportion of the polymorphic loci, and the expected average heterozygosity ranged from 1.75 to 4.70, from 0.55 to 1.00, and from 0.21 to 0.67, respectively. Microsatellite alleles being unique to a particular population were detected in some populations. The $D_A$ genetic distance between populations was obtained from allele frequency for every pair of the populations to construct a neighbor-joining tree. According to the phylogenetic tree, excluding a few exceptions, native Japanese chicken breeds and foreign breeds were clearly separated from each other. Furthermore, the tree topology divided native Japanese chickens into four main classes, which was almost in accordance with the classification based on body morphology; that is, (1) Cochin type, (2) Malay type, (3) layer type, and (4) intermediate type between Malay and layer types. This is the first finding for native Japanese chickens.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.10
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• pp.1399-1405
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• 2014

The effective management of endangered animal genetic resources is one of the most important concerns of modern breeding. Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. This study aimed to analyze the genetic diversity and population structure of six Korean native chicken breeds (n = 300), which were compared with three imported breeds in Korea (n = 150). For the analysis of genetic diversity, 30 microsatellite markers from FAO/ISAG recommended diversity panel or previously reported microsatellite markers were used. The number of alleles ranged from 2 to 15 per locus, with a mean of 8.13. The average observed heterozygosity within native breeds varied between 0.46 and 0.59. The overall heterozygote deficiency ($F_{IT}$) in native chicken was $0.234{\pm}0.025$. Over 30.7% of $F_{IT}$ was contributed by within-population deficiency ($F_{IS}$). Bayesian clustering analysis, using the STRUCTURE software suggested 9 clusters. This study may provide the background for future studies to identify the genetic uniqueness of the Korean native chicken breeds.

• Korean Journal of Poultry Science
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• v.25 no.2
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• pp.55-64
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• 1998

This study was carried out to investigate the postmortem changes in physico-chemical characteristics of chicken meat with different breeds. Thigh and breast meats from Korean Native Chicken(KNC, 15-wk old), Wangchoo(15-wk old), and broiler(7-wk old) were stored at 5 ˚C. Differences in postmortem pH changes were not recognized among breeds, and pH showed by the lowest value at the 1st day of postmortem in all breeds. Breast meat had tendency to drop pH faster than thigh meat. Heme pigment contents showed no differences among breeds. KNC showed the lowest cholesterol contents in all breeds, total collagen contents showed the lowest value at the 1st day of postmortem, and thereafter it was gradually increased. Heat soluble collagen contents was lowest in Wangchoo. Water soluble and salt soluble protein showed the lowest extractability at the 1st day of storage. Broiler showed the highest extractability of these proteins and Wangchoo showed the lowest. Water holding capacity(WHC) had increasing tendency whilst cooking loss had decreasing tendency by the ageing. WHC of breast and thigh meat showed the highest values in KNC and broiler, respectively. Myofibrillar fragmentation index (MFI) was significantly increased in all breeds by the ageing. Breast and thigh meat showed almost same MFI in KNC and broiler, and in KNC and Wangchoo, respectively. Hardness of breast meat showed decreasing tendency by the ageing.