• Korean Journal of Poultry Science
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• v.36 no.4
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• pp.317-322
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• 2009

The chicken major histocompatibility complex (MHC) is known to be associated with disease resistance and susceptibility to several pathogens. The microsatellite marker LEI0258 is physically located between the BG and BF of MHC region and variations near this marker have been well documented. In this report, the LEI0258 marker was used to find specific alleles for the Korean native chicken. The MHC haplotype was analyzed by PCR screening and sequencing of LEI0258 region in four different breeds including black Korean native chicken, brown Korean native chicken, Cornish and Rhode island red. The serologically same MHC haplotypes showed the differences in repeat numbers, a few indels or single nucleotide polymorphisms by sequencing analysis. Even though we could not identify specific alleles for Korean native chickens, the genotypes analyzed in these breeds can give valuable information for the relationships with disease resistance and establishment of breeding strategies for the Korean native chicken.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.2
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• pp.157-165
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• 2002

Genetic variations of seven egg white protein loci in 1,112 samples from eight Asian countries (Yunnan province of China, Mongolia, Nepal, Vietnam, Laos, Thailand, Myanmar, Indonesia) and 360 samples from two improved breeds (Isa Brown, Boris Brown) were investigated by using starch gel and polyacrylamide gel electrophoresis. Five egg white protein loci (Ov, $G_3$, $G_2$, $G_1$ and $Tf_{EW}$) were found to be polymorphic in Asian native chicken populations. The proportion of polymorphic loci ($P_{poly}$) and average heterozygosity ($\bar{H}$) of Asian native populations varied from 0.143 to 0.714 and 0.014 to 0.225, respectively, and were higher than those of improved breeds. The subdivision index ($G_{ST}$) value among 18 native chicken populations in Asia is lower (0.0827) than among improved chicken populations (0.1693). This value means that the degree of subdivision among Asian native populations is lower than among improved breeds and gene constitutions among populations in Asia are similar.

• Journal of Animal Science and Technology
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• v.54 no.6
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• pp.401-409
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• 2012

The objective of this study was to determine genetic variation of five Korean native chicken lines using 30 microsatellite (MS) markers, which were previously recommended by ISAG (International Society for Animal Genetics). The initial study indicated that two microsatellite markers, MCW0284 and LEI0192, were not amplified in these lines and excluded for further analysis. Twenty eight microsatellite markers were investigated in 83 birds from five Korean native chicken lines. The identified mean number of alleles was 4.57. Also, the expected, observed heterozygosity (He, Ho) and polymorphism information content (PIC) values were estimated in these markers and they ranged from 0.31~0.868, 0.145~0.699, and 0.268~0.847, respectively. The results were used for the discrimination of five chicken lines using genetic distance values and also neighbor-joining phylogenetic tree was constructed. Based on the He and PIC values, eighteen markers are enough for the discrimination of these Korean native chicken lines for the expected probability of identity values among genotypes of random individuals (PI), random half sibs ($PI_{half-sibs}$) and random sibs ($PI_{sibs}$). Taken together, these results will help the decision of conservation strategies and establishment of traceability system in this native chicken breed. Also, the use of ISAG-recommended microsatellite markers may indicate that the global comparison with other chicken breeds is possible.

• 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.

• Korean Journal of Poultry Science
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• v.38 no.3
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• pp.191-195
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• 2011

The objectives of this study are to identify specific functional genes which are related with growth and protein structure of the pectoral muscle of Korean native chicken. Pectoral muscle was isolated from three Korean native chickens (KNC, red brown, 12 months old, 2.41 ${\pm}$ 0.24 kg) and three Cornish chickens (16 month old, 2.76 ${\pm}$ 3.0 kg). The subtraction cDNA library was prepared in PCR4 Blunt-TOPO vector. The DNA sequence homology was compared with other breeds and species in GenBank. A clone NDS-81 was found to be unique for the DNA sequence homology with UBX family. Their partial sequence has high homology (98%) with chicken UBX domain D. Chicken UBX domain has chicken (93%), cattle (68%), dog (67%), mouse (64%) and, human (63%) nucleotide sequence homology. Several regions were mutated from T in chicken to C or G in the NDS-81 clone. The first site is LAD in chicken, but it was expressed as (L)RM in clone NDS-81. In this site, amino acids were changed from Ala to Arg, and from Asp to Met. The second site was changed from ER (Arg) in chicken to ED (Asp) in clone NDS-81. They are both containing functional side chains and play an important role in binding other proteins. Therefore, the clone NDS-81 could be a different candidate gene for the UBX family gene and could related with pectoral muscle structure of Korean native chicken.

• Korean Journal of Poultry Science
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• v.37 no.1
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• pp.81-87
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• 2010

To estimate the genetic characteristics and cumulative power of discrimination (CPD) Korean Native Chicken. We used a total of 195 genomic DNAs from four breeds population (Korean Native Red chicken: R, Korean Native Yellow chicken: Y, Korean Native Black chicken: L, Ogal chicken: S). Frequencies of microsatellites markers were used to estimate heterozygosities and genetic distances. The lowest distance (0.05) was observed between the R and L strains and the highest distance (0.158) between the L and S strains. Korean native chicken strains (R, Y, K) have each other comparatively near genetic distance. Cumulative power of discriminate (CPD) was 99.999% by including the 10 microsatellites loci individual identification system. And then matching probability in that two different individuals incidentally have same genotype was estimated to $0.36{\times}10^{-7}$. The system employing the 10 markers therefore provided to be applicable to individual identification in Korea native chicken.

• Korean Journal of Poultry Science
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• v.45 no.3
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• pp.175-182
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• 2018

The carcass and meat quality of new native chicken strains (A, C, and D) being developed in the Golden Seed Project for Samgyetang were compared with a commercial native chicken (Hanhyup No. 3, H) and Baeksemi (white semi broiler, W) strains. In total, 250 male chicks were raised under the same feeding and raising conditions for 5 weeks. After slaughter, the carcass weight and percentage yield of parts from each strain were measured and the physicochemical quality traits (general composition, color values, fatty acid composition, and sensory evaluation) of breast muscles were comparatively analyzed. The carcass weight (875.10 g) of the W strain was significantly heavier than that of the other native chicken strains, while that of A strain (537.54 g) was the lowest. The percentage yield of breast meat was also higher in the W strain than in the other strains. The fat content of W strain was higher than that of the other native chicken strains. The new native chicken strains (A, C, D) had higher contents of linoleic acid (C18:2) than the H strain. The A and D strains especially showed relatively high content of arachidonic acid (C20:4), a characteristic fatty acid in native chicken meats. On the other hand, the fatty acid composition of C strain was similar to that of the W strain. This study provides important information on specific quality characteristics than can be used to select new native chicken lines for breeding program.

• Korean Journal of Poultry Science
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• v.41 no.4
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• pp.305-311
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• 2014

Copy number variation (CNV) is a form of structural variation that shows various numbers of copies in segments of the DNA. It has been shown to account for phenotypic variations in human diseases and agricultural production traits. Currently, most of chicken breeds in the poultry industry are based on European-origin breeds that have been mostly provided from several international breeding companies. Therefore, National Institute of Animal Science, RDA has been trying to restore and improve Korean native chicken breeds (12 lines of 5 breeds) for about 20 years. Thanks to the recent advance of sequencing technologies, genome-wide CNV can be accessed in the higher resolution throughout the genome of species of interest. However, there is no systematic study available to dissect the CNV in the native chicken breed in Korea. Here, we report genome-wide copy number variations identified from a genome of Korean native chicken (Line L) by comparing between the chicken reference sequence assembly (Gallus gallus) and a de novo sequencing assembly of the Korean native chicken (Line L). Throughout all twenty eight chicken autosomes, we identified a total of 501 CNVs; defined as gain and loss of duplication and deletion respectively. Furthermore, we performed gene ontology (GO) analysis for the putative CNVs using DAVID, leading to 68 GO terms clustered independently. Of the clustered GO terms, genes related to transcription and gene regulation were mainly detected. This study provides useful genomic resource to investigate potential biological implications of CNVs with traits of interest in the Korean native chicken.

• Journal of Life Science
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• v.20 no.7
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• pp.1086-1092
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• 2010

To estimate the genetic characteristics and cumulative power of discrimination (CPD) within Korean native commercial chicken, we used a total of 395 genomic DNAs from six breeds population (Korean Native Red chicken: R, Korean Native Yellow chicken: Y, Korean native Commercial Chicken: C, Ogal chicken: S, Hy-Line Brown: H, White Leghorn: W). Genetic diversity indices including mean allele number among loci, unbiased heterozygosity ($h_i$) within locus, effective number of alleles ($N_e$) and polymorphism information content (PIC) as well as the unbiased average heterozygosity (H) among loci in the populations were calculated using the generated allele frequencies by each marker. Frequencies of microsatellites markers were used to estimate heterozygosities and genetic distances. The nearest distance (0.119) was observed between the C and Y strains. The generated unbiased average heterozygosity among loci in each population was integrated to the global formula of CPD and the result demonstrated that the CPD within the six chicken populations was 99.461%.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.12
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• pp.1637-1643
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• 2011

Korean native chickens are a very valuable chicken population in Korea and their prices are higher than that of commercial broilers. In order to discriminate two commercial Korean native chicken populations (CCP1 and CCP2), single nucleotide polymorphisms (SNPs) from mitochondrial (mt) DNA D-loop sequences and LEI0258 marker polymorphisms in the major histocompatibility complex (MHC) region were investigated. A total of 718 birds from nine populations were sampled and 432 mtDNA sequences were obtained. Of these, two commercial Korean native chicken populations (363 birds) were used for investigation of their genetic relationship and breed differentiation. The sequence data classified the chickens into 20 clades, with the largest number of birds represented in clade 1. Analysis of the clade distribution indicated the genetic diversity and relation among the populations. Based on the mtDNA sequence analysis, three selected SNPs from mtDNA polymorphisms were used for the breed identification. The combination of identification probability (Pi) between CCP1 and CCP2 using SNPs from mtDNA and LEI0258 marker polymorphisms was 86.9% and 86.1%, respectively, indicating the utility of these markers for breed identification. The results will be applicable in designing breeding and conservation strategies for the Korean native chicken populations and also used for the development of breed identification markers.