• Journal of Life Science
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• v.25 no.11
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• pp.1204-1213
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• 2015

A comprehensive analysis of the population structure of the sandfish (Arctoscopus japonicas), the most abundant fishery resource in the East Sea of Korea, has not been carried out, despite its importance in Korea. The present study examined the genetic diversity and differences between five populations (two Japanese and three Korean populations) of A. japonicas captured in the East Sea using both the 401 bp sequence of mitochondrial DNA (mtDNA, cytochrome b) and five microsatellite DNA (msDNA) markers. The results of the analysis using the Cyt b sequence revealed 27 haplotypes. Based on msDNA variations, the estimated expected heterozygosity (H_E) in each population ranged from 0.68 (Gampo, Korea) to 0.7765 (Erimo, Japan). Pairwise F_ST and AMOVA tests using both the Cyt b sequence and msDNA data pointed to significant differences between the Korean and Japanese populations (mtDNA; F_ST=0.2648, p<0.05, msDNA; F_ST=0.0814, p<0.05). These results were similar to the results of UPGMA, PCA, and structure analysis. In these analyses, the five populations were assigned to two groups (Korean populations and Japanese populations). These results shed light on the genetic diversity and relationships of A. japonicas and contribute to research on the evaluation, conservation, and utilization of Korean A. japonicas as genetic resources.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.3
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• pp.316-322
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• 2013

In order to evaluate the genetic diversity and discrimination among five Korean native chicken lines, a total of 86 individuals were genotyped using 150 microsatellite (MS) markers, and 15 highly polymorphic MS markers were selected. Based on the highest value of the number of alleles, the expected heterozygosity (He) and polymorphic information content (PIC) for the selected markers ranged from 6 to 12, 0.466 to 0.852, 0.709 to 0.882 and 0.648 to 0.865, respectively. Using these markers, the calculated genetic distance (Fst), the heterozygote deficit among chicken lines (Fit) and the heterozygote deficit within chicken line (Fis) values ranged from 0.0309 to 0.2473, 0.0013 to 0.4513 and -0.1002 to 0.271, respectively. The expected probability of identity values in random individuals (PI), random half-sib ($PI_{half-sibs}$) and random sibs ($PI_{sibs}$) were estimated at $7.98{\times}10^{-29}$, $2.88{\times}10^{-20}$ and $1.25{\times}10^{-08}$, respectively, indicating that these markers can be used for traceability systems in Korean native chickens. The unrooted phylogenetic neighbor-joining (NJ) tree was constructed using 15 MS markers that clearly differentiated among the five native chicken lines. Also, the structure was estimated by the individual clustering with the K value of 5. The selected 15 MS markers were found to be useful for the conservation, breeding plan, and traceability system in Korean native chickens.

• Journal of Animal Science and Technology
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• v.62 no.6
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• pp.790-800
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• 2020

The Yeonsan Ogye (YO) chicken is a natural heritage of Korea, characterized by black feathers, skin, bones, eyes, and comb. The purebred of YO population has been reared under the natural mating system with no systematic selection and breeding plan. The purpose of this study was to identify the genetic diversity and find the optimal number of population sub-division using 12 polymorphic microsatellite (MS) markers to construct a pedigree-based breeding plan for the YO population. A total of 509 YO birds were used for this study. Genetic diversity and population structure analysis were conducted based on the MS marker genotype information. The overall average polymorphic information content value and expected heterozygosity of the population were 0.586, and 0.642, respectively. The K-mean cluster analysis based on the genetic distance result confirmed that the current YO population can be divided into three ancestry groups. Individuals in each group were evaluated based on their genetic distance to identify the potential candidates for a future breeding plan. This study concludes that a future breeding plan with known pedigree information of selected founder animals, which holds high genetic diversity, could be the best strategy to ensure the conservation of the Korean YO chicken population.

• Korean Journal of Agricultural Science
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• v.48 no.4
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• pp.693-702
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• 2021

The aim of this study was to analyze the genetic diversity and distance of the Korean native black goat line. Thus far, this Korean native black goat line has not been studied intensively, especially in genetic diversity and relationship studies in comparison with other breeds. In total, eleven microsatellite (MS) markers were used to evaluate alleles from 391 Korean native black goats and foreign hybrid animals. The genetic diversity index was evaluated based on the allele distributions. Four Korean native black goat lines showed expected ranges of observed heterozygosity, expected heterozygosity, and polymorphism information content (PIC) values for use in genetic diversity research (0.509 - 0.643, 0.434 - 0.623 and 0.356 - 0.567). Lines from the Korean native black goat and foreign hybrid were clearly separated according to principal coordinates analysis (PCoA), phylogenetic tree and tended to be clustered in each Korean native black goat line. Thus, this study can be used for analyzing the genetic relationships between Korean native black goats and foreign breeds for line preservation and for fundamental information to determine breed improvement strategies.

• The Korean Journal of Malacology
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• v.28 no.3
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• pp.269-274
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• 2012

The genetic variation of Ark Shell, Scapharca broughtonii black was estimated using six polymorphic microsatellite (MS) loci in 443 individuals collected from five populations in Korea. The mean numbers of alleles per locus in five populations were 10-28. The mean number of alleles per locus in Jinhae Hatchery (JHH) population showed the least value as 15.5, but that in Gangjin (GJ) population showed the most value as 20.3. The mean expected heterozygosity in Saryangdo (SR) population showed the least value as 0.817, but that in Gangjin (GJ) population showed the most value as 0.831. In Jinhae hatchery(JHH) population, the mean expected heterozygosity was 0.822, there was no significant difference from those of wild population. The $F_{ST}$ values in Gangjin (GJ) population showed significant difference from those of the other populations, which revealed Gangjin (GJ) population is genetically different from the other populations. The $F_{ST}$ values among Jinhae Hatchery (JHH) population, Jinhae (JH) population and Saryangdo (SR) population showed lower values than the others, which implies there was a gene flow among these three populations. The $F_{ST}$ value and genetic distance between Jinhae (JH) population and Saryangdo (SR) population showed the least value as 0.0001 and 0.0386, indicating that these two populations were genetically the same.

• Animal Bioscience
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• v.37 no.4
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• pp.600-608
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• 2024

Objective: In this study, we aimed to evaluate the usability single nucleotide polymorphisms (SNPs) for parentage testing of horse breeds in Korea. Methods: The genotypes of 93 horse samples (38 Thoroughbred horses, 17 Jeju horses, 20 Quarter horses, and 18 American miniature horses) were determined using 15 microsatellite (Ms) markers (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG10, LEX3, and VHL20) and 101 SNP markers. Results: Paternity tests were performed using 15 Ms markers and 101 SNP markers in Thoroughbred horses and Quarter horses. AHT5, ASB2, ASB17, ASB23, CA425, HMS7, HTG10, and LEX3 did not follow Mendelian inheritance in Thoroughbred horses, whereas in Quarter horses, only AHT4, ASB2, and HMS2 showed Mendelian inheritance, consequently, paternity was not established. Meanwhile, 31 markers, including MNEc_2_2_2_98568918_BIEC2_502451, in Thoroughbred horses, and 30 markers, including MNEc_2_30_7430735_BIEC2_816793, in Quarter horses did not conform with Mendelian inheritance and therefore, could not be used for establishing parentage. Conclusion: The possibility of replacing Ms markers with SNP markers for paternity testing in horses was confirmed. However, further research using more samples is necessary.

• Journal of Animal Science and Technology
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• v.51 no.4
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• pp.273-282
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• 2009

DNA marker information is used to identify or distinguish cattle breeds or individual animal. The purpose of this study was to apply Bovine Genotypes Kit Version 1.1/2.1 to bovine DNA samples (National Institute of Animal Science) taken from Australian / American beef (n=148), Holstein beef (n=170) and Hanwoo cattle (n=177) bred in Jeongeub, Jeonbuk, Korea, so that it could distinguish Hanwoo breed. The Bovine Genotype Kits consist of 16 ISAG MS markers, which were used to build a database of genotypes in each group. Genotyping results were analyzed using MS Tool kit and Phylip program to create phylogenetic tree. The GeneClass 2.0 was used to estimate breed identification. These analyses found that this kit had 100% capacity to distinguish Hanwoo beef, 95.3% capacity to differentiate Australian / American beef and 90% capacity to identify Korean Holstein steer beef. Hence, it is expected that 16 commercial microsatellite markers is useful to categorizegenetic characteristics of Hanwoo breed and also identify Hanwoo individuals and the origin of beef. In particular, it is expected that these markers will be advantageous in discriminating domestic Holstein beef from Australian / Americanbeef.

• 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.

• Korean Journal of Poultry Science
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• v.42 no.1
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• pp.15-26
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• 2015

In this study, genotyping was executed by using 27 microsatellite markers for genetic diversity of 469 Korean Native Chickens [20 population, each population is 24 samples but Hanhyup A line is 13 samples). in total 469 samples were collected from National Institute of Animal Science (Korean Native Chicken (NR, NY, NG, NL and NW), Ogye (NO), Leghorn F,K (NF and NK), Black and Brown cormish (NH and NS), Rhode Island Red C, D (NC and ND), Total is 12 populations] and Hanhyup [H line (HH), F line (HF), G line (HG), V line (HV), S line (HS), W line (HW), Y line (HY), A line (HA), total is 8 populations]. [The allele number were observed 5 (ADL0268) to 20 (MCW0127) each markers. Observed heterozygostiy ($H_{obs}$), expected heterozygosity ($H_{exp}$), polymorphism Information Content (PIC) were observed 0.359 to 0.677, 0.668 to 0.881 and 0.646 to 0.869, respectively. Using these markers, the calculated the heterozygote deficit within chicken line ($F_{is}$) value each population from mean 0.117. Phylogenetic tree showing the genetic relationship among 20 population using standard genetic distance calculated from 27 microsatellite markers. genetic distances revealed the closest (0.175) between NC and ND. on the other hand, Farthest genetic distances (0.710) revealed between NF and HV. STRUCTURE analysis and Principal Components Analysis (PCA) showed that results of similar phylogenetic tree. The expected probability of identity values on random individuals (Total population and only Hanhyup line) was estimated at $8.80{\times}10^{-83}$ and $3.87{\times}10^{-117}$, respectively. In conclusion, This study shows the useful data that be utilized as a basic data of Korean Native Chicken breeding and development for commercial chicken industry to meet the consumer's demand.

• Journal of Animal Science and Technology
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• v.53 no.1
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• pp.35-42
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• 2011

The study was conducted to select and optimize microsatellite (MS) markers for evaluation of Korean native pig (KNP) populations in order to provide standard for the classification and breed definition of the indigenous breeds. The study also aimed to characterize and classify each KNP populations. A total of 648 pigs from 17 pig populations including six KNP, four Chinese native pig and four commercial pig populations were analyzed with 26 MS markers. KNP populations formed separate cluster from those of Chinese native pig and introduced pig populations. Expected heterozygosity (He) of KNP populations were 0.48~0.55 except two populations with 0.65. Genetic distances between KNP populations were relatively shorter: 0.12-0.34. Among six KNP populations, three showed high genetic uniformity, two showed lower uniformity and one showed high level of impurity and heterozygosity. The results can be used to evaluate and manage animal genetic resources at national scale.