• Animal Bioscience
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• v.36 no.10
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• pp.1499-1507
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• 2023

Objective: The study investigated the origin of the Akhal-Teke horse using genome-wide single-nucleotide polymorphism (SNP) data and mitochondrial hypervariable region 1 (HVR-1) nucleotide sequences Methods: Genome-wide SNP data from 22 breeds (481 horses) and mitochondrial HVR-1 sequences from 24 breeds (544 sequences) worldwide to examine the origin of the Akhal-Teke horse. The data were analyzed using principal component analysis, linkage disequilibrium analysis, neighbor-joining dendrograms, and ancestry inference to determine the population relationships, ancestral source, genetic structure, and relationships with other varieties. Results: A close genetic relationship between the Akhal-Teke horse and horses from the Middle East was found. Analysis of mitochondrial HVR-1 sequences showed that there were no shared haplotypes between the Akhal-Teke and Tarpan horses, and the mitochondrial data indicated that the Akhal-Teke horse has not historically expanded its group. Ancestral inference suggested that Arabian and Caspian horses were the likely ancestors of the Akhal-Teke horse. Conclusion: The Akhal-Teke horse originated in the Middle East.

• Development and Reproduction
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• v.18 no.4
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• pp.275-286
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• 2014

To successful molecular breeding, identification and functional characterization of breeding related genes and development of molecular breeding techniques using DNA markers are essential. Although the development of a useful marker is difficult in the aspect of time, cost and effort, many markers are being developed to be used in molecular breeding and developed markers have been used in many fields. Single nucleotide polymorphisms (SNPs) markers were widely used for genomic research and breeding, but has hardly been validated for screening functional genes in olive flounder. We identified single nucleotide polymorphisms (SNPs) from expressed sequence tag (EST) database in olive flounder; out of a total 4,327 ESTs, 693 contigs and 514 SNPs were detected in total EST, and these substitutions include 297 transitions and 217 transversions. As a result, 144 SNP markers were developed on the basis of 514 SNP to selection of useful gene region, and then applied to each of eight wild and culture olive flounder (total 16 samples). In our experimental result, only 32 markers had detected polymorphism in sample, also identified 21 transitions and 11 transversions, whereas indel was not detected in polymorphic SNPs. Heterozygosity of wild and cultured olive flounder using the 32 SNP markers is 0.34 and 0.29, respectively. In conclusion, we identified SNP and polymorphism in olive flounder using newly designed marker, it supports that developed markers are suitable for SNP detection and diversity analysis in olive flounder. The outcome of this study can be basic data for researches for immunity gene and characteristic with SNP.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.5
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• pp.2625-2628
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• 2016

ABCC11 is reported to be associated with breast cancer. However, whether ABCC11 polymorphisms relate to breast cancer risk remains unclear. This study aimed to evaluate any association of a single nucleotide polymorphism (SNP), rs17822931, in ABCC11 with breast cancer in Koreans. Genomic DNA samples of 170 women with breast cancer and 100 controls were assessed for SNP rs17822931 of ABCC11 by single-strand conformation polymorphism (SSCP) and DNA sequencing. A 27-bp deletion (${\Delta}27$) of ABCC11 was analyzed by PCR amplification. The genotype of SNP rs17822931 was confirmed to be AA in all samples from breast cancer patients and ${\Delta}27$ was found in none of the samples. Our finding indicated that the SNP rs17822931 in ABCC11 is not associated with breast cancer. However, this study does provide information on fundamental genetic aspects of ABCC11 with regard to breast cancer risk in Koreans.

• Proceedings of the Plant Resources Society of Korea Conference
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• v.18 no.1
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• pp.143-143
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• 2005

• Bulletin of the Korean Chemical Society
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• v.31 no.7
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• pp.1902-1906
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• 2010

A microchip electrophoresis (ME) method was developed using a programmed field strength gradients (PFSG) for the single nucleotide polymorphism (SNP) based fast identification of cattle breeds. Four different Korean cattle (Hanwoo) and Holstein SNP markers amplified by allele-specific polymerase chain reaction were separated in a glass microchip filled with 0.5% poly(ethyleneoxide) ($M_r$ = 8 000 000) by PFSG as follows: 750 V/cm for 0 - 14 s, 166.7 V/cm for 14 - 31 s, 83.3 V/cm for 31 - 46 s, and 750 V/cm for 46 - 100 s. The cattle breeds were clearly distinguished within 45 s. The ME-PFSG method was 7 times and 5 times faster than the constant electric field ME method and the capillary electrophoresis- PFSG method, respectively, with a high resolving power ($R_s$ = 5.05 - 9.98). The proposed methodology could be a powerful tool for the fast and simultaneous determination of SNP markers for various cattle breeds with high accuracy.

• The Korean Journal of Mycology
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• v.43 no.4
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• pp.231-238
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• 2015

Genome-wide reanalyzed data of 25 Flammulina strains were compared against the reference genome (KACC42780) to establish a genome-wide single nucleotide polymorphism (SNP). The rate of mapping differences between the strains reflected in the strain variation in its result. Genome-wide SNPs distribution divided into types of homozygous SNP and heterozygous SNP moreover all of the strains demonstrated a wide variation in all of the regions. In the further study of topological relationship between the collected strains, phylogenetic tree was separated into 3 major groups. Group I contained F. velutipes var. related strains of ASI 4062, 4148, 4195. Group 2 contained strains that are different species of ASI 4188 F. elastica, ASI 4190 F. fennae, and ASI 4194 F. rossica. The other 19 strains F. velutipes were classified as a single group. However, further experiment to discriminate its genetic relationship between the white group and brown group did not verify its validity. The inferred tree exhibited a phylogenetic relationship between Korea white fruitbody forming strains of ASI 4210, 4166, 4178 and Japan white fruitbody forming strains of ASI 4209, 4167 confirmed to be genetically closely related.

• Journal of Life Science
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• v.33 no.12
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• pp.1025-1035
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• 2023

In this study, we analyzed SNPs that appear between Korean and Chinese Scapharca subcrenata using the nucleotide sequence data of S. subcrenata analyzed by genotyping by sequencing (GBS). To distinguish the country of origin for S. subcrenata in Korean and Chinese, we developed a primer set as single nucleotide polymorphism (SNP) markers for quantitative real-time PCR (qPCR) analysis and validated by sequencing SNPs. A total of 180 samples of S. subcrenata were analyzed by genotyping by sequencing, and 15 candidate SNPs were selected. SNP marker selection for country of origin were identified through real-time qPCR. Insertion 1 and SNP 21 markers showed the most distinct separation between the sequence types as well as the country of origin through qPCR, with the observed amplification patterns matching the expected outcomes.. Additionally, in a blind test conducted by mixing samples of S. subcrenata at random, Insertion 1 showed 74% accuracy, 52% sensitivity, and 96% specificity, and SNP 21 showed 86% accuracy, 79% sensitivity, and 93% specificity. Therefore, the two SNP markers developed are expected to be useful in verifying the authenticity of the country of origin of S. subcrenata when used independently or in combination.

• The Journal of Korean Academy of Prosthodontics
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• v.49 no.4
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• pp.341-345
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• 2011

Genetic association study has been progressed in medicine along with advance in genetic technology. It focused on the individual differences in genotype due to errors occurring during DNA duplication, which can cause vulnerability to specific diseases. Polymorphism defines the varieties in phenotype due to those genetic variations. Polymorphism due to change in one DNA base sequence is called as a Single Nucleotide Polymorphism. In the near future, the evaluation of relative risk to specific disease according to SNP will be essential part of fundamental of medicine for the diagnosis, treatment and prevention. Dental caries and periodontal diseases has been first subject to genetic association study in dentistry and broaden out to other areas like bone formation and resorption. This article presents the current state of genetic association study and its application to dentistry.

• The Korean Journal of Applied Statistics
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• v.16 no.2
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• pp.195-202
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• 2003

Haplotype analysis in SNP is very useful for the study of complex genetic disease due to low cost and high efficiency comparing to individual analysis of each SNP, and is functionally important in biological view. But, the gametic phase of haplotypes is usually unknown in SNP group, and it is difficult to predict haplotype proportions. In this study, haplotype proportions were estimated using EM algorithm from diploid data of SNP group in solid tumor group and normal group. From these results, linkage disequilibrium among SNPs was analyzed.

• International Journal of Oral Biology
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• v.31 no.3
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• pp.107-112
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• 2006

Aldehyde dehydrogenase (ALDH) plays an important role in alcohol metabolism; ALDH is responsible for the oxidation of acetaldehyde generated during alcohol oxidation. ALDH is also known to oxidize various other endogenous and exogenous aldehydes. Cytochrome P-450 2E1 (CYP2E1), a liver microsomal enzyme, also metabolizes acetaldehyde and ethanol and can be induced by other inducers including acetone and ethanol. We examined single nucleotide polymorphisms (SNP) of ALDH and CYP2E1 genotypes in Korean. Restriction fragment length polymorphism (RFLP) method was used to determine ALDH and CYP2E1 SNP. Mutation in ALDH was 60% (heterozygote 46.7% and homozygote 13.3%) among 15 cases. CYP2E1 mutation was 52.7% (heterozygote 47.4% and homozygote 5.3%) among 19 cases.