• Environmental Mutagens and Carcinogens
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• v.23 no.1
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• pp.16-22
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• 2003

Single nucleotide polymorphisms (SNPs) are alterations in DNA base that occur most frequently throughout the human genome. The SNPs of DNA repair genes, hMLH1, hMSH2 and ATM, among 100 Korean people were analyzed using Dynamic Allele specific Hybridization (DASH) techniques. Mutation at the position of exon 38 (GA) and exon 10 (CG) of ATM gene, mutation at the position of exon 8 (AG), and exon 1 (AG) of hMLH1 gene and exon 14 (AG) of hMSH2 gene were investigated. No mutation at the selected position of ATM gene and hMSH1 gene was found. However, while there was no mutation at the position of exon of hMSH2 gene, mutation was found at the promotion region (CT) with the frequency of 24% CC, 36% CT and 62% TT genotyes. This results might be used as baseline data for research on SNP of Korean population.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.2
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• pp.151-157
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• 2015

Fatness qualities in pigs measured by the amount of fat deposition and composition of fatty acids (FAs) in pork have considerable effect on current breeding goals. The stearoyl-CoA desaturase (SCD) gene plays a crucial role in the conversion of saturated FAs into monounsaturated FAs (MUFAs), and hence, is among the candidate genes responsible for pig fatness traits. Here, we identified a single nucleotide polymorphism (SNP, $c.^*2041T$ >C) in the 3' untranslated region by direct sequencing focused on coding and regulatory regions of porcine SCD. According to the association analysis using a hundred of Berkshire pigs, the SNP was significantly associated with FA composition (MUFAs and polyunsaturated FAs [PUFAs]), polyunsaturated to saturated (P:S) FA ratio, n-6:n-3 FA ratio, and extent of fat deposition such as intramuscular fat and marbling (p<0.05). In addition, the SNP showed a significant effect on the SCD mRNA expression levels (p = 0.041). Based on our results, we suggest that the SCD $c.^*2041T$ >C SNP plays a role in the gene regulation and affects the fatness qualities in Berkshire pigs.

• Korean Journal of Schizophrenia Research
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• v.23 no.2
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• pp.71-77
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• 2020

Objectives: Tardive dyskinesia (TD) is a movement disorder that is characterized by hyperkinetic movements. Previous studies have suggested that the serotonergic systems are correlated with TD vulnerability. In this study, the association between a single-nucleotide polymorphism (SNP) of the serotonin 1A receptor gene (HTR1A) rs6295 and TD was investigated. Methods: We investigated whether HTR1A rs6295 SNP is associated with antipsychotic-induced TD in 280 Korean patients with schizophrenia. Patients with schizophrenia having TD (n=105) and those without TD (n=175) were matched for their antipsychotic exposures and other relevant variables. The HTR1A rs6295 SNP was analyzed using polymerase chain reaction (PCR)-based methods. Results: There was no significant difference in the distribution of genotypic (χ²=2.70, p=0.26) and allelic (χ²=1.87, p=0.17) frequencies between the patient groups with TD and without TD. There was no significant difference in total abnormal involuntary movement scale score (F=0.39, p=0.68) among the genotype group either. Conclusion: Although there were no differences in genotypic and allelic frequency between patient groups with and without TD, further studies on association of TD with other SNPs of HTRA1 are needed to understand the pathophysiological mechanism of TD.

• Korean Journal of Poultry Science
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• v.41 no.1
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• pp.29-37
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• 2014

The Feather Color of chicken is considered as most obvious, and the purpose of this study is to identify the genotype following the SNP of MC1R, MITF and TYRP1, which are genes related to Feather Color, and develop a SNP marker that can be classified per breed. When a haplotype is observed through the combination of markers, a Korean Native Chicken can especially be distinguished when it is a CGG type in the SNP combination of the MC1R gene. In case of the TAG, TGG and TAA types, only Araucana was identified, and for the CAA type, Leghorn could specifically be distinguished. In the SNP combination of TYRP1 gene, only Leghorn was differentiated in case of the TTTCA and CCTCA types, and only Silky Fowl was identified in case of the CTTTA type. The SNP combination of MC1R gene enabled for Korean Native Chicken, Leghorn, and Araucana to be distinguished and each of the SNP and combination of TYRP1 gene allowed for all 4 breeds to be classified. If many researches are conducted about genetic polymorphism between breeds, then it is considered that the differences between breeds will be understood from a molecular biological aspect instead of simply distinguishing the breeds through Feather Color.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.21 no.1
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• pp.240-246
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• 2020

This study was conducted to develop specific Single Nucleotide Polymorphism (SNP) markers to identify the genetic characteristics and breed of White Hanwoo (WH) using a molecular biological method. SNP genotyping was performed with an Illumina Bovine HD 777K SNP chip using DNA extracted from 48 Hanwoo and 22 WH. The minor allele frequency (MAF) difference of each SNP was calculated and the statistical significance (P-value) of the MAF difference was calculated through Fisher's Exact test (Genotype). SNPs with 100% difference in the MAF difference were selected based on marker selection criteria. The nine SNP markers with genetic differences were selected. The selected markers have different alleles as being Hanwoo- and WH- specific. Therefore, based on these results, it can be concluded that the Hanwoo and WH varieties can be clearly distinguished by using these SNPs. So, the patent of the WH breed identification markers was registered. WH is a breed that shows the characteristics of a Korean native species that is separate from the native Hanwoo. It is expected that genetic characteristics research on the WH can be used to identify the breed and as a knowledge base for enhancing the value of breeding stock.

• Korean Journal of Agricultural Science
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• v.46 no.1
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• pp.27-31
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• 2019

It is well documented that intensive selection in dairy cattle for economic value such as increased milk yield led to a decline in reproductive performance. Recent studies using genome-wide association studies (GWASs) discovered candidate genes involved in the lower fertility including embryo development and conception rates. However, the information, which showed a lower reproductive performance, is limited to dairy cattle, especially Holstein, and the candidate genes were not examined in the Korean native cattle Hanwoo which has been intensively selected and bred for meat in the last few decades. We selected the candidate genes WBP1 and PARM1 reported to be associated with cow and/or heifer conception in dairy cattle and analyzed the genotype because those genes have non-synonymous single nucleotide polymorphisms (SNPs). To determine the single base change, we used the high resolution melting (HRM) assay which is rapid and cost-effective for a small number of genes. We found that most heifers with higher conception (1: service per conception) have the AA genotype coding Threonine rather than Proline in the WBP1 gene. We did not detect an association for a SNP in PARM1 in our analysis. In conclusion, the genetic variation of WBP1 can be used as a selective marker gene to improve reproductive performance, and HRM assay can be used to identify common SNP genotypes rapidly and cost effectively.

• Food Science of Animal Resources
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• v.32 no.6
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• pp.776-782
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• 2012

Marbling (intramuscular fat) is the most economically important meat quality trait in Hanwoo (Korean cattle). The endothelial differentiation G-protein coupled receptor 1 (EDG1) gene, involved in blood vessel formation, is located within the genomic region of a quantitative trait locus (QTL) for marbling on bovine chromosome 3. Thus, the EDG1 gene can be considered as a positional and functional candidate gene for meat quality in beef cattle. This study aimed to identify single nucleotide polymorphisms (SNPs) in the EDG1 gene and to evaluate their associations with carcass traits in Hanwoo population. We have sequenced a fragment of 5'-UTR of the EDG1 gene and identified one SNP. Genotyping of the g.166A>G SNP marker was carried out using PCR-RFLP analysis in 309 Hanwoo steers in order to evaluate their association with carcass traits. The g.166A>G SNP marker showed a significant effect on the marbling score. Animals with the GG genotype had higher marbling score compared with AA and AG genotypes (p<0.05). This SNP marker also showed a significant additive effects for the marbling score (p<0.05). These results suggest that the EDG1 gene can be used as a molecular marker for DNA marker-assisted selection in order to increase the levels of the marbling score in Hanwoo.

• Communications for Statistical Applications and Methods
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• v.15 no.2
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• pp.265-271
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• 2008

It is commonly believed that diseases of human or economic traits of livestock are caused not by single genes acting alone, but multiple genes interacting with one another. This issue is difficult due to the limitations of parametric-statistic methods of gene effects. So we introduce multifactor-dimensionality reduction(MDR) as a methods for reducing the dimensionality of multilocus information. The MDR method is nonparametric (i. e., no hypothesis about the value of a statistical parameter is made), model free (i. e., it assumes no particular inheritance model) and is directly applicable to case-control studies. Application of the MDR method revealed the best model with an interaction effect between the SNPs, SNP1 and SNP3, while only one main effect of SNP1 was statistically significant for LMA (p < 0.01) under a general linear mixed model.

• Proceedings of the Korean Information Science Society Conference
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• 2006.06a
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• pp.19-21
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• 2006

Single Nucleotide Polymorphism(SNP)는 인간 유전자 서열의 0.1%에 해당하는 부분으로 이는 각 개인의 체질 및 각종 유전질환과 밀접한 관련이 있다고 알려져 있다. 최근 이 SNP정보의 패턴을 이용 질병의 진단 및 치료에 연관지으려는 노력이 시도되고 있다. 그러나 아직 SNP를 이용한 효율적인 분석방법에 대한 전산학적 연구는 많지 않다. 본 논문에서는 대표적인 패턴인식기 중 하나인 Support Vector Machine(SVM)을 이용 한국인의 대표적인 유전질환으로 알려진 만성간염에 대해서 관련된 SNP에 대한 패턴 인식율 측정을 실험하였다. 실험 데이터는 간 및 소화기 질환 유전체 센터에서 얻어진 만성간염 환자와 관련 SNP정보를 사용하였으며, 실험 결과 전체 SNP 정보를 모두 가지는 환자그룹에 대한 학습인식율이 66.46%로 나타났으며, 부분그룹에서는 72.91%로 높은 인식율을 보였다. 이 결과는 SNP 정보를 이용한 만성간염의 초기진단예측에 SVM을 효율적으로 사용할 수 있음을 보인다.

• Journal of Life Science
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• v.26 no.1
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• pp.1-7
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• 2016

Fatness is one of the most important economic traits in pigs. The leptin receptor (LEPR) gene may be a potential candidate for the fatness quantitative trait locus (QTL) on porcine chromosome 6, due to its position and physiological role. Thus, this study was carried out to evaluate the associations between structural variants in the LEPR gene and economic traits in pigs. We obtained an approximately 114-kb sequence containing the complete genomic DNA of the porcine LEPR gene, using shotgun sequencing of a bacterial artificial chromosome clone. We report the complete genomic structure of the porcine LEPR gene. Dozens of transcription factor-binding sites were found in the 1.2 kb upstream region from the transcription start point. An association study was performed with 550 Duroc pigs for 24 single-nucleotide polymorphisms (SNPs), including 6 SNPs within exons and 18 SNPs within the putative 5‘ regulatory region of the porcine LEPR gene. Among them, one SNP (−790C/G) was significantly associated with backfat thickness and lean meat percentage, whereas the others, including two SNPs with missense polymorphisms, had no effect on any phenotype. These results suggest that SNP −790C/G may be a useful marker for genetic improvements of fatness and leanness in Duroc pigs.