• Plant Breeding and Biotechnology
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• v.6 no.4
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• pp.391-403
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• 2018

Genome resequencing by next-generation sequencing technology can reveal numerous single nucleotide polymorphisms (SNPs) within a closely-related cultivar group, which would enable the development of sufficient SNP markers for mapping and the identification of useful genes present in the cultivar group. We analyzed genome sequence data from 13 Korean japonica rice varieties and discovered 740,566 SNPs. The SNPs were distributed at 100-kbp intervals throughout the rice genome, although the SNP density was uneven among the chromosomes. Of the 740,566 SNPs, 1,014 SNP sites were selected on the basis of polymorphism information content (PIC) value higher than 0.4 per 200-kbp interval, and 506 of these SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers. The 506 KASP markers were tested for genotyping with the 13 sequenced Korean japonica rice varieties, and polymorphisms were detected in 400 KASP markers (79.1%) which would be suitable for genetic analysis and molecular breeding. Additionally, a genetic map comprising 205 KASP markers was successfully constructed with 188 $F_2$ progenies derived from a cross between the varieties, Junam and Nampyeong. In a phylogenetic analysis with 81 KASP markers, 13 Korean japonica varieties showed close genetic relationships and were divided into three groups. More KASP markers are being developed and these markers will be utilized in gene mapping, quantitative trait locus (QTL) analysis, marker-assisted selection and other strategies relevant to crop improvement.

• The Journal of Internal Korean Medicine
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• v.36 no.4
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• pp.547-561
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• 2015

Objectives In this study, we divided Korean asthma patients into excess syndrome or deficiency syndrome groups according to clinical phenotype. Genetic analysis was conducted to investigate the association of exonic SNPs in the CD46 gene polymorphism with the clinical phenotype based on the differentiation syndrome of the bronchial asthma patients.Methods There were 95 healthy patients (control group) and 53 asthma patients. (The deficiency syndrome group included 24 and the excess syndrome group 29). We searched the exonic areas of the CD46 gene in the NCBI website SNPs with <0.01 minor allele frequency (MAF) and <0.01 heterozygosity. We finally selected two SNPs: rs138843816, Ser13Phe and rs7144, 3’-UTR. Hardy-Weinberg equilibrium was calculated using SNPStats.Results There were significant differences in the codominant 1 model and the dominant model between the healthy group and the asthma group. There were significant differences between deficiency syndrome group and the excess syndrome group in the genotype frequencies and in the codominant 1 model, the dominant model, and the log-additive model. The allele frequency of rs7144C showed a significant difference between the deficiency syndrome group and the excess syndrome group. Two-SNP haplotype analysis showed a significant difference in frequency in the deficiency syndrome group and in the excess syndrome group. There were significant differences between the healthy group and the excess syndrome group in the codominant 1 model, the dominant model, and the log-additive model. The frequency of the rs7144 C allele exhibited a significant difference in the demonstration. SNP haplotype analysis between the healthy group and the excess syndrome group showed a significant difference in the frequency of the CT haplotype and the CC haplotype.Conclusions The results indicate that two CD46 SNPs (rs138843816, Ser13Phe and rs7144, 3′–UTR) might be associated with the symptomatic excess syndrome in Korean asthma patients.

• Clinical and Experimental Reproductive Medicine
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• v.33 no.1
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• pp.61-61
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• 2006

Objectives : This study was performed to understand the influence of the methylenetetrahydrofolate reductase (MTHFR C677T and A1298C) genotypes on the spontaneously aborted embryos. Methods : DNA was extracted from tissue samples of 95 spontaneously aborted embryos and 100 samples of normal children randomly and 449 samples of normal adults were selected as the controls. MTHFR genotypes were determined by a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. Results : The aborted embryo group had higher frequency of MTHFR 677CC type (p=0.014) and lower 677CT type (p=0.063) than the controlled child group. The frequency of MTHFR 677CT type was drastically lower than that of controlled adult group (p=0.032). In the MTHFR C677T/A1298C combination, 677CC/1298AC genotype of the aborted embryo was significantly higher (p=0.034) than that of controlled child group, but it was not statistically significant in controlled adult group (p=0.063). Conclusion : MTHFR 677CC and MTHFR 677CC/1298AC genotypes may represent genetic markers for the risk of spontaneously aborted embryos at least in Koreans.

• Journal of Life Science
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• v.23 no.9
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• pp.1088-1095
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• 2013

The swimming crab, Portunus trituberculatus, inhabits seafloor habitats containing sand or pebbles and is widely distributed throughout the world. The present study investigated genetic polymorphisms of 10 microsatellites in 281 samples of P. trituberculatus collected from four locations along the coastal water of the Korean side of the Yellow Sea (Yeonggwang, Taean, Sorea, and Yeonpyeong-do Island). The number of alleles per locus ranged from 50 to 129, with a mean of 69.5. The observed and expected hetrozygosity varied from 0.111 to 1.000 and from 0.609 to 0.979, respectively. The inbreeding coefficients (Fis) varied among the loci from -0.0207 to 0.8175. The genetic differentiation (Fst) was less than 0.05 (range 0.0020-0.0124). Therefore, the four groups of P. trituberculatus appeared to exhibit little genetic differentiation. The lack of differentiation was confirmed in a phylogenetic tree constructed by the unweighted pair group method with the arithmetic average (UPGMA). The hypervariation between the populations and the lack of genetic differentiation may reflect active gene flow among the Yellow Sea populations and the absence of geographical boundaries. The highly polymorphic microsatellite loci will be useful for molecular and phylogenetic studies, as well as stock management, of swimming crab, which is an important fishery resource.

• ANNALS OF ANIMAL RESOURCE SCIENCES
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• v.29 no.4
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• pp.150-157
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• 2018

The Zygote arrest 1 (ZAR1) gene is known to affect early embryonic development in various vertebrates. In this study, we performed the association analysis to check whether there is any significant relationship between semen kinematic characteristics and the ZAR1 gene. To determine semen kinematic characteristics, we measured motility (MOT), straight-line velocity (VSL), curvilinear velocity (VCL), average path velocity (VAP), linearity (LIN), straightness (STR), amplitude of lateral head displacement (ALH), and beat cross frequency (BCF) of spermatozoa in boars. In order to detect single nucleotide polymorphisms (SNPs), we extracted genomic DNA from multiple Duroc boars, and then subsequently used them in sequencing reactions. As a result, three SNPs were detected in the intronic region of ZAR1 gene (g.2435T>C in intron 2, g.2605G>A and g.4633A>C in intron 3 ). SNPs g.2435T>C and g.2605G>A were significantly associated with MOT (p<0.01) and VSL (p<0.05), and g.4633A

• Korean Journal of Food Science and Technology
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• v.37 no.1
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• pp.134-141
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• 2005

To characterize genotypic and phenotypic traits of Staphylococcus aureus isolates (n = 86) from lettuces and raw milk, major virulence-associated genes and antibiotic susceptibility were detected using PCR-based methods and disk diffusion method, respectively. All isolates possessed coagulase gene and showed five polymorphism types [500 bp (2.4%), 580 bp (17.4%), 660 bp (61.6%), 740 bp (17.4%), and 820 bp (1.2%)] due to variable numbers of tandem repeats present within the gene. Two or three different loci of hemolysin gene family were dominant in isolates, 47 of which (55%) possessed combination of hla/hld/hlg-2 genes as the most prevalent types. Among enterotoxin-encoding genes, sea was detected from 32 isolates (37%), sed from 1 isolate (1%), and sea and sed genes were co-detected from 4 isolates (5%), whereas seb, sec, and tsst-1 genes were not detected. All isolates were susceptible to ciprofloxacin, trimethoprim/sulfamethoxazole, oxacillin, and vancomycin, 85 isolates (99%) to penicillin G, 54 isolates (63%) to chloramphenicol, 51 isolates (59%) to erythromycin, and 7 isolates (8%) to clindamycin. Among resistant isolates, seven displayed multiantibiotic-resistance against two different antibiotics.

• The Journal of Internal Korean Medicine
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• v.25 no.4
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• pp.18-24
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• 2004

연구배경 : 플라스미노겐 활성 억제인자-1 (plasminogen activator inhibitor-1; PAI-1)은 허혈성 뇌경색의 발생의 원인이 되는 섬유소 용해작용의 저하를 매개하는 인자로서, PAI-1의 작용이 촉진되면 섬유소 용해기능이 저하되어 관상동맥 및 뇌혈관질환의 발생을 증가시키게 된다. PAI-1 유전자의 촉진자(promoter) 영역에는 -675 4G/5G (4G/5G)와A -844G (A/G)의 두 개의 유전자 다형성이 존재하며, 이는 PAI-1의 유전자 전사과정에 영향을 미쳐 혈청 PAI-1의 농도를 증가시키고 결과적으로 허혈성 뇌경색의 발생확률을 높이는 작용을 하게 된다. 연구방법 : 허혈성 뇌경색으로 진단 받은 167명의 환자와 173명의 건강인의 말초혈액에서 DNA를 분리한 후 PAI-1의 4G/5G와 A/G 유전자 다형성에 대한 연쇄중합반응 및 제한효소 절편길이 다형성 (polymerase chain reaction-restriction fragment length polymorphism; PCR-RFLP) 방법을 이용하여 허혈성 뇌경색 발생과 유전자 다형성과의 관계를 비교 분석하였다. 결과 : 허혈성 뇌경색 환자에서의 4G/4G의 유전자형의 빈도는 15.0%으로 정상 대조군의 33.5%에 비해 현저하게 낮게 나타났다 (P < 0.0001). 각각의 유전자형과 허혈성 뇌경색의 발생 위험도 (odd ratio ; OR)와의 관계를 분석했을 때 4G/4G 유전자형을 가질 경우 위험도는 0.35배로 현저하게 낮아졌으며, (P < 0.0001), 5G/5G 유전자형을 가질 경우 위험도는 4.49배 로 현저하게 높아졌다 (P < 0.0001). 그러나, A/G 유전자 다형성과 허혈성 뇌경색의 발생과는 유의한 연관성을 발견하지 못하였다. 결론 : 이상의 결과로 볼 때 PAI-1 유전자의 4G/4G 유전자형은 허혈성 뇌경색의 발생 비율을 감소시키는 작용을 하는 것으로 여겨진다.

• Korean Journal of Microbiology
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• v.42 no.2
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• pp.103-110
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• 2006

T-RFLP analysis and clone sequencing analysis based on bacterial 16S rDNA were conducted to assess bacterial community structure and diversity in Zoysia japonica soil treated with liquid fertilizer containing amino acids(LFcAA) after spray with herbicide. The results of T-RFLP (terminal restriction fragment length poly-morphism) analysis using restriction enzyme Hae III showed that the T-RFs of various size appeared evenly in the 32 clones of KD3 and 38 clones of KD4 respectively that had been treated with liquid fertilizer containing amino acid(LFcAA) compared to 23 clones of KD2 hat had not been treated with LFcAA. The microbial com- munity structure in KD2 appeared less diverse than those in KD3 and KD4. Analysis of partial sequences for 110 clones from KDI (control), KD2 (non-treated), KD3 (LFcAA 1X), KD4 (LFcAA 2X), respectively, revealed that most bacteria were related with uncultured bacteria in a 16S rDNA sequence similarity range of 91-99% through blast search. Otherwise, the other clones were members of proteobacteria, Acidobacteria, Act-inobacteria, Sphingobacteria and Planctomyces groups. Especially in KD4, members of Alpha Proteobacteria, Rhizobiales, Sphigomonadales, Caulobacterales, Gamma Proteobacteria, the genus Pseudomonas, Betapro-teobacteria, Nitrosomonadales and genus Nitrosospira appeared to be dominant. In addition, Acidobacteria group, Actinobacteria group, Planctomycetacia and Sphingobacteria were also shown. The microbial com-munity structure in Z. japonica soil sprayed with herbicide was affected by LFcAA.

• Journal of Animal Science and Technology
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• v.54 no.1
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• pp.1-8
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• 2012

This study aimed to investigate the single nucleotide polymorphisms (SNPs) of the porcine MC4R gene and validate the effect of the MC4R genotype for marker assisted selection (MAS). Six amplicons were produced to analyze the entire base sequences of the porcine MC4R gene and six SNPs were detected (c.-780C>G, c.-135C>T, c.175C>T-Leu59Leu, c.707A>G-Arg236His, c.892A>G-Asp298Asn, and c.*430A>T). Linkage disequilibrium (LD) of the six SNPs was analyzed by performing haploid analysis. There was a perfect linkage disequilibrium in c.-780C>G, c.-135C>T, c.175C>T-Leu59Leu, c.707A>G-Arg236His, and c.*430A>T. Only the c.892A>G (Asp298Asn) SNP showed a very low LD with an $r^2$ value of 0.028 and the D' value of 0.348. As a result, the two SNPs-c.707A>G (Arg236His) and c.892A>G (Asp298Asn)-were selected to extract the genotype frequencies from the 5 pig breeds by using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) genotype analysis method. The SNP frequency of c.707A>G (Arg236His) indicated the presence of the A (His) allele only in Yorkshire, while the G allele was fixed in the KNP, Landrace, Berkshire, and Duroc. Association analysis was carried out in 484 pigs with the c.707A>G (Arg236His) SNP and the meat quality traits of four different pig cross populations: a significant association was noted in crude fat, sirloin moisture, meat color, and the degree of red and yellow coloration. The frequency of the c.892A>G(Asp298Asn) SNP genotype varied among the breeds; while Duroc showed the highest frequency of the A (Asn) allele, KNP showed the highest frequency of the G (Asp) allele. Association analysis was carried out in 1126 pigs with the c.892A>G (Asp298Asn) SNP and the meat quality traits of four pig populations: a highly significant linkage was noted in the back-fat thickness (P<0.002). It was found that the back-fat thickness was higher in individuals with the AA genotype than in those with the AG or GG genotype. Thus, in this study, we verified that the c.892A>G (Asp298Asn) SNP in the pig MC4R gene has a sufficient effect as a gene marker for MAS in Korean pork industry.

• The korean journal of orthodontics
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• v.44 no.2
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• pp.96-102
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• 2014

Objective: A recent study suggested that rs6504340, a polymorphism within the homeobox B (HOXB) gene cluster, is associated with the susceptibility for malocclusions in Europeans. The resulting malocclusions require orthodontic treatment. The aim of this study was to investigate the association of rs6504340 and other dentition-implicated polymorphisms with dental and occlusal traits in Korean and Japanese populations. Methods: The study participants included 223 unrelated Koreans from the Busan area and 256 unrelated Japanese individuals from the Tokyo metropolitan area. DNA samples were extracted from saliva specimens. Genotyping for rs6504340 and four single nucleotide polymorphisms (SNPs) that have been shown to be associated with the timing of first tooth eruption and the number of teeth at 1 year of age (rs10506525, rs1956529, rs9674544, and rs8079702) was performed using TaqMan assays. The Index of Orthodontic Treatment Need (IOTN), overjet, overbite, arch length discrepancy, crown sizes, and length and width of the dental arches were measured. Spearman's correlation coefficients were calculated to evaluate relationships between rs6504340 and these dental/occlusal traits. Results: We evaluated the aesthetic components and dental health components of the IOTN in the Korean and Japanese populations and found that neither rs6504340 nor the other four SNPs showed any association with dental and occlusal traits in these East Asian populations. Conclusions: These negative results suggest that further research is needed to identify the genetic determinants of malocclusions in order to reach a consensus.