• Journal of Plant Biotechnology
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• v.47 no.2
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• pp.124-130
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• 2020

The sweet potato (Ipomoea batatas [L.] Lam.) is the sixth-most important crop in the world following rice, wheat, potato, maize, and cassava. Four varieties ('Beniharuka', 'Annobeni', 'Pungwonmi', 'Hogammi') and their Japanese cultivars are broadly distributed in South Korea. In the Korean marketplace, sweet potatoes are classified by color and shape, not by variety, making it necessary to differentiate varieties for uniform production and consumption. In this study, molecular markers were developed to distinguish the four varieties of sweet potato using SNPs and genotyping-by-sequencing (GBS) analysis via a tetra-primer amplification refractory mutation system (ARMS)-PCR. The results revealed that three variety-specific fragments (164 bp and 241 bp of SNP 04-27457768 and 292 bp of SNP 03-16195623) were amplified in the 'Beniharuka', 'Pungwonmi', and 'Annobeni' sweet potato varieties. There were instances where some varieties produced three bands within the gel electrophoresis, indicating heterozygosity at the given SNPs loci. DNA sequencing analysis also confirmed the results of electrophoresis at the SNPs loci. Overall, these molecular markers would provide a useful, rapid, and, simple evaluation method for the Korean sweet potato marketplace, where the mixing of varieties is a serious issue.

• Korean Journal of Clinical Laboratory Science
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• v.39 no.3
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• pp.147-150
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• 2007

Most expressed HLA (human leukocyte antigen) loci exhibit a remarkable degree of allelic polymorphism, which derives from sequence differences predominantly localized to discrete hypervariable regions of the amino terminal domain of the molecule. In this study, the HLA-B genotypes were determined in twenty students unrelated koreans using the PCR-SSP (polymerase chain reaction-sequence specific primer) technique. Several specific primer pairs in assigning the HLA-B gene were used ($B^{\ast}4001/4007$, $B^{\ast}4901/5001/4501$, $B^{\ast}3701$, $B^{\ast}5801$). The results of PCR-SSP, the HLA-B3701 primer was detected one (5%), the $HLA-B^{\ast}5801$ were detected four (20%), the $HLA-B^{\ast}4001/4007$ were detected nineteen (95%) and the $HLA-B^{\ast}4901/5001/4501$ were detected twenty. This study shows that the PCR-SSP technique is relatively simple, fast and a practical tool for the determination of the HLA-B genotypes. Moreover, these results genotype frequency of the HLA-B gene could be useful for database study before being applied to individual identification and transplantation immunity.

• The Korean Journal of Malacology
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• v.30 no.3
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• pp.197-210
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• 2014

Single nucleotide polymorphisms (SNPs) are widely acknowledged as the marker of choice for many genetic and genomic applications because they show co-dominant inheritance, are highly abundant across genomes and are suitable for high-throughput genotyping. Here we evaluated the applicability of SNP markers developed from Crassostrea gigas and C. virginica expressed sequence tags (ESTs) in closely related Crassostrea and Ostrea species. A total of 213 putative interspecific level SNPs were identified from re-sequencing data in six amplicons, yielding on average of one interspecific level SNP per seven bp. High polymorphism levels were observed and the high success rate of transferability show that genic EST-derived SNP markers provide an efficient method for rapid marker development and SNP discovery in closely related oyster species. The six EST-SNP markers identified here will provide useful molecular tools for addressing questions in molecular ecology and evolution studies including for stock analysis (pedigree monitoring) in related oyster taxa.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.1
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• pp.28-32
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• 2012

In the present study, we evaluated the informativeness of SNPs genotyped by the Illumina Bovine SNP50K assay in different cattle breeds. To investigate these on a genome-wide scale, we considered 52,678 SNPs spanning the whole autosomal and X chromosomes in cattle. Our study samples consists of six different cattle breeds. Across the breeds approximately 72 and 6% SNPs were found polymorphic and fixed or close to fix in all the breeds, respectively. The variations in the average minor allele frequency (MAF) were significantly different between the breeds studied. The level of average MAF observed in Hanwoo was significantly lower than the other breeds. Hanwoo breed also displayed the lowest number of polymorphic SNPs across all the chromosomes. More importantly, this study indicated that the Bovine SNP50K assay will have reduced power for genome-wide association studies in Hanwoo as compared to other cattle breeds. Overall, the Bovine SNP50K assay described in this study offer a useful genotyping platform for mapping quantitative trait loci (QTLs) in the cattle breeds. The assay data represent a vast and generally untapped resource to assist the investigation of the complex production traits and the development of marker-assisted selection programs.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.7
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• pp.927-934
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• 2012

The efficiency of insertion and/or deletion (indels) polymorphisms as genetic markers was evaluated by genotyping 102 indels loci in native chicken populations from Myanmar and Indonesia as well as Red jungle fowls and Green jungle fowls from Java Island. Out of the 102 indel markers, 97 were polymorphic. The average observed and expected heterozygosities were 0.206 to 0.268 and 0.229 to 0.284 in native chicken populations and 0.003 to 0.101 and 0.012 to 0.078 in jungle fowl populations. The coefficients of genetic differentiation (Gst) of the native chicken populations from Myanmar and Indonesia were 0.041 and 0.098 respectively. The genetic variability is higher among native chicken populations than jungle fowl populations. The high Gst value was found between native chicken populations and jungle fowl populations. Neighbor-joining tree using genetic distance revealed that the native chickens from two countries were genetically close to each other and remote from Red and Green jungle fowls of Java Island.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.6
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• pp.2491-2494
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• 2012

The current study was performed to assess any association between the methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism and risk of lung cancer in Henan province. This case-control study involved94 patients with newly histological confirmed lung cancer and 78 healthy controls. Genotyping was achieved with peripheral blood lymphocytes DNA and association of the polymorphism with risk of lung cancer was estimated by unconditional logistic regression analysis. The frequencies of the MTHFR 667TT genotype were 37.2% in cases compared with 23.1% in controls (${\chi}^2$ = 4.008, P = 0.045). Individuals with the 667CC/CT genotype displayed a significantly reduced risk of lung cancer compared with those with the TT genotypes [adjusted odds ratio (OR), 0.506; 95% confidence interval (95% CI), 0.258 - 0.991]. The C667T polymorphism might have a significant effect on the occurrence of lung cancer in Henan province.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.6
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• pp.2541-2545
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• 2012

Objective: To investigate any association between XRCC1 and XRCC3 polymorphisms and outcome of platinum-based chemotherapy in ovarian cancer patients. Methods: With a prospective study design was cases were consecutively collected from January 2005 to January 2007. All 310 included patients were followed-up until the end of January 2010. Genotyping of XRCC1 and XRCC3 polymorphisms was conducted by TaqMan Gene Expression assays. Results: A total of 191 patients died during follow-up. Our study showed a lower survival rate in XRCC1 399 Arg/Arg genotype than Gln/Gln, with a significant increased risk of death (HR=1.69, 95%CI=1.07-2.78). Similarly, those carrying XRCC3 Thr/Thr genotype had a increased risk as compare to the Met/Met genotype, with a HR (95% CI) of 1.90 (1.12-3.41). There was no significant association between XRCC1 Arg194Trp and XRCC1Arg280His gene polymorphisms and ovarian cancer death. Conclusion: Our study demonstrates that polymorphisms in DNA repair genes have roles in the susceptibility and survival of ovarian cancer patients.

• Journal of Microbiology and Biotechnology
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• v.16 no.5
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• pp.740-747
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• 2006

Amplification by universal consensus sequences in pathogenic bacterial DNA would allow rapid identification of pathogenic bacteria, and amplification of genus-specific and species-specific sequences of pathogenic bacterial DNA might be used for genotyping at the genus and species levels. For design of probes for molecular diagnostics, several tools are available as stand-alone programs or as Web application. However, since most programs can design only a few probe sets at one time, they are not suitable for large-scale and automatic probes design. Therefore, for high-throughput design of specific probes in diagnostic array development, an automated design tool is necessary. Thus, we developed a Web-based automatic system for design of genus-specific and species-specific probes for pathogen detection. The system is available at http://www.miprobe.com.

• Journal of Microbiology and Biotechnology
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• v.24 no.10
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• pp.1445-1454
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• 2014

Severe acute respiratory syndrome (SARS), a disease that spread widely in the world during late 2002 to 2004, severely threatened public health. Although there have been no reported infections since 2004, the extremely pathogenic SARS coronavirus (SARS-CoV), as the causative agent of SARS, has recently been identified in animals, showing the potential for the re-emergence of this disease. Previous studies showed that 27 single nucleotide polymorphism (SNP) mutations among the spike (S) gene of this virus are correlated closely with the SARS pathogenicity and epidemicity. We have developed a SNP DNA microarray in order to detect and genotype these SNPs, and to obtain related information on the pathogenicity and epidemicity of a given strain. The microarray was hybridized with PCR products amplified from cDNAs obtained from different SARS-CoV strains. We were able to detect 24 SNPs and determine the type of a given strain. The hybridization profile showed that 19 samples were detected and genotyped correctly by using our microarray, with 100% accuracy. Our microarray provides a novel method for the detection and epidemiological surveillance of SARS-CoV.

• Animal cells and systems
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• v.9 no.2
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• pp.95-100
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• 2005

Essential hypertension results from the complex interaction between genetic and environmental factors. A C825T polymorphism of the gene encoding G-protein ${\beta}3$ subunit (GNB3), associated with enhanced G-protein coupled signaling and increased $Na^+-H^+$ exchanger, has been implicated in the development of essential hypertension in several human populations, especially in Caucasian population. We examined the disease relevance of this candidate gene by performing an association study in a study group of Korean heritage. Participants comprised 109 essential hypertensives and 109 normotensives, respectively. Genotyping was performed with PCR-BsaJI restriction digestion method. Observed genotype frequencies were in Hardy-Weinberg equilibrium in all groups. Genotype and allele frequencies did not differ significantly between normotensives and essential hypertensives (P>0.05). However, the serum total cholesterol (TC) and LDL-cholesterol levels were significantly higher in subjects with the TT genotype compared to those with the CC or CT genotypes in normotensives of our study subjects (P<0.05). Thus, these results suggest that GNB3/C825T polymorphism might be significantly associated with abnormality in serum lipid metabolism.