• Microbiology and Biotechnology Letters
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• v.34 no.1
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• pp.23-27
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• 2006

Molecular subtyping of Listeria monocytogenes, including type strains and isolates from Korean foods, were performed using random amplification of polymorphic DNA (RAPD). Each Listeria species showed specific RAPD band patterns, and L. monocytogenes serotypes and isolates were divided into two clusters. RAPD results showed that L. monocytogenes isolates from Korean foods were divided into two groups. Group I contained L. monocytogenes serotypes 1/2b and 4b, whereas Group II contained serotypes 1/2a and 1/2c. These results suggested RAPD as possible subtyping methods for Listeria species. Also, RAPD Results showed significant correlation between molecular subtyping and serotyping of L. monocytogenes, and classified two different groups of L. monocytogenes isolated from Korean foods.

• Journal of Ginseng Research
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• v.17 no.2
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• pp.153-158
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• 1993

The study was carried out for comparison of variants and development of genetic markers using Randomly Amplified Polymorphic D사A (RAPD) analysis method. The ginseng variants used were as follows: Chungkyung-Chong, Hwangskoog-Chong, KG101 selected by the pureline selection method, and 6 kinds of Jakyung-Chong strains Uinjakyung, Jakyung-Chong 81783, Jakyung-Chong 847913, Jaky tong-Chong 79742, Jinjakyung of USSR, and Mimaki of Japan). Four of 10 RAPD primers showed the distinctive polymorphism among 9 ginseng variants and lines, and were selected for more detailed polymorphic analysis. The sequences of 4 selected primers were TGCCGAGCTG (Primer#2), AATCGGGCTG (#4), GAAACGGGTG (U7), and GTGACGTAGG (#8). All primers produced several common bands among the strains. However, when primer # 2 was applied, the electrophoregram showed the specific band at 1.8 kb region in Chungkyung-Chong, Hwangskoog- chong, and KG101, and 1 kb in the Jakyung-Chong 847913. In primer #4, 1.1 kb band was shown in Chungkyung-Chong, Hwangskoog-Chong, KG101, and Jakyung-Chong 79742. In primer # 7, 700 bp band was appeared in Jakyung-Chong 81783 and Jinjakyung of USSR In primer # 8, 800 bp band was observed only in Mimaki, comparing to another strains. When Similarity Index (SI) was calculated, Chungkyung-Chong and Hwngskoog-Chong, and Jakyung- chong 81783 and Jinjakyung of USSR showed the most close SI, 0.11 and 0.08, respectively. The data of KG101, which showed the SI of 0.13 with the group of Chungkyung-Chong and Hwangskoog-Chong, coincided with the fact that it was released from Hwangskoog-Chong by breeding process. The data of Jakyung strains indicated the significant variation among the strains. From these results, RAPD analysis method could be succesively applied to the classification and genetic analysis for breeding of Korean ginseng.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.49 no.4
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• pp.358-362
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• 2004

In order to develop molecular markers related to stay green phenotype, AFLP analysis was conducted using near-isogenic lines for either stay green or non stay green trait. Both lines have characteristics of multi-ear and tillers (MET). Two out of 64 primer combinations of selective amplification identified three reproducible polymorphic fragments in MET corn with stay green. Both of E+AGC/M+CAC and E+AAG/M+CAA primer combinations produced two and one specific polymorphic fragments linked to stay green trait, respectively. For the conversion of AFLPs to sequence tag sites (STSs), primers were designed form both end sequences of each two polymorphic fragments. One fragment, which was amplified with E+AAG/M+CAA primer combinations, possessed 298 bp long and showed a $91\%$ homology with maize retrotransposon Cinful-l. One out of two polymorphic fragments produced with E+AGC/M+CAC primer combination had 236 bp long and matched a $96\%$ homology with an intron region of 22kDa alpha zein gene cluster in Zea mays. One out of two PCR fragments amplified with MET2 primer set in the stay green MET was not produced in the non-stay green MET. The developed AFLP and STS marker could be used as an efficient tool for selection of the stay green trait in the MET inbred.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.12
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• pp.1543-1551
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• 2010

A major aim of cattle genome research is to identify candidate genes associated with meat quantity and quality through QTL analysis for application in the livestock industry. Therefore, this study focused on discovery of useful SNPs within the LOC534614 gene, containing 12273_165 SNP which is located on the same site as the QTL on chromosome 6, and evaluation of the association between SNP and body weight and cold carcass weight in Hanwoo (Korean cattle) As a result of a BLAST search of the NCBI web site, we discovered that the mRNA sequence of the LOC534614 gene was similar to that of the coiled-coil domain containing 158 (CCDC158) for dog and human. According to the direct DNA sequence from the CCDC158 gene, we identified 19 polymorphic SNPs within exons and their flanking regions. Among them, 17 polymorphic SNPs were selected for genotyping in Hanwoo (n = 476) and seventeen marker haplotypes containing 12273_165 SNP (frequency >0.1) were identified. As a result of the association between 17 polymorphic SNPs and Hanwoo (n = 476), g.8778G>A SNP in exon 6 was found to be a non-synonymous SNP, and was significantly associated with body weight and cold carcass weight (p<0.05). We discovered 19 polymorphic SNPs in the CCDC158 gene on the QTL region of BTA 6 in Hanwoo and identified that the g.8778G>A SNP was significantly associated with body weight and cold carcass weight (p<0.05), which causes an amino acid variation from valine to methionine. Furthermore, statistical analysis demonstrated that the CCDC158 gene is strongly associated with body weight and cold carcass weight in Hanwoo. In this regard, the g.8778G>A SNP in the CCDC158 gene can be useful as a positional candidate for body weight and cold carcass weight for marker-assisted selection in Hanwoo.

• Mycobiology
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• v.47 no.4
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• pp.527-532
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• 2019

We designed 170 new simple sequence repeat (SSR) markers based on the whole-genome sequence data of button mushroom (Agaricus bisporus), and selected 121 polymorphic markers. A total of 121 polymorphic markers, the average major allele frequency (M_AF) and the average number of alleles (N_A) were 0.50 and 5.47, respectively. The average number of genotypes (N_G), observed heterozygosity (H_O), expected heterozygosity (H_E), and polymorphic information content (PIC) were 6.177, 0.227, 0.619, and 0.569, respectively. Pearson's correlation coefficient showed that M_AF was negatively correlated with N_G (-0.683), N_A (-0.600), H_O (-0.584), and PIC (-0.941). N_G, N_A, H_O, and PIC were positively correlated with other polymorphic parameters except for M_AF. UPGMA clustering showed that 26 A. bisporus accessions were classified into 3 groups, and each accession was differentiated. The 121 SSR markers should facilitate the use of molecular markers in button mushroom breeding and genetic studies.

• Radiation Oncology Journal
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• v.11 no.1
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• pp.83-90
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• 1993

During the period from January, 1975, to June, 1989, one hundred patients with histopathologically proven polymorphic reticulosis in the upper respiratory tract were treated with radiation therapy and the analysis of treatmemt results was undertaken. One hundred patients (69 males, 31 females) with a mean age of 46 years (range 12-79 years) were presented. Nasal cavity was the most frequent site of involvement ($56{\%}$), and 44 cases had multifocal sites of involvement. The incidence of cervical lymph node metastasis at initial diagnosis was $24{\%}$. Staging was determined by Ann-Arbor classification, retrospectively. The number of patients of stage IE, IIE, IIIE and IVE were 35, 60, 1, and 4, respectively. The overall 5 year actuarial survival rates were $38.4{\%}$. The difference in 5 year survival rates between patients with stage IE and IIE, with solitary and multiple, with CR and PR after irradiation were significant statistically. For the analysis of failure patterns, failure sites include the following: local failure alone (30/55=$54.6{\%}$), systemic failure alone (9/55=$16.4{\%}$), both local and systemic failure (16/55=$29.0{\%}$). Retrograde slide review was available in 29 cases of PMR with respect to histopathologic bases, and immunohistochemical studies were performed using MT1 and DACO-UCHL-1 as T-cell markers, MB2 as a B-cell marker and alpha-1-antichymotrypsin as a histiocytic markers. All that 29 cases showed characteristic histologic features similar to those of peripheral T-cell lymphoma and showed positive reactio to the T-cell marker. These findings suggest strongly that quite a significant portion of PMR may be in fact T-cell lymphoma.

• The Korean Journal of Mycology
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• v.25 no.3 s.82
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• pp.219-225
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• 1997

Random Amplified Polymorphic DNA (RAPD) assay was used to identify seven typical Lentinula edodes (Berk.) Pegler strains isolated in Korea. Twenty primers from OPA-01 to OPA-20 were applied to generate the recognition of L. edodes strains. Out of 20 primers, nine primers showed efficient RAPD patterns to classify the 7 strains tested, but the rest eleven primers were not useful to be used. Even though there was no single primer that could classify all of the strains, any combination of two primers among the nine primers could identify the strains tested. Thus, RAPD assay turned out to be very precise method for classifying L. edodes strains.

• Korean Journal of Weed Science
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• v.18 no.1
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• pp.76-83
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• 1998

Echinochloa species maintained by selling for more than 10 years were classified using random amplified polymorphic DNAs(RAPDs) analysis. Seventy-four decamer of randomly sequence markers were used to classify intraspecific variation irt Echinochloa species. The number of amplification products increased with increasing GC content of the primer in the range between 60% and 70% GC. Single-base substitutions of a primer altered amplification, providing new polymorphisms. The size of amplified DNA was mostly between 0.40kbp and 1.4kbp with the most common bands at 1.1kbp. Echinochloa species were detected with 6 primers which generated 26 polymorphic amplified DNAs. By hierarchical cluster analysis, Echinochloa species collected in Korea were divided into three groups. These results revealed that RAPD markers are useful tools for the determination of genetic variations in Echinochloa species.

• Journal of Life Science
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• v.16 no.1
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• pp.88-94
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• 2006

The random amplified polymorphic DNA (RAPD) technique was investigated as a potential tool for the origin identification of olive flounder (Paralichthys olivaceus) and redlip croaker (Pseudosciaena polyactis). Olive flounder specimens were collected from North Korea and several locations of South Korea (Jumunjin, Tongyoung and Geoje). Fishes obtained from Tongyeong and Geoje were cultured products. Redlip croaker specimens were collected from South Korea and China. Consistent and distinct diagnostic bands were easily identified in the RAPD patterns of the olive flounder specimens. Although consistent diagnostic bands rarely appeared in the RAPD pattern of redlip croaker specimens because of their genetic heterogeneity, we were able to find potential diagnostic bands in the average RAPD pattern of each origin.

• Journal of Crop Science and Biotechnology
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• v.10 no.2
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• pp.98-105
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• 2007

Phylogenetic relationships in Korean watermelons were evaluated by genetic similarity coefficients using 15 SSR(simple sequence repeat), 14 SCAR(sequence characterized amplified region) and 14 CAPS(sequence characterized amplified region) markers. The SSR markers were selected from previously reported melon and watermelon SSRs through testing polymorphisms within a set of commercial $F_1$ varieties. The SCAR and CAPS markers were developed from polymorphic AFLP(amplified fragment length polymorphism) markers between inbred lines 'BN4001' and 'BN4002'. From the AFLP analysis, 105 polymorphic fragments were identified between the inbred lines using 1,440 primer combinations of EcoRI+CNNN and XbaI+ANNN. Based on the sequencing data of these polymorphic fragments, we synthesized sequence specific primer pairs and detected clear and reliable polymorphisms in 27 primer pairs by indels(insertion/deletion) or RFLP(restriction fragment length polymorphism). A total of 43 sequence-based PCR markers were obtained and polymorphic information content(PIC) was analyzed to measure the informativeness of each marker in watermelon varieties. The average PIC value of SCAR markers was 0.41, which was similar to that of SSR markers. Genetic diversity was also estimated by using these markers to assess the phylogenetic relationships among commercial varieties of watermelon. These markers differentiated 26 Korean watermelon varieties into two major phylogenetic groups, but this grouping was not significantly correlated with their morphological and physiological characteristics. The mean genetic similarity was 66% within the complete set of 26 commercial varieties. In addition, these sequence-based PCR markers were reliable and useful to identify cultivars and genotypes of watermelon.