• Korean Journal of Medicinal Crop Science
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• v.13 no.4
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• pp.141-145
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• 2005

The genetic relationships of Hypericum erectum, H. ascyron and H. perforatum Thunb. by RAPD using total 46 primers were analysed 30 primers among primers tested showed the amplification band in all. The amplified DNA fragment ranged from 0.25 to 6.6 kb in size. The 411 bands (34.4%) among 1194 bands derived from 30 primers were polymorphic, and 13.7 bands per primer were observed. The phenograms for six analyzed individuals by RAPD markers were not matched well with those of the result by morphological characters. They were clustered monophyletic at the similarity coefficient value ranged from 0.24 to 0.96.

• Food Science and Biotechnology
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• v.17 no.6
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• pp.1171-1177
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• 2008

This study was undertaken to classify Enterobacter sakazakii isolates from 13 powdered infant formula products, 25 powdered weaning diet products, and 33 weaning diet ingredients on polymerse chain reaction (PCR) methods. The numbers of the isolates from 1 powdered infant formula product, 7 powdered weaning diet products, and 6 weaning diet ingredients were 1, 14, and 8, respectively. The contaminated ingredients were 1 rice powder, 2 millet powders, 2 vegetable powders, and 1 fruit and vegetable premix. PCR with the primer of repetitive extragenic palindromic element (REP-PCR) and random amplification of polymorphic DNA(RAPD) were effective in discriminating among the isolates, but tRNA-PCR and PCR with the primer of l6S-23S internal transcribed spacer (ITS-PCR) were not. Some of E. sakazakii isolates from vegetable powders, fruit and vegetable premix, and millets powders were classified into the clonal groups based on the DNA patterns in the REP-PCR and RAPD analysis. A close genetic relationship among the isolates from some of the powdered weaning diet products and the rice powder was also detected in the cluster analysis based on the DNA patterns in RAPD.

• Journal of Microbiology and Biotechnology
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• v.20 no.3
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• pp.558-562
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• 2010

SDS-PAGE of extracted surface-associated proteins of Lactobacillus rhamnosus strains E/N, Oxy, and Pen, was performed. The obtained protein patterns allowed differentiation of the examined strains, which was not accomplished by the commonly used RAPD genotypic method. The differentiation by the SDS-PAGE method proved to be a useful tool for strain-specific identification, which was further confirmed by 2DE analysis. Therefore, it can be used as an alternative or complementary method for both conventional and genotypic identification procedures, especially when closely related lactobacilli isolates are identified.

• Mycobiology
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• v.39 no.2
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• pp.71-78
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• 2011

The phylogenetic relationships of the most dominant and morphologically cryptic endophytic fungal isolates from each of five selected medicinal plants, namely Potentilla fulgens, Osbeckia stellata, Osbeckia chinensis, Camellia caduca, and Schima khasiana of the biodiversity rich state of Meghalaya, were assessed with random amplification of polymorphic DNA and PCR-restriction fragment length polymorphism profiles. Sequencing of the internal transcribed spacer 1, small subunit rRNA and partial ${\beta}$-tubulin gene fragments was also conducted to determine the phylogenetic relationships of these isolates with fungal sequences available in Genbank, NCBI. The identity of the fungal isolates is suggested based on the molecular phylogenetic data.

• Mycobiology
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• v.30 no.3
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• pp.139-145
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• 2002

Gibberella fujikuroi is species complex. This species complex includes Fusarium tabacinum, F. moniliforme(=F. verticillioides), F. nygamai, F. proliferatum as well as F. subglutinans. Our objective was to develop a technique to differentiate between isolates of F. subglutinans, F. proliferatum and F. verticillioides. Thirty-two strains of F. subglutinans, six strains from F. verticillioides and five strains of F. Proliferatum isolated from maize in Austria were studied using random amplified polymorphic DNA(RAPD). F. subglutinans strains clustered very closely, with similarity ranging from $87{\sim}100%$. On the other hand, all the amplification patterns of F. verticillioides were identical, as well as in the case of F. proliferatum. Our results indicated that these Fusaria species are distinct species and hence RAPD markers can be quick and reliable for differentiating them.

• Mycobiology
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• v.35 no.3
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• pp.154-156
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• 2007

A database application, namely MushBase, has been built based on Microsoft Access in order to store and manage different kinds of data about mushroom biological information of species, strains and their physiological characteristics such as geometries and growth condition(s). In addition, it is also designed to store another group of information that is experimental data about mushroom classification by Random Amplification of Polymorphic DNA (RAPD). These two groups of information are stored and managed in the way so that it is convenient to retrieve each group of data and to cross-refer between them as well.

• Journal of The Korean Society of Grassland and Forage Science
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• v.18 no.4
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• pp.277-284
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• 1998

Random amplified polymorphic DNA (RAPD) analysis was used to detect the genetic diversity of soybean (Glycine max (L.) Merr.) varieties and field bean (Glycine soza Sieb. and Zucc.) Five soybean varieties and one field bean were analysed with random primers using the polymerase chain reaction (PCR). Nine primers of a total twenty random primer were selected to amplify DNA segments. A total of 74 PCR products were amplified and 67.6% of which were polymorphic. The size of DNA molecule is ranged 0.13~2.0Kb and typically generated four to eight major bands. Specific genetic marker were revealed in primer sequence 5'-CAG GCC CIT C-3', 5'-TGC TCT GCC C-3' and 5'-GTC CAC ACG G-3', respectively. Genetic similarity between each of the varieties were calculated from the pair-wise comparisons of amplification products and a dendrogram was constructed by an unweighted pair-group method with arithmethical means (UPGMA). The results indicate that intervarietal relationships of soybean have a narrow genetic base and between the varieties, Hwanggum-kong and Seckryang-bootkong is more closely related than the rest of varieties, and field bean is related quite distant.

• The Plant Pathology Journal
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• v.22 no.1
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• pp.36-45
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• 2006

Twenty isolates of Didymella bryoniae were isolated from infected cucurbit plants in various growing areas of southern Korea in 2001 and 2002. Random Amplified Polymorphic DNA (RAPD) group [RG] I of D. bryoniae was more virulent than RG IV to watermelon. Virulence of the RG I isolate was strong to moderate to cucumber, whereas that of the RG IV varied from strong, moderate to weak. Two hundred seventy-three amplified fragments were produced with 40 primers, and were analyzed by a cluster analysis using UPGMA method with an arithmetic average program of NTSYSPC. At the distance level of 0.7, two major genomic DNA RAPD groups were differentiated among 20 isolates. The RG I included 7 isolates from watermelon and one isolate from melon, whereas the RG IV included 12 isolates from squash, cucumber, watermelon and melon. Amplification of internal transcribed spacer (ITS) region and small subunit rRNA region from the 20 isolates yielded respectively a single fragment. Restriction pattern with 12 restriction enzymes was identical for all isolates tested, suggesting that variation in the ITS and small subunit within the D. bryoniae were low. Amplification of the genomic DNAs of the tested isolates with the sequence characterized amplified regions (SCAR) primer RG IF-RG IR specific for RG I group resulted in a single band of 650bp fragment for 8 isolates out of the 20 isolates. Therefore, these 8 isolates could be assigned into RG I. The same experiments done with RG IIF-RG IIR resulted in no amplified PCR product for the 20 isolates tested. An about 1.4 kb-fragment amplified from the RG IV isolates was specifically hybridized with PCR fragments amplified from genomic DNAs of the RG IV isolates only, suggesting that this PCR product could be used for discriminating the RG IV isolates from the RG I isolates as well other fungal species.

• Parasites, Hosts and Diseases
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• v.47 no.3
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• pp.293-297
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• 2009

Improved methods for detection of Cryptosporidium oocysts in environmental and clinical samples are urgently needed to improve detection of cryptosporidiosis. We compared the sensitivity of 7 PCR primer sets for detection of Cryptosporidium parvum. Each target gene was amplified by PCR or nested PCR with serially diluted DNA extracted from purified C. parvum oocysts. The target genes included Cryptosporidium oocyst wall protein (COWP), small subunit ribosomal RNA (SSU rRNA), and random amplified polymorphic DNA. The detection limit of the PCR method ranged from $10^3$ to $10^4$ oocysts, and the nested PCR method was able to detect $10^0$ to $10^2$ oocysts. A second-round amplification of target genes showed that the nested primer set specific for the COWP gene proved to be the most sensitive one compared to the other primer sets tested in this study and would therefore be useful for the detection of C. parvum.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.54 no.4
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• pp.346-350
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• 2009

The cultivated radish (Raphanus sativus L.) is a major vegetable crop in the world wide and fast-growing species that grows inhabitats of six continents. It is very important to determine hybrid seed purity in the production of hybrid Brassica vegetable seeds to avoid unacceptable contamination with self-inbred (sib) seeds. The use of random amplified polymorphic DNA (RAPD) markers for evaluating seed purity in $F_2$-hybrid radish cultivars demonstrated. One hundred eighty seeds from the F1 male and female harvest were subsequently screened for seed purity using 13 primers. The 13 primers result in 17 cultivar-specific bands and 23 variable RAPD bands scored for cultivar. RAPD analysis of hybrid seeds from the harvest revealed 128 seeds tested except underdevelopment and decayed seeds were sibs. Especially, $F_2$ hybrids of radish, OPC13, OPD20 were presented clear hybrid bands. It maintains higher than average level of genetic diversity compared with their correspondent parents. RAPD amplification of DNA extracted from germinated individuals from the female harvest reveal that 10 of 208 seeds tested were self-inbred (4.8%). RAPD analysis of hybrid seeds from the male harvest revealed 7 of the 208 seeds tested were sibs (3.4%). The RAPD may lead to a better insight in to the hybrid seed purity.