• Korean Journal of Medicinal Crop Science
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• v.10 no.3
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• pp.194-199
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• 2002

Extracted genomic DNA from 16 accessions of Codonopsis lanceolata collected from South Korea and the Baekdoo Mt. areas of China were analyzed for their genetic relationships by RAPD. Twenty 10-mer-oligonucleotide primers having reproductive polymorphism were selected for the RAPD analysis. The size of amplified DNA was almost between 125 bp and 2.0 kbp. Sixteen collected Codonopsis lanceolata were analyzed with 20 primers which generated 73(49.3%) polymorphic bands among 148 PCR products. The mean number of polymorphic bands were 7.4 and varied $1{\sim}9$ per primer. It was, thus, demonstrated that RAPD was useful for detecting polymorphism in Codonopsis lanceolata. The range of 1-F value(genetic similarity) was from 0.682 to 0.959. These results indicate variable genetic similarities. By UPGMA (Unweighted Pair Group Method using an Arithmetic average) cluster analysis based on 1-F value, genetic distance among the 16 collected Codonopsis lanceolata was $0.133{\sim}0.400$. It was certainly classified into two groups between collected accessions from Korea and China, and the genetic distance was about 0.281. Both accessions collected from Korea and China showed miner differences, while the genetic relationships of Tonghua Xian and Liuhe Xian from China was farthest with other accessions collected.

• Korean Journal of Plant Resources
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• v.22 no.5
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• pp.446-453
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• 2009

RAPD analyses were performed to investigate genetic relationships and useful molecular maker for 3 species and their 17 regional populations of the Pueraria lobata and related taxa. The length of amplified DNA fragments ranged from 200 to, 2,800 bp. Two hundred and eight scorable polymorphic makers and three scorable monomorphic makers were found from the PCR reactions with 15 random oligo primers, and those were analyzed by Nei's genetic distance coefficient. Based on the UPGMA phenogram from RAPD analyses, two major groups (9 populations from Korea; 3 populations from foreign countries) were recognized. And it showed distinct genetic differences from related taxa. The RAPD results was very useful to define the samples by geographical distribution and to discuss the relationships among the populations and their related taxa of the Pueraria lobata.

• Korean Journal of Microbiology
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• v.41 no.1
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• pp.60-66
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• 2005

To select the rapid and efficient molecular subtyping method for epidemiologic monitoring of Staphylococcus aureus (S. aureus) strains at clinical laboratory levels, a total 116 of S. aureus and MRSA (methicillin-resistant S. aureus) strains from diverse animal species [Korean cattle, goat, pig, dog, chicken, mouse] and also humans were analyzed. To evaluate the discriminatory ability (DA) of individual PCR methods, random amplified polymorphic of DNA [RAPD; 4M & RA primer], repetitive extragenic palindromic sequences PCR (REP-PCR), and enterobacterial repetitive intergenic consensus sequences PCR (ERIC-PCR) methods were conducted and then compared on their Simpson's index of diversity (SID) values based on the dendrogram patterns, which was produced by software program (BiolD2+ & GelCompar II). In first, RAPD using the 4M primer (SID 0.915) was expressed more higher SID value than that of RA primer (SID 0.874). 4M primer was expressed more powerful DA than RA. Both REP-PCR (SID 0.930) and ERIC-PCR (SID 0.929) methods showed much more higher DA than that of RAPD. According to the present results, both REP-PCR and ERIC-PCR among the tested analysis methods were found as the most reliable and discriminative molecular subtyping method, because they expressed the highest DA for the present S. aureus and MRSA strains.

• Journal of Life Science
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• v.30 no.1
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• pp.1-9
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• 2020

Pseudomonas syringae pv. actinidiae, the causal agent of a bacterial canker disease in kiwifruit, is subdivided into five genetically distinct populations, namely biovars 1, 2, 3, 5, and 6. Of these, strains belonging to biovar 3 are responsible for a pandemic bacterial canker of kiwifruits since 2008. This study aimed to characterize the structure of the biovar 3 population and investigate the origin of biovar 3 strains isolated in Korea. The genetic variability of fifteen biovar 3 strains, thirteen Korean and two Chinese, were evaluated through random amplified polymorphic DNA (RAPD)-PCR. The RAPD results revealed the presence of eight lineages, designated as subgroups I-VIII, across the biovar 3 strains used in this study. As the strains in subgroups II and III from China were not found in the Korean examples, we concluded that six genetically different biovar 3 subgroups (I, IV, V, VI, VII, and VIII) are present in Korea. In PCR analysis using primers specific to the strains of New Zealand and Europe, Korean strains in subgroups V and VI amplified the relevant DNA bands, suggesting that these were introduced from these two origins, respectively. PCR primers specific to subgroup VIII were developed to monitor the spread of the first biovar 3 strain in Korea, and investigations revealed that this strain was not found in Korea after its first occurrence.

• Korean Journal of Medicinal Crop Science
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• v.13 no.5
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• pp.249-253
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• 2005

This study was carried out to develop convenient and reproducible methods for identifying the genetic relationship among germplasms of Panax species based on molecular genetics. Using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) analyses, genetic polymorphism of the Panax species was investigated with following cultivars and accessions, such as Chunpoong, Yunpoong, Kopoong, Sunpoong, and Kumpoong in domestic cultivars, Hwangsuk, Jakyung and Suckju in domestic accessions, and Panax quinquefolius L. and Panax japonicus C.A. Meyer in foreign introduced accessions, respectively. Specific DNA fragments ranging from 200 to 3,000 base pairs in size could be obtained with various ISSR and RAPD primers under the optimized PCR conditions. The dissimilarity coefficients among the genetic polymorphisms of ginseng cultivars and accessions were calculated from 0.26 to 0.90 in RAPD and from 0.12 to 0.89 in ISSR analysis, respectively. Eleven plant samples were grouped siblings together with cultivars and parents based on cluster analysis of genetic distance depending on genetic property such as origin of the species. In results, both RAPD and ISSR analyses were useful for identifying the genetic relationship among cultivars and accessions of Panax species at DNA level.

• Korean Journal of Plant Resources
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• v.20 no.4
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• pp.272-280
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• 2007

In order to presume the genetic relationship about two species and their 30 regional populations of the Saururus and Houttuynia of Saururaceae, RAPD analyses were performed. The length of amplified DNA fragments ranged from 300 to 2,000 bp. 156 scorable RAPD makers were found from PCR reactions with sixteen random oligoprimers. Also, some regional populations were clustered separately from the UPGMA phenogram. The OTUs between cultivated and natural populations were distinguished distinctly on the UPGMA phenogram. And the regionals populations of the treated taxa were clustered. Among the regional populations of two species, GN populations had the close relationship JJ populations rather than JN populations. The RAPD data was very useful to define the genetic relationship and distinguish the cultivated populations from natural populations by regional distributions in this study.

• Fisheries and Aquatic Sciences
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• v.18 no.4
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• pp.387-393
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• 2015

Biotyping of Vibrio vulnificus strains isolated from marine environments along the south coast of Korea showed that the majority of the isolates (94.7%) belonged to biotype 1 and the remaining isolates (5.3%) belonged to biotype 2. Analysis of 16S rRNA V. vulnificus strains isolated from marine environments using a multiplex polymerase chain reaction (PCR) revealed that 78.7% were type A and 21.3% were type B. Random amplified polymorphic DNA (RAPD) was used to analyze the genomic differences in V. vulnificus among the biotype 2 strains isolated from marine environments (newly isolated strains group) and reference strains obtained from infected eels (reference strains group). The two groups had distinctly different profiles of the amplicons produced from RAPD. Additionally, biochemical comparison of these strains revealed that all four strains isolated from marine environments differed from the strains isolated from eels in their ability to promote D-mannitol fermentation. Two (NH 1 and NH 2) out of four isolates of biotype 2 from marine environments showed pathogenicity in eels Anguilla japonica in a challenge test. These isolates did not agglutinate with antisera against V. vulnificus NCIMB 2137 (serovar E), ATCC 27562 (non-serovar E), and ATCC 33816 (atypical serovar E).

• Journal of Life Science
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• v.21 no.4
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• pp.502-508
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• 2011

The purpose of this study was to evaluate the methods of identifying zygotic seedlings of crosses between 'Morita unshiu' (Citrus. unshiu Marc.) and 'Ponkan' (C. reticulata Blanco). In order to investigate the frequency and position of zygotic seedlings and to determine the efficiency of zygotic seedling identification, random amplified polymorphic DNA (RAPD) and sequence-related amplified polymorphism (SRAP) were performed using UBC (9, 27, 229, 230, and 254) primers and F4/R27, F7/R14, F12/R10, and F44/R62 primer sets, respectively. A total of 37 putative zygotic seedlings out of 55 individuals were selected by RAPD and SRAP. The F7/R14 primer pair showed a screening ability of 45.5% (25/55), whereas the primer UBC27 revealed the highest efficiency of zygotic seedling identification (50.9%, 28/55). When both UBC27 and F7/R14 were properly used for selection of hybridized seedlings of 'Morita unshiu' (C. unshiu Marc.) and 'Ponkan' (C. reticulata Blanco), screening efficiency was increased to 60% (33/55) for putative zygotic seedlings. Thus, it is possible to select putative hybrid zygotic seedlings in an accurate and effective manner by RAPD and SRAP.

• Microbiology and Biotechnology Letters
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• v.49 no.2
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• pp.239-248
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• 2021

The emergence of multidrug-resistant Acinetobacter baumannii has partly increased treatment failure and patient mortality. Class D β-lactamases is an important mechanism of resistance to beta-lactam antibiotics in this species. This study aimed to investigate the relationship between the presence oxacillinase gene and genetic fingerprints of A. baumannii isolates from the intensive care unit of an Egyptian tertiary care hospital. One hundred and twenty A. baumannii clinical isolates were collected. Multiplex PCR was performed to detect genes encoding oxacillinases (OXA-23, OXA-24, OXA-51, OXA-58 and OXA-143). Molecular typing of all collected isolates was performed using random amplified polymorphic DNA (RAPD)-PCR assay. Out of 120 examined isolates, 92, 88 and 84% were resistant to ertapenem, imipenem and meropenem, respectively. The species-specific, commonly present OXA-51 gene was found in all isolates while OXA-23 showed a high prevalence of 88% of isolates. OXA-24 and OXA-143 genes were detected in 3% and 1% of isolates, respectively. No OXA-58 gene was detected. Five clusters consisting of 19 genotypes were detected using RAPD-PCR. Genotype A was the most prevalent, it was observed in 62% of the isolates followed by genotype B (12%). These results revealed that genotypes A and B are common in the hospital. Results also demonstrate that RAPD-PCR is a rapid and reliable method for studying the clonal similarity among A. baumannii isolated from different clinical specimens.

• Journal of Practical Agriculture & Fisheries Research
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• v.3 no.1
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• pp.48-69
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• 2001

A lot of clones of the genus Dioscorea have been introduced from some tropical and subtropical regions since 1997. In 33 clones of water yams (Dioscorea alata L.), some morphological characteristics were investigated at the field. Variation ranges of the total weight and tuber number per stump were within the ranges from 90 to 2,147 g with an average of 610 g ; and 1.3-4.7 with an average of 2.8, respectively. The color tones observed on the tuber-flesh were sorted into 3 color-categories, i.e., white, pale brown and pale purple, and those on leaves were sorted into 3 color-categories, i.e., green, heavy green and purplish green. Intraspecific genetic relationship of 19 variation types of the Yam classified by their external morphological characteristics such as leaf and tuber shape was assessed by DNA using random and specific primers. Twenty two out of 113 primers (100 random[10-mer] primers, two 15 mer [M13 core sequence, and (GGAT)4 sequence]) had been used in PCR-amplification. Only 12 primers, however, were successful in DNA amplification in all of the analyzed plants, resulting in 93 randomly and specifically amplified DNA fragments. The analyzed taxa showed very high polymorphisms(69 bands, 71.0%), allowing individual taxon to be identified based on DNA fingerprinting. Monomorphic bands among total amplified DNA bands of each primer was low under the 50%. Similarity indices between accessions were computed from PCR(polymerase chain reaction) data, and genetic relationships among intraspecific variations were closely related at the levels ranging from 0.66 to 0.90.