• Journal of Forest and Environmental Science
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• v.25 no.2
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• pp.93-100
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• 2009

In Malaysia, Labisia pumila Benth & Hook f, popularly known as 'Kacip Fatimah' has been used traditionally to treat various elements of the woman's health in Malay community. The objective of this study was to develop randomly amplified polymorphic DNA (RAPD) based DNA markers for the identification of L. pumila and to distinguish its three varieties from each other. Total DNA from nine accessions of L. pumila was extracted by CTAB method and polymerase chain reactions (PCR) were carried out to amplify the segments of DNA using different primers to develop DNA barcode using RAPD technique. To find out variety-specific DNA marker/s, twenty different 10-mer primer sequences with annealing temperature from 36-$40^{\circ}C$ were evaluated in triplicate. Out of 20 random primers, two primers (OPA-1 and OPA-2/A10) were selected which produced reliable RAPD band patterns. To have DNA based handle, two RAPD amplification products were cloned and sequenced to determine the identity of the DNA. RAPD analysis using two random primers generated 72 discrete bands ranging in size 200 bp-3,000 bp. Fifty nine of these were polymorphic loci (82%) and thirteen were non-polymorphic loci (18%). A total of 32 bands polymorphic loci (72%) were amplified with primer OPA-1 and analyzed by cluster analysis and UPGMA (Unweighted Pair Group Method with Arithmetic) to present a dendogram depicting the degree of genetic relationship among nine accessions of L. pumila. Our results shows the reasonable genetic diversity among the L. pumila varieties and within varieties; and two RAPD marker sequences obtained could be used to identify L. pumila at species level.

• Food Engineering Progress
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• v.21 no.2
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• pp.174-179
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• 2017

For preliminary molecular typing, PCR-based fingerprinting using random amplified polymorphic DNA (RAPD) is the method of choice. In this study, 14 bacterial strains were isolated from different Korean food sources, identified using 16S rRNA gene sequencing, and characterized through RAPD-PCR. Two PCR primers (239 and KAY3) generated a total of 130 RAPD bands, 14 distinct PCR profiles, 10 polymorphic bands, one monomorphic band, and four unique bands. Dendrogram-based analysis with primer 239 showed that all 14 strains could be divided into seven clades out of which clade VII had the maximum of seven. In contrast, dendrogram analysis with the primer KAY3 divided the 14 L. citreum strains into four clades out of which clade IV consisted of a maximum of 10 strains out of 14. This research identified and characterized bacterial populations associated with different Korean foods. The proposed RAPD-PCR method, based on sequence amplification, could easily identify and discriminate the lactic acid bacteria species at the strain-specific level and could be used as a highly reliable genomic fingerprinting tool.

• 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.

• Korean Journal of Plant Resources
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• v.16 no.1
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• pp.55-60
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• 2003

The genetic variation of random amplified polymorphic DNA (RAPD) patterns of genomic DNAs was investigated in dioecious plant Rumex acetosa L., which carries different sex chromosome complements in female (2n=12A+XX) and male (2n=12A+XY$_1$Y$_2$). One hundred and twenty random primers consisted of 10-mer were used for PCR amplification. Polymorphic bands were found in 24 primers. Specific bands for female and male were 16 and 18, respectively. Especially, a band of 1,440 bp from the OPC-10 primer was male specific. These sex specific RAPD markers are used to understanding the sex determination mechanism in plants.

• Journal of Sericultural and Entomological Science
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• v.37 no.2
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• pp.167-171
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• 1995

To develope a microbial pesticide for the control of mulberry longicorn beetle, Apriona germari, Beauveria spp. were isolated from the infected Apriona germari larvae. The morphology of Beauveria spp. was observed by phase contrast and scanning electron microscope. In addition, the Beauveria spp. isolated from Apriona germari were identified by the random amplification of polymorphic DNA using polymerase chain reaction. The results showed that the Beauveria spp., SFB-1A and SFB-3A, isolated from Apriona germari were identified with B. bassiana and B. brongniartii, respectively, suggesting that the random amplification of polymorphic DNA is effective for the identification of Beauveria spp.

• Korean Journal of Animal Reproduction
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• v.25 no.4
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• pp.359-369
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• 2001

Polymerase chain reaction (PCR) amplification of DNA as 30 different arbitrary primers and random amplified polymorphic DNAs (RAPD) analysis were performed on genomic DNA extracted from the blood of the marine rockfish (Sebastes schlegeli) from the Yellow Sea and the Southern Sea. The unique properties of the genomic DNA were used to investigate the features of the population dynamics and origins of the species. Out of 30 primers, seven generated 207 highly reproducible RAPD polymorphic products, producing approximately 2.7 polymorphic bands per primer. About 67.4% of total amplified products (307) were either polymorphic (207) to rockfish. The degree of similarity varied from 0.22 to 0.63 as calculated by bandsharing analysis. Also, the average level of bandsharing was 0.39$\pm$0.02 within the rockfish strains. The electrophoretic analysis of RAPD-PCR products showed the relatively high levels if variation between different individuals in rockfish from the Yellow Sea. However, the RAPD outlines obtained with DNA of different rockfish strains from the Yellow Sea and the Southern Sea in Korea were very similar. Also, a small number of polymorphic bands were identified. Even if further analyses or more rockfish populations are required, this result implies RAPD analysis reflects genetic differences between the geographical strains of the rockfish.

• Animal cells and systems
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• v.5 no.4
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• pp.333-339
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• 2001

Common carp (Cyprinus carpio) and its aquaculture breed Israeli carp samples were obtained from two separate aquaculture facilities under the similar raising conditions during two years in the Kunsan National University, Korea. Genomic DNA was isolated from the common carp and Israeli carp for identification of genetic characteristics and genomic polymorphisms by polymerase chain reaction amplification of DNA using arbitrary primers. The arbitrary primer No.21 (ACTTCGCCAC) yielded the highest number of fragments with the average of 15.0 among the primers used in Israeli carp. A tota1 of 294 polymorphic products in common carp and 336 in Israeli carp were observed by random primers. The average number of polymorphic products generated by random RAPD primer No. 2 (GTAGAC-CCGT) showed 8.0 in Israeli carp. On average, each random RAPD primer produced 5.4 amplified polymorphic products in common carp and 6.2 in Israeli carp. An average genetic similarity (BS value) was 0.44$\pm$0.05 within the common carp and 0.32$\pm$0.04 within the Israeli carp. The degree of similarity frequency (BS) between two carps was 0.67 as generated by the primer No. 19 (GACGGATCAG). The average level of bandsharing was 0.57$\pm$0.03 between the two carps. Accordingly, the two carp populations were genetically a little distant. The electrophoretic analysis of PCR-RAPD products showed middle levels of variation between the two carp populations. This result implies that the genetic diversity among intra-population may be higher when compared with that between the two carps. The RAPD polymorphism generated by these random primers might be used as a genetic marker for populations or lines identification in important aquacultural carp.

• Korean Journal of Veterinary Research
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• v.49 no.4
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• pp.319-328
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• 2009

This study investigated the epidemiology of Listeria (L.) monocytogenes, a food-borne pathogen. The epidemiology of food-borne pathogens is of great importance for clarifying bacterial origin and preventing bacterial contamination and infection. This work examined 68 L. monocytogenes strains, including 11 reference strains and 57 isolates from imported US beef, domestic meats (beef, pork, chicken meat), raw milk, and milk plants. The random amplified polymorphic DNA (RAPD) techniques were optimized to develop a standard molecular epidemiological analysis of L. monocytogenes. There was great genetic variability among the isolates, which produced 24 and 34 RAPD patterns with primer HLWL85 and HLWL74, respectively. The discriminatory power of the RAPD methods with HLWL85 and HLWL74 primer were very high (DI = 0.957; S ${\geq}$ 80%, S ${\geq}$ 95%). Some RAPD types were specific to origin. A few RAPD types were specific for L. monocytogenes strains belonging to a particular serotype. Using the HLWL85 primer, the strains isolated from milk plants could be distinguished from the other strains. And using the HLWL74 primer, the strains isolated from imported beef (US) could be distinguished completely from the other strains.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.4
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• pp.475-481
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• 2006

The genetic polymorphism and relationships of Muscovy, Cherry Valley Meat ducks, Partridge ducks and their crossbreds $F_1$ and $F_2$, respectively, were studied using a random amplified polymorphic DNA (RAPD) technique. The results showed that RAPD markers were effective for the analysis of genetic relationships among ducks. Amplification with 20-primers gave 760 reproducible amplified fragments. The percentage of polymorphic marker band was 74.70%, which indicates that the RAPD technique had higher efficiency of polymorphism detection and sensitivity in studying the genetic variations among ducks and showed that the genetic polymorphism was abundant between two species of duck populations. The average index of genetic distance in hybrid $F_2$ was 0.2341 and higher than that of its parents, which indicates that the genetic diversity was improved by crossbreeding with Muscovy.

• Journal of Life Science
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• v.9 no.1
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• pp.15-21
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• 1999

The random amplified ploymorphic DNAs (RAPD) assay is a simple and useful tool in identification of appropriate genetic markers, that requires no knowledge of target DNA sequence. RAPD products were generated directly from seaweed tissues, without prior nucleic acid extraction, of Porphyra yezoensis, Ulva pertusa and Undaria pinnatifida. The nuclear rDNA internal transcribed spacer (ITS) fragment however was not amplified directly from the seaweed tissues. Using DNA extracted by the LiCl method, both the ITS and RAPD's have been amplified by the polymerase chain reaction. RAPD of P yezoensis, thallus (n) and conchocelis (2n) produced lots of different polymorphic bands (36-50$\%$) depending on the arbitrary primers used. Difference was also observed between direct tissues amplification and DNA extracts amplification (53-57$\%$). Thus it is important to use the same ploidy of tissue for DNA extraction and as a RAPD template.