• Microbiology and Biotechnology Letters
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• v.22 no.6
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• pp.577-583
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• 1994

To classify Lactobacillus casei strains on the basis of difference in their chromosomal DNA sequence, we have performed polymerase chain reactions on their chromosomal DNA by using random primers, and followed by analyzing randomly amplified polymorphic DNA fragments. We also developed a mini-preparative method to isolate PCR-grade chromosomal DNA from Lacto- bacillus casei strains within 3 hours. Based on RAPD pattems by polymerase chain reactions with degenerated random primers, 4 Lactobacillus casei strains and 2 mutant strains were successfully discriminated. Results were very sensitive, strain-specific and reproducible. It was also reliable. These results suggest that RAPD may be applied efficiently for the identification of several Lactoba- cillus casei strains.

• Journal of Plant Biotechnology
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• v.1 no.2
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• pp.109-115
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• 1999

A linkage map of Capsicum annuum L. was constructed by random amplified polymorphic DNA (RAPD) markers followed in a backcross population of an intraspecific cross between cultivars HDA210 and Yatsufusa. A total of 420 random primers were tested and 311 polymorphic bands were generated by 158 random primers. Among them, 86 Yatsufusa specific bands generated by 52 primers were examined for mapping. Most bands except three segregated in Mendelian fashion fitting the expected 1:1 ratio. The total length of the map was 533 cM distributed in 15 linkage groups. The map distance between adjacent markers ranged 0 to 32.8 cM, with an average distance of 9.1 cM (63 markers). Some markers were clustered and this may be due to the amplification of a repetitive sequence by the RAPDs. Primer pairs for a sequence characterized amplified region (SCAR) were developed and the segregation scores by the SCAR primers were in accordance with the RAPD data. Two QTL markers for number of axillary shoots and for early flowering were developed. One QTL for early flowering located in the linkage group 3 and explained 61 "io of the phenotypic variation. The other QTL for the number of axillary shoots located in the linkage group 4 explained 55 % of the phenotypic variation.tion.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.4
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• pp.470-476
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• 2002

Random amplified polymorphic DNA (RAPD) analysis based on numerous polymorphic bands have been used to investigate genetic similarity and diversity among and within two cultured and wild populations represented by the species crucian carp (Carassius carassius). From RAPD analysis using five primers, a total of 442 polymorphic bands were obtained in the two populations and 273 were found to be specific to a wild population. 169 polymorphic bands were also produced in wild and cultured population. According to RAPD-based estimates, the average number of polymorphic bands in the wild population was approximately 1.5 times as diverse as that in cultured. The average number of polymorphic bands in each population was found to be different and was higher in the wild than in the cultured population. Comparison of banding patterns in the cultured and wild populations revealed substantial differences supporting a previous assessment that the populations may have been subjected to a long period of geographical isolation from each other. The values in wild population altered from 0.21 to 0.51 as calculated by bandsharing analysis. Also, the average level of bandsharing values was $0.40{\pm}0.05 $ in the wild population, compared to $0.69{\pm}0.08$ in the cultured. With reference to bandsharing values and banding patterns, the wild population was considerably more diverse than the cultured. Knowledge of the genetic diversity of crucian carp could help in formulating more effective strategies for managing this aquacultural fish species and also in evaluating the potential genetic effects induced by hatchery operations.

• 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.

• The Korean Journal of Malacology
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• v.25 no.1
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• pp.41-49
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• 2009

Random amplified polymorphic DNA (RAPD) marker and sequence analyses of the internal transcribed spacer (ITS) region of ribosomal DNA were used to assess phylogenetic relationships of four Korean oyster species. The average number of species-specific markers identified from five universal rice primers (URPs) by RAPD-PCR was 1.8 for Crassostrea gigas, 3.2 for C. nippona, 3.6 for C. ariakensis, and 4.6 for Ostrea denselamellosa. The length of the ITS (ITS1-5.8S-ITS2) region ranged from 1,001 to 1,206 bp (ITS1, 426-518 bp; 5.8S, 157 bp; and ITS2, 418-536 bp), while the GC content ranged from 55.5-61.1% (ITS1, 56.8-61.8%; 5.8S, 56-57.3%; and ITS2, 54.1-62.2%). A phylogenetic analysis of the oysters based on our RAPD, ITS1, and ITS2 sequence data revealed a close relationship between C. gigas and C. nippona and a distant relationship between the genera Crassostrea and Ostrea. Our results indicated that RAPD and ITS sequence analysis was a useful tool for the elucidation of phylogenetic relationships and for the selection of species-specific markers in Korean oysters.

• Korean Journal of Veterinary Research
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• v.45 no.3
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• pp.359-367
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• 2005

This study was carried out to understand the contamination patterns of Listeria in pork processing plants. A total of 402 samples were collected from carcass, pork during processing, surfaces of equipment and environment, and 238 isolates of Listeria species were identified. L. innocua was found in 64.7% of the isolates, L. monocytogenes in 33.2%, and L. welshimeri in 2.1%. Random amplified polymorphic DNA (RAPD) analysis performed to investigate the origin and routes of Listeria contamination, showed 21 composite types of L. monocytogenes and 26 composite types of L. innocua. It was confirmed that Listeria contamination begins with contaminated incoming carcass and ever-present contaminants in the processing environments. The persistence and dissemination of the same strain of L. monocytogenes and L. innocua throughout the processing line revealed that the sanitation standard operating procedure should be implemented to minimize the risk of colonization in the workplace. Molecular subtyping of L. innocua allowed us to tracing the possibility of cross-contamination during processing.

• Journal of Life Science
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• v.14 no.3
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• pp.521-524
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• 2004

This experiment was carried out to analyze genetic characteristics and to develop the breed specific DNA marker for Cheju-native horse. If this marker contains high repetitive sequences, it is possible to convert a RAPD marker of interest into a single-locus PCR marker called a sequence characterized amplified region(SCAR). Twenty six Cheju-native horse and Fifty thoroughbred genomic DNA were pooled and PCR. were accomplished using 800 random primers. Comparing the pooled DNA from Cheju-native horse and thoroughbred, we found 9 primers which identified markers present in the pooled DNA from breed but absent in the other breed. Among 9 random primers, 6 primers were thoroughbred specific and 3 primers were Cheju-native horse specific. Testing individual horse revealed that 5 marker showed the similar band pattern between Cheju-native horse and Thoroughbred. However, 4 marker were wholly absent in breed while present in the other breed. UBC $126_{3500bp}$, UBC $162_{500bp}$, and UBC $244_{1200bp}$ was detected only Thoroughbred and UBC $562_{560bp}$was detected Cheju-native horse, respectively. After determining of the cloned breed-specific fragment sequence, we designed the SCAR-primers and carried out PCR. Compared to random primer, RAPD-SCAR primer didn't show significantly higher specific band. However, RAPD analysis is useful for genetic characterization of Cheju-native horse.

• 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.

• International Journal of Industrial Entomology and Biomaterials
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• v.29 no.2
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• pp.169-178
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• 2014

In this study, we investigated genetic diversity of 22 microsporidian isolates infecting tropical tasar silkworm, Antheraea mylitta collected from various geographical forest locations in the state of Jharkhand, India, using polymerase chain reaction (PCR)-based marker assay: random amplified polymorphic DNA (RAPD). A type species, NIK-1s_mys was used as control for comparison. The shape of mature microsporidians was found to be oval to elongate, measuring 3.80 to $5.10{\mu}m$ in length and 2.56 to $3.30{\mu}m$ in width. Of the 20 RAPD primers screened, 16 primers generated reproducible profiles with 298 polymorphic fragments displaying high degree of polymorphism (97%). A total of 14 RAPD primers produced 45 unique putative genetic markers, which were used to differentiate the microsporidians. Calculation of genetic distance coefficients based on dice coefficient method and clustering with un-weighted pair group method using arithmetic average (UPGMA) analysis was conducted to unravel the genetic diversity of microsporidians infecting tasar silkworm. The similarity coefficients varied from 0.059 to 0.980. UPGMA analysis generated a dendrogram with four microsporidian groups, which appear to be different from each other as well as from NIK-1s_mys. Two-dimensional distribution based on Euclidean distance matrix also revealed considerable variability among different microsporidians identified from the tasar silkworms. Clustering of few microsporidian isolates was in accordance with the geographic origin. The results indicate that the RAPD profiles and specific/unique genetic markers can be used for differentiating as well as to identify different microsporidians with considerable accuracy.

• Journal of Life Science
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• v.20 no.7
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• pp.983-990
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• 2010

Genus Spiraea is a woody species primarily distributed throughout Asia. Many species of this genus are important plants medicinally and ecologically. I evaluated a representative sample of the sixteen taxa with random amplified polymorphic DNA (RAPD) markers to estimate genetic relationships within genus Spiraea. In addition, RAPD analysis was also conducted to estimate the genetic diversity and population structure of these species. As the typical populations of Spiraea were small, isolated, and patchily distributed for natural populations, they maintained a low level of genetic diversity for polymorphic primers. The mean H was 0.117 across species. The Korean endemic species (S. chartacea) and patchily distributed species (S. betulifolia) showed fewer alleles per locus (mean 1.240 vs. 1.297), lower percent polymorphic locus (24.0 vs. 29.7), and lower diversity (0.092 vs. 0.121) than a relatively widely spread species. An assessment of the proportion of diversity present within species, $H_{POP}/H_{SP}$, indicated that about 87.8% the total genetic diversity was among species. Thus, the majority of genetic variation (87.8%) resided within species. The phylogenic tree showed three distinct groups. One clade includes S. prunifolia for. simpliciflora, S. thunbergii, S. chamaedryfolia var. ulmifolia, S. media, and S. cantoniensis. Another clade includes S. blumei, S. pubescens, S. chartacea, and S. chinensis. The other clade is the remaining seven species.