Random Amplified Polymorphic DNA Results Research Articles

Morphology, Biochemical, and Molecular Characterization of Pasteurella multocida Causing Hemorrhagic Septicemia in Indonesia.

Pasteurella multocida is a Gram-negative bacterium that causes hemorrhagic septicemia (HS) in buffaloes and cattle. The disease causes serious problems in Indonesian livestock and is classified as a serious transmissible animal disease. Previous research has determined the diversity of P. multocida using a serotyping method based on the antigenic properties of capsule polysaccharides. An alternative method for analysis utilizes sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and random amplified polymorphic DNA (RAPD). This study aimed to characterize and determine P. multocida diversity in several regions of Indonesia based on phenotypic character, protein profile, and the band pattern of RAPD results. Bacterial identification was performed using traditional biochemical techniques and API® 20NE systems and then confirmed molecularly using polymerase chain reaction (PCR). The freeze-thawing technique was performed to obtain the bacterial protein extract, and DNA extraction was executed using DNAzol. The extracted protein and RAPD product were then electrophoresed on 12% polyacrylamide gel and 1.5% agarose gel, respectively. The results indicate that the molecular weight range of the protein bands is 12-209 kDa, and the band pattern of the RAPD results ranged from 307-3,100 bp. Based on phenotypical analysis, P. multocida from South Sulawesi Province exhibited a variety of growth characteristics in MacConkey agar media. Using the hierarchical clustering analysis of the band patterns of RAPD and the whole-cell protein profiles, four and five clusters were formed, respectively. These results indicate molecular diversity among P. multocida from several regions of Indonesia.

Analysing South Sumatra red rice polymorphism using random amplified polymorphic DNA (RAPD) markers

this research aims to determine genetic variation based on polymorphism bands and the relationship between red rice in south sumatra based on PCR- RAPD (Polymerase Chain Reaction- Random Amplified Polymorphic DNA) tecnique using the mathematical modeling application NTSys 2.1. Collecting data using observation methods where samples are collected genetic variation and presented in quantitative form. Research instruments include tools and laboratory materials that facilitate the research process such as electrophoresis, thermal cycle machines, gel documentation and others. DNA bands obtained electrophoresized PCR sample is converted into binary data which is stated by the presence or absence of DNA bands, if there is a DNA band then marked with (1), whereas if the DNA band does not appear then marked with (0). Data were analysed using the NTSys version program. 2.1. Dendrogram created using unweighted pair-group with arithmetic average with genetic similarity coefficient using Jaccard Coefficient of Similarity and presented in the form of dendrogram. Based on the DNA band profile of RAPD results which 43 DNA bands show polymorphism (93.47%). Based on the analysis using the NTSys 2.1 program, a dendogram was obtained where red rice in South Sumatra was divided into two main clusters at a genetic similarity coefficient level of 0.19, namely cluster A consisting of red rice with CT code (Cahya Tani) and cluster B consisting of red rice SJ code (Sumber Jaya), SP (Sp Padang), and K (Kelirejo). The four red rice individuals taken from different places have a low genetic similarity coefficient of 0.15-0.37, meaning that the fourth genetic variation of red rice is very high.

Genetic impacts induced by BaP and Pb in Mytilus coruscus: Can RAPD be a validated tool in genotoxicity evaluation both in vivo and in vitro?

Benzo(α)pyrene (BaP) and lead (Pb) are common pollutants discharged greatly in ocean and causing detrimental impacts on marine organisms. Although mussels are one of the most prominent and frequently studied biological models, the research on their genomic alterations induced by the mixture of two totally different chemicals, is still rare. In present study, local marine mussels Mytilus coruscus were exposed in vivo to BaP (53.74 ± 19.79 μg/L), Pb (2.58 ± 0.11 mg/L) and their mixture for 6 days. The genotoxic damages were assessed by comet assay, micronucleus (MNi) test, and random amplified polymorphic DNA (RAPD) analysis. Significantly increased though transitory genomic damage was investigated after the exposure and showed consistency using various detecting methods. Additive genotoxicity was only found after 3 days combined exposure by means of MNi test, suggesting that BaP and Pb may play with alternative biological targets during metabolism and/or interaction with the genome. The geno-stability and the recovery capability were further detected both in vivo and in vitro after challenged by BaP. RAPD results showed coherence in BaP induced genotoxicity, together with time-specific alterations. The genomic instability was found to recover in both in vivo and in vitro exposure scenarios in present study. To our knowledge, this is the first study to focus on the genotoxicitiy induced by BaP, Pb and their mixture by multiple detecting techniques. The attempt to utilize model pollutants and marine organism to validate the potential value of RAPD analysis highlighted that it might be a useful tool in the research of genotoxicology, especially on the effect-mechanism interplay at genetic level.

Analyses of somaclonal variation in endosperm-supported mature embryo culture of rye (Secale cereale L.)

ABSTRACTGenetic variations, and especially somaclonal variations, are undesirable in genetic transformation. In this study, random amplified polymorphic DNA (RAPD) and coupled restriction enzyme digestion-random amplification (CRED-RA) markers were used for detection of the variation in calli that were obtained from endosperm-supported mature embryo of rye on Murashige and Skoog (MS) medium containing different auxins (2,4-D, dicamba and picloram) at a range of different concentrations (2, 4, 6, 8, 10 and 12 mg/L). High level of auxins caused a reduction in the genomic template stability (GTS) value. While the highest GTS was observed in the calli maintained on MS medium with 2 mg/L dicamba (98.4%), the calli maintained on MS medium with 12 mg/L picloram were found to show the least GTS (81.7%) when RAPD patterns were analysed. Epigenetic changes were more frequent and variable than genetic changes when compared to RAPD and CRED-RA results. DNA hypermethylation was observed at higher concentrations of 2,4-D and picloram, whereas DNA hypomethylation was observed in dicamba. These results indicate that RAPD and CRED-RA techniques can be used for detection of somaclonal variation in in vitro cultures, which is a fundamental step in plant genetic transformation.

Development of RAPD and SCAR markers related to watermelon mosaic virus and zucchini yellow mosaic virus resistance in Cucurbita moschata

Squash (Cucurbita spp.) is a major vegetable crop in the Cucurbitaceae family, and has high economic value. Squash is an important foodstuff and has possible health benefits because of its antioxidant, anti-diabetic, anti-carcinogenic, and anti-microbial potential. However, the highly virulent watermelon mosaic virus (WMV) and zucchini yellow mosaic virus (ZYMV) are serious problems for squash worldwide. Single or mixed infections of WMV and ZYMV can destroy entire squash plants. Therefore, breeding squash cultivars with resistance to WMV and ZYMV is of major importance for squash cultivation. In this study, random amplified polymorphic DNA (RAPD) and sequence-characterized amplified region (SCAR) markers were developed using C. moschata lines resistant or susceptible to WMV and ZYMV. A total of 100 random primers were tested for their ability to discriminate between resistant and susceptible lines in RAPD analysis, and 4 RAPD markers (OPF10, OPF19, OPF20, and OPL19) related to WMV and ZYMV resistance were selected. Based on the RAPD results, genetic similarities were calculated and cluster analysis was conducted using unweighted pair group method with arithmetic mean (UPGMA) method. C. moschata lines were clearly segregated into resistant and susceptible lines by cluster analysis. One of the RAPD markers was successfully converted into a SCAR marker (VirSq-F19). This marker could be used as a tool for selecting WMV- and ZYMV-resistant squash in the early selection stages of a practical squash breeding program.

Diversity analysis of green gram (Vigna radiata (L.) Wilczek)through morphological and molecular markers

Twenty-three genotypes of green gram (Vigna radiata (L.) Wilczek) were collected to determine the extent of genetic diversity through morphological characters as well as random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), and simple sequence repeat (SSR) fingerprinting results. Analysis of variance revealed significant mean square values that indicated a substantial degree of genetic variability among the genotypes. Significant genetic variance was observed for days to 50% maturity, days to maturity, plant height (cm), number of branches/plant, number of pods/plant, pod length (cm), 1000-seed weight (g), seed yield/plant (g), biological yield (g), and harvest index (%) during cultivation in three different environments. Hierarchical Euclidean and cluster analysis based on 10 morphological characteristics grouped all 23 genotypes into three divergent clusters. RAPD (15), ISSR (13), and SSR (10) markers produced a total of 216 bands, of which 190 exhibited polymorphism. The similarity coefficients were significant for all markers; however, they were higher in ISSR than in RAPD or SSR. In the UPGMA dendrogram based on the combined morphological, RAPD, ISSR, and SSR results, the 23 genotypes were divided into three main clusters. The present study revealed that morphological and molecular markers may be successfully utilized for determining genetic diversity and relationships in green gram genotypes and could be used in green gram breeding programs.

Determination of genetic and epigenetic effects of glyphosate on Triticum aestivum with RAPD and CRED-RA techniques

In this study, the most commonly used herbicide, glyphosate, was investigated for its genotoxic effects on the genome of Triticum aestivum. Five different concentrations of the herbicide were used, and alterations to DNA were measured quantitatively based on their RAPD (Randomly Amplified Polymorphic DNA) profiles. The genomic template stability (GTS%) at each concentration was evaluated, and a decrease was observed with increasing glyphosate concentration. Thus the highest concentration was concluded to be the most effective for causing alteration to DNA. Additionally, the coupled restriction enzyme digestion-random amplification (CRED-RA) technique was used to determine an epigenetic mechanism, e.g. DNA methylation. The polymorphic percentages of all concentration were calculated after herbicide applications. When in glyphosate doses compared with control group, all applications of glyphosate observed to consist of methylation. The methylation levels range from 28.3 to 73.9 % (DNA hypermethylation). In conclusion, based on the RAPD and CRED-RA results, glyphosate causes DNA alterations and methylation.

Assessment of genetic characteristics of Aconitum germplasms in Xinjiang Province (China) by RAPD and ISSR markers

Aconitum is a medicinal treasure trove that grows extensively on fertile pastures in Xinjiang Province (China); however, its molecular genetic characteristics are still poorly studied. We studied Aconitum kusnezoffii Reichb., Aconitum soongaricum Stapf., Aconitum carmichaelii Debx. and Aconitum leucostomum Worosch, using random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) techniques, to evaluate their genetic relationship and potential medicinal value. Our results showed that A.kusnezoffii Reichb. and A.soongaricum Stapf. have close genetic relationship and cluster together. Polymorphism rates of 97.25% and 98.92% were achieved by using 15 RAPD and 15 ISSR primers, respectively. Based on Nei's gene diversity (H) and Shannon's index (I), the inter-population diversity (Hs) was higher when compared with the intra-population diversity (Hp). Among the three Aconitum populations, the coefficient of gene differentiation (Gst) was 0.4358 when evaluated by RAPD and 0.5005 by ISSR. The genetic differentiation among the three Aconitum populations was highly significant, suggesting low gene flow (Nm). This was confirmed by the estimates of gene flow (Nm = 0.6473 and Nm = 0.4991, based on ISSR and RAPD data, respectively). Comparing the RAPD and ISSR results, the two DNA markers proved similarly effective in the assessment of the genetic characteristics of the studied Aconitum populations and could be used for reliable fingerprinting and mapping in studies on Aconitum diversity in view of Aconitum suitability for development and protection.

Genetic analysis of litchi (Litchi chinensis Sonn.) in southern China by improved random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR)

Litchi (Litchi chinensis Sonn., L. chinensis), a type of tree growing in most areas of southern China, produces an edible fruit that is also a source of traditional medicine. Genetic identification of litchi species or cultivars using molecular markers is very important. In this study, a total of six litchi samples from Fujian, Hainan, Guangdong, Guangxi and Sichuan province, as well as one wild Dimocarpus confinis (D. confinis) sample from Guangxi province were collected for genetic analysis. The cluster dendrograms were constructed for genetic analysis on the basis of DNA amplification results by RAPD and ISSR. The improved RAPD amplified DNA with consistent and clear banding patterns. A total of 176 bands were found, indicating a 72.7 % polymorphism in L. chinensis DNA samples. Significant genetic distances were found among the different species or cultivars, with an index of similarity coefficient ranging from 0.59 to 0.87. Similar to RAPD results, ISSR analysis of the L. chinensis DNA samples showed a range of 0.70-0.93 similarity coefficients. The genetic distance between Hainan sample and Sichuan samples was the farthest, which is consistent with their geographic distance. Furthermore, the index of similarity coefficient between D. confinis and L. chinensis was 0.35-0.41 by RAPD and 0.38-0.48 by ISSR, indicating that these two species have significant genetic difference. This study reveals the high level of genetic differences between different litchi species or cultivars, and confirms the significance of the improved RAPD method in genetic characterization of organisms. Taken together, the improved RAPD combined with ISSR analysis can be used frequently for the genetic diversity, germplasm resources preservation, molecular-assisted breeding, and genetic characterization of various organisms.

Study on Classification and Genetic Diversity of Kentucky Bluegrasses by Using RAPD Markers

A total of 69 random primers were screened by using random amplified polymorphic DNA (RAPD) markers to analyze the genetic bands of 32 Kentucky bluegrass cultivars. A total of 197 bands were amplified from 46 primers, among which 195 bands were polymorphic. Each primer could amplify one to nine polymorphic bands with an average of 4.3 per primer. Based on similarity coefficient analysis of RAPD results and by using NTSYS software to cluster analyze with the average UPGMA method, the result showed that 18 cultivars of the 32 were in group 1, three cultivars were in group 2, two cultivars were in group 3, eight cultivars were in group 4, and only one cultivar in group 5.

Molecular Characterization of Seven Different Species of <i>Aspergillus</i> through Random Amplified Polymorphic DNA (RAPD) and Enzyme Analysis

The aim of this study was to characterize seven species of Aspergillus at molecular level, using random am- plification of polymorphic DNA (RAPD). RAPD- PCR conditions were optimized for two primers of series B, GL Decamer B-09 and GL Decamer B-10 out of 10 total primers. RAPD results were evaluated by a statistical software Minitab and a phylogenetic tree was prepared. GL Decamer B-09 showed 38 bands and GL Decamer B-10 gave 46 bands, showing 50% and 57% similarity respectively, among species. Biochemical characterization was done by screening of zones production with particular enzyme activity of each specie resulted in particular substrate degradation.

English

In this study, we identified novel family- and genus-specific DNA markers in Mugilidae fish. Genomic DNA was isolated from the blood of fish of 15 families and eighty (80) random primers were used for random amplified polymorphic DNA (RAPD) fingerprinting. When the primer OPAV04 was employed, a novel specific PCR product was observed in the Mugilidae family. In addition, another novel specific PCR product was also observed in the Liza genus while using primer OPAV10. Sequencing analysis revealed that the novel family- and genus-specific DNA fragments were 857 and 419 bp, respectively, and no similar sequences were found in GenBank. Two primers sets were designed based on the family- and genus-specific sequences to confirm the RAPD results and the 571 and 187 bp predicted bands were successfully amplified by PCR. Intriguingly, these two novel specific DNA markers were also effectively used for terrestrial and aquatic animal discrimination. Therefore, the novel family- and genus-specific DNA markers identified in this study can be used as an effective tool for rapid and accurate determination of the Mugilidae family and Liza genus, and even for cross-species identification.   Key words: Mugilidae, family- and genus-specific sequences, DNA markers.

ANALYSIS OF DONGBI LONGAN WITH ISOENZYME AND RAPD TECHNOLOGIES

Longan (Dimocarpus longan Lour.) is one of the most important subtropical fruit trees in Fujian province. Due to little genetic background, the development of longan resources study was restricted. Random amplified polymorphic DNA (RAPD) and POD isoenzyme techniques were used to study the genetic polymorphism and relationship among strains of Dongbi longan. Twenty two arbitrary 10mer primers were used in RAPD analysis of 13 Dongbi longan strains. A total of 124 bands were amplified from 13 samples, each primer pair produces 3 (S299) to 9 (S60) bands, and the average bands were 5.64. The RAPD results showed that the genetic comparability was significantly high and there was high genetic stability among 13 strains, but genes varied with the time and environment. Compared to RAPD results, there was no significant difference in POD isoenzyme among 13 samples from POD isoenzyme gel. According to the results, we concluded that RAPD technology is more suitable than POD isoenzyme technology for longan germplasm resources analysis.

Biochemical and Molecular Characterization of Some Centaurea Species Growing in the Eastern Anatolia Region of Turkey

Random amplified polymorphic DNA (RAPD) and fatty acid (FAME) profiles were used to examine phenotypic and genetic relationships among 16 Centaurea species growing wild in the eastern Anatolia region of Turkey. Thirteen decamer primers were used to examine polymorphism. According to the RAPD results, 99 amplicons in the size range of 50-1000 bp were produced from 13 primers in 16 Centaurea species. Genetically four distinct groups were determined among the species of Centaurea, which represents high genetic variation. In the 16 species, 14 fatty acids were determined according to FAME results. Both FAME and RAPD results showed that C. virgata is genetically different from other species. The differences in the composition of fatty acids among Centaurea species suggest that fatty acid profiles could be used to differentiate among some of these species. Results of this study show that RAPD and FAME analyses are consistent.

Genetic and Withaferin A Analysis of Iranian Natural Populations ofWithania SomniferaandW. Coagulansby RAPD and HPTLC

For successful conservation and breeding of a medicinal species, it is important to evaluate its genetic diversity as well as its content of phytochemical compounds. The aim of the present study was to investigate the genetic variation of Iranian natural populations of W. somnifera and W. coagulans, using the RAPD (random amplified polymorphic DNA) markers, and their withaferin A content. Using 16 RAPD primers, a total of 282 RAPD bands were achieved. The highest and lowest percentages of polymorphism were observed with primers OPAD-15 (100.0%) and OPC-06 (75.0%), respectively. Cluster analysis of the genotypes was performed based on data from polymorphic RAPD bands, using Dice's similarity coefficient and the UPGMA clustering method. Variations in the RAPD results were found to reflect geographical distribution and genetic factors of the plant populations. The HPTLC analysis of the studied samples revealed the presence of withaferin A in W. coagulans and W. somnifera. Moreover, the concentration of withaferin A had a range from 2.2 to 32.5 microg/g DW and was higher in the aerial part than in the root in all used samples. The results of the present study show that there is a high level of variation in the Iranian natural population of Withania, which is significant for conservation and breeding programs to improve production of withaferin A.

Phenotypic and molecular evaluation of genetic diversity of rapeseed ( Brassica napus L.) genotypes

The genetic diversity and relationships among rapeseed genotypes were evaluated using quantitative analysis and random amplified polymorphic DNA (RAPD) markers. Ten morphological and biochemical traits (plant height, height to the first branch, stem diameter, branch number, leaf number, pod number, seed yield per plant, 1000-seed weight, oil content and protein content) were analyzed in a three-year field experiment with 30 winter rapeseed genotypes. RAPD analysis was performed with 13 primers, chosen according to previous results. Significant genetic variability among the genotypes was obtained at both the morphological and molecular level. Nine out of the thirteen RAPD primers that were used for the analysis enabled the estimation of DNA polymorphism of the genotypes, while the other primers were monomorphic. Dendrograms obtained for morpho-biochemical traits and for the RAPD results were compared. In both cases partial grouping of genotypes based on their geographical origin was established.

GENETIC DIVERSITY OF NEOTYPHODIUM ENDOPHYTES ISOLATED FROM <EM>ACHNATHERUM SIBIRICUM</EM> POPULATIONS IN MID_ AND EASTERN INNER MONGOLIA STEPPE, CHINA

Background and Aims The fungal endophytes in grasses grow intercellularly and systemically in aboveground plant tissues. Vertically transmitted asexual endophytes (Neotyphodium) forming asymptomatic infections of cool-season grasses have been repeatedly derived from sexual species (Epichlo) that abort host inflorescences. The phylogenetic distribution of seed-transmitted endophytes is strongly suggestive of cocladogenesis with their hosts. Endophytes are considered plant mutualists: they receive nutrition and protection from the host plant while the host plant may benefit from enhanced competitive abilities and increased resistance to herbivores, pathogens, and various abiotic stresses. Most studies of grass-endophyte associations have been undertaken with two economically important plant species, Lolium perenne and Festuca arundinacea. The interactions between endophytes and other grasses in natural plant communities, however, are seldom concerned. Much less attention has been paid to native grasses in Inner Mongolia Steppe, which lies in the north of China and is an important part of Steppe in Eurasia, and only limited published symbiosis studies are available in this natural ecosystem. Thereby, a more comprehensive view of the ecology, diversity of endophytes and their interactions with host plants becomes essential. Methods Our research of grass (Achnatherum sibiricum) associated with Neotyphodium endophyte (a new grass-endophyte association) was carried out in the Inner Mongolia Steppe, China. Twenty-seven endophyte strains were isolated from four A. sibiricum populations including Hulingol (H), Xi Ujimqin Qi (X), Inner Mongolia Grassland Ecosystem Research Station of the Chinese Academy of Sciences (IMGERS-CAS) (I), and the Leymus chinensis plot of the IMGERS-CAS (L), respectively. Colony morphology, growth rate on potato dextrose agar (PDA) and conidial measurements of isolates were used to characterize diversity of endophytes hosted by A. sibiricum. The genetic polymorphisms of Neotyphodium species from the four A. sibiricum populations were also analyzed using random amplified polymorphic DNA (RAPD) markers. Key Results Four morphological groups of Neotyphodium species and five individual morphological types were described based on the colony morphology, growth rate, and conidial shape and size. A total of 463 bands were obtained using 20 RAPD primers, of which 461 bands were polymorphic. A total of 93 unique loci were obtained, accounting for 20.1% of the total amplified loci. Nei's diversity index (h) and Shannon's diversity index (I) were 0.238 and 0.387, respectively. In the four populations (H , X , I, and L), the value of h was 0.122 0, 0.180 4, 0.146 3 and 0.210 7, respectively. The four populations may be ranked in a descending order as L X I H, and the I of the four populations had a similar trend. The fixation index (F ST ), the coefficient of gene differentiation (G ST ), and the genetic differentiation (Hsp-Hpop)/Hsp (estimated by Shannon's diversity index) were 0.205 1, 0.300 4, and 0.355 0, respectively. The genetic variation of Neotyphodium species mainly existed within populations. Genetic similarities within each population were found to be in the range of 0.647 9-0.943 8 in similarity, and the average genetic distance among the four populations was 0.285 8, varying from 0.057 8 to 0.433 9. Clustering analysis based on Nei's unbiased genetic distance and UPGMA method showed that there were seven distinct RAPD genetic groups. Conclusions The high incidence of endophytic infection in A. sibiricum was indicative that the presence of the endophyte gave the grass a competitive advantage over non-infected grasses. The study also indicated that there were higher genetic diversity based on morphological and RAPD results, and that there were relatively high genetic variations among the four populations and higher genetic differentiation of Neotyphodium sp. within a geographical region. Most of the genetic groups were related to geographical origins of the strains. The dendrogram of genetic distance matched rather well with the morphological data, as reflected by the four morphotypes.

Population genetic studies on the Australian freshwater crayfish,Cherax destructor(Crustacea: Parastacidae) using allozyme and RAPD markers

Allozyme and Random Amplified Polymorphic DNA (RAPD) variation was surveyed in the freshwater crayfish Cherax destructor Clark, an ecologically and commercially important species that is widespread throughout the freshwater systems of central Australia. At the intra-population level, allozymes revealed a similar level of variation to that found in other freshwater crayfish; RAPDs showed less diversity than allozymes, which was unexpected. At the inter-population level, both techniques revealed significant population structure, both within and between drainages. RAPD results were consistent with phylogeographic patterns previously identified using mtDNA. Although allozyme data showed little geographic pattern in relation to genetic variation based on multidimensional-scaling (MDS) plots on matrices of genetic distance, results of AMOVA and Mantel tests indicated significant population structuring. Each of the mtDNA lineages proposed in a previous study also showed significant genetic structure at similar levels as revealed by RAPDs but different levels by allozymes. These results reject hypotheses previously put forward on genetic homogenisation within the species due to wide-scale translocation. The implications of the findings for conservation and aquaculture of C. destructor are also discussed.

Evaluation of randomly amplified polymorphic DNA and pulsed field gel electrophoresis techniques for molecular typing of Dermatophilus congolensis

This study aimed to evaluate molecular typing methods useful for standardization of strains in experimental work on dermatophilosis. Fifty Dermatophilus congolensis isolates, collected from sheep, cattle, horse and a deer, were analyzed by randomly amplified polymorphic DNA (RAPD) method using twenty-one different primers, and the results were compared with those obtained by typing with a pulsed field gel electrophoresis (PFGE) method using the restriction digest enzyme Sse8387I. The typeability, reproducibility and discriminatory power of RAPD and Sse8387I-PFGE typing were calculated. Both typing methods were highly reproducible. Of the two techniques, Sse8387I-PFGE was the least discriminating (Dice Index (DI), 0.663) and could not distinguish between epidemiologically related isolates, whereas RAPD showed an excellent discriminatory power (DI, 0.7694–0.9722). Overall, the degree of correlation between RAPD and PFGE typing was significantly high ( r, 0.8822). We conclude that the DNA profiles generated by either RAPD or PFGE can be used to differentiate epidemiologically unrelated isolates. The results of this study strongly suggest that at least two independent primers are used for RAPD typing in order to improve its discriminatory power, and that PFGE is used for confirmation of RAPD results.

Molecular differentiation ofPanax species by RAPD analysis

Traditional taxonomic methods used for the identification and differentiation of ginsengs rely primarily on morphological observations or physiochemical methods, which cannot be used efficiently when only powdered forms or shredded material is available. Randomly amplified polymorphic DNA (RAPD) was used to determine the unique DNA profiles that are characteristic not only of the genus Panax but also of various Panax subgroups collected from five different countries. RAPD results of OP-5A primer showed a specific single band that is characteristic of all ginseng samples. RAPD results of OP-13B primer demonstrated that OP-13B primer could be used as a unique RAPD marker to differentiate Panax species. These results support that this approach could be applied to distinguish Korean Ginseng (Panax ginseng) from others at the molecular level.