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RAPD
About: RAPD is a research topic. Over the lifetime, 15960 publications have been published within this topic receiving 360391 citations.
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TL;DR: Assessment of a subset of the germplasm array using RAPDs resulted in genetic distance measurements more similar to published genetic distance estimates by RFLP markers than estimates by isozyme markers, indicating that RAPD markers have utility for analysis of genetic diversity and germplasms management in cucumber.
Abstract: Isozyme and restriction fragment length polymorphisms (RFLPs) have been applied to studies of genetic relationships and germplasm management in cucumber (Cucumis sativus L.). However, isozymes identify relatively few polymorphisms, and RFLPs are technically complex, expensive, and not compatible for the high through-put required for rigorous assessment of this narrow-based germplasm. Since random amplified polymorphic DNA (RAPD) markers do not manifest such shortcomings, a study was conducted in cucumber to examine genetic relationships in diverse germplasm, assess the usefulness of RAPD markers in distinguishing elite accessions, and compare the relative effectiveness of RAPD markers to that of isozyme and RFLP markers. One hundred and eighteen C. sativus accessions were analyzed using variation at 71 RAPD loci (44 mapped and 27 unmapped). Genetic distances among accessions were estimated using the simple matching coefficient complement, and analyzed using multi-dimensional scaling. Each accession had a unique marker profile, indicating that RAPD analysis was useful in genotypic differentiation. Germplasm grouping patterns were consistent with individual accession origins, theoretical dispersal routes and discriminating morphological characters (i.e., sex expression and fruit length to diameter ratio). Although elite accessions were discriminated by RAPD profiling, their genetic distances were relatively small (between 0.01 and 0.58), indicating limited genetic diversity in this germplasm array. Assessment of a subset of the germplasm array using RAPDs resulted in genetic distance measurements more similar to published genetic distance estimates by RFLP markers (Spearman rank correlation, rs = 0.7–0.8) than estimates by isozyme markers (rs = 0.4). Data indicate that RAPD markers have utility for analysis of genetic diversity and germplasm management in cucumber.
102 citations
TL;DR: In this article, a laboratory study was conducted to evaluate the response of soil enzyme activities (namely dehydrogenase, phosphatase and urease) to different levels of trace element pollution in soil representative area.
Abstract: A laboratory study was conducted to evaluate the response of soil enzyme activities (namely dehydrogenase, phosphatase and urease) to different levels of trace element pollution in soil representative area. The improved ecological dose model and random-amplified polymorphic DNA (RAPD) were used to assess soil health. The 50% ecological dose (ED50) values modified by toxicant coefficient were calculated from the best-fit model, and determination values from the regression analysis for the three enzyme activities were studied after the incubation periods. The results showed that the elevated heavy metal concentration negatively affects the total population size of bacteria and actinomycetes and enzymatic activity; dehydrogenase (ED50 = 777) was the most sensitive soil enzyme, whereas urease activity (ED50 = 2,857) showed the lowest inhibition; combined pollution or elevated toxicant level would increase disappearing RAPD bands, and the number of denoting polymorphic bands was greater in combined polluted soils. All three mathematical modified models satisfactorily described the inhibition of soil enzyme activities caused by Cd and Pb, by giving the best fit.
102 citations
TL;DR: All Mediterranean Pleurotus populations growing on umbellifers seem to have recently diverged through a sympatric speciation process, that is based on both intrinsic reproductive barriers and extrinsic ecogeographical factors.
Abstract: The Pleurotus eryngii species-complex includes populations of choice edible mushrooms, growing in the greater Mediterranean area in close association with different genera of plants of the family Apiaceae. Their distinct host-specialization served as the principal criterion for the discrimination of several taxa; however, the genetic relationships among the various P. eryngii ecotypes remain ambiguous. In the present study, 46 Pleurotus strains with a wide range of geographical origins were isolated from Eryngium spp., Ferula communis, Cachrys ferulacea, Thapsia garganica and Elaeoselinum asclepium subsp. asclepium, and were subjected to isozyme and random amplified polymorphic DNA-PCR (RAPD) analysis. The 16 enzyme activities tested were controlled by 28 loci, 11 of which were monomorphic. Host-exclusive zymograms for the Aph (acid phosphatase) and Phe-1 (dopa-phenoloxidase) loci were obtained from Pleurotus strains associated with C. ferulacea. Allele frequencies, genetic diversity and mean diversity were high for isolates from Eryngium spp. and Ferula communis. In RAPD analysis, the use of five primers allowed the production of 45 (out of 48) polymorphic bands, while four molecular markers specific for the identification of Pleurotus strains growing on E. asclepium subsp. asclepium and C. ferulacea were obtained. The Pleurotus strains produced 35 distinct electrophoretic types and 42 RAPD patterns, which independently permitted the separation of the fungal populations into five clusters in accordance with their host-specificity. In addition, the evaluation of the principal ecological and morphological characters provided further evidence for discriminating between P. nebrodensis growing on C. ferulacea and the rest of the host-associated populations. The latter represent taxa at the varietal level: P. eryngii var. eryngii, P. eryngii var. ferulae and P. eryngii var. elaeoselini. The position of taxa of dubious validity, such as P. hadamardii and P. fossulatus, is discussed in relation to the new findings. All Mediterranean Pleurotus populations growing on umbellifers seem to have recently diverged through a sympatric speciation process, that is based on both intrinsic reproductive barriers and extrinsic ecogeographical factors.
102 citations
TL;DR: The results indicate that the random amplification of polymorphic DNA (RAPD) may be an extremely useful approach to the identification of schistosome strains and species.
102 citations
TL;DR: Within food strains, one RAPD profile was more common than others, suggesting this to be a common type among strains from this source, and discrimination within serogroups was allowed, although five RAPD profiles which were not confined to one serotype were found.
Abstract: The 10-mer primer OPM-01 (5'-GTT GGT GGC T-3') was used to generate random amplification of polymorphic DNA (RAPD) profiles by polymerase chain reaction for 91 strains of Listeria monocytogenes from raw milk, food, and veterinary, medical, and food-environmental sources. The profiles obtained contained 1 to 10 bands within the molecular size range of 0.5 to 5.0 kbp. Reproducibility was enhanced by annealing at low stringency and introducing a 1-min ramp time between annealing and extension temperatures. Thirty-three RAPD profiles were observed, with specific profiles being observed for strains from each source. RAPD profiles allowed discrimination within serogroups, although five RAPD profiles which were not confined to one serotype were found. Within food strains, one RAPD profile was more common than others, suggesting this to be a common type among strains from this source.
102 citations