scholarly journals Clonal Nature of Enterotoxigenic Escherichia coliSerotype O6:H16 Revealed by Randomly Amplified Polymorphic DNA Analysis

1998 ◽  
Vol 36 (7) ◽  
pp. 2099-2102 ◽  
Author(s):  
Ana B. F. Pacheco ◽  
Kelen C. Soares ◽  
Darcy F. de Almeida ◽  
Gloria I. Viboud ◽  
Norma Binsztein ◽  
...  
Keyword(s):  
Dna Analysis ◽  
Genetic Relatedness ◽  
Geographical Origin ◽  
Rapd Analysis ◽  
Randomly Amplified Polymorphic Dna ◽  
Significant Similarity ◽  
Single Strain ◽  
Heat Stable ◽  
Clonal Nature ◽  
Different Parts

The genetic relatedness among 29 enterotoxigenic Escherichia coli strains of serotype O6:H16 was investigated by randomly amplified polymorphic DNA (RAPD) analysis. The strains were isolated in different parts of the world, displayed CS1-CS3 or CS2-CS3 profiles, and expressed heat-labile toxin (LT) and heat-stable toxin; a single strain expressed only LT. Ten RAPD types were distinguished and showed significant similarity, having on average 82% of the amplified bands in common. These results indicated that, irrespective of the different geographical origin or virulence factors, these strains belonged to a widespread clonal group.

scholarly journals RAPD analysis of genetic relatedness among selected quince (Cydonia oblonga Mill.) accessions from different parts of Turkey

2011 ◽  
Vol 38 (No. 4) ◽  
pp. 134-141 ◽  
Author(s):  
S. Bayazit ◽  
B. Imrak ◽  
A. Küden ◽  
M. Kemal Güngör
Keyword(s):  
Rapd Markers ◽  
Genetic Relatedness ◽  
Geographical Origin ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Randomly Amplified Polymorphic Dna ◽  
Cydonia Oblonga ◽  
A Minor ◽  
Almost All ◽  
Different Parts

Quince (Cydonia oblonga Mill.) is a minor fruit crop, which is primarily used for marmalade, jam, sauce and as rootstocks for pears. Different cultivated and local quince genotypes are grown in almost all parts of Turkey for fruit usage. In this study, randomly amplified polymorphic DNA (RAPD) technology was used to study the genetic relationships among 13 quince accessions selected from different parts of Turkey. Thirty decamer primers were used and 14 of them did not produce any polymorphism. The remaining 16 primers ranged in their amplification fragments between one (P-402, P-437, OPA 10, OPA 16, OPA 18 and OPA-19) and five (OPA-06 and OPA-07). The size of fragments varied from 100 to 1500 bp. Similarity values among the studied genotypes ranged between 0.483 and 0.925. The resulting dendrogram clustered into two groups (0.69 similarity value) based on evaluation of genetic similarities and differences. The results suggest that RAPD analysis could be used to distinguish and determine genetic variation among quince accessions. Also, the obtained clustering based on RAPD markers agreed to some extent with the geographical origin of the studied set of quince accessions.

scholarly journals Use of Random Amplified Polymorphic DNA Markers for Cultivar Identification in Mint

HortScience ◽  
2001 ◽  
Vol 36 (4) ◽  
pp. 761-764 ◽  
Author(s):  
A.L. Fenwick ◽  
S.M. Ward
Keyword(s):  
United States ◽  
Genetic Diversity ◽  
Dna Markers ◽  
Geographical Origin ◽  
Cultivar Identification ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
The United States ◽  
Randomly Amplified Polymorphic Dna ◽  
Commercial Oil

Seventeen mint accessions representing the three species grown for commercial oil production in the United States were characterized using randomly amplified polymorphic DNA (RAPD) analysis. The RAPD profiles readily identified the different Mentha species; calculation of genetic distance, based on the number of shared bands, indicated that M. spicata L. is more closely related to M. × gracilis than to M. × piperita. The RAPD profiles also distinguished among eight peppermint accessions of different geographical origin. However, only limited polymorphism was observed among the most widely grown peppermint and Scotch spearmint cultivars. These results indicate a potential lack of genetic diversity in mint cultivars grown for oil in the United States.

scholarly journals Genetic Diversity in Muscadine and American Bunch Grapes Based on Randomly Amplified Polymorphic DNA (RAPD) Analysis

1996 ◽  
Vol 121 (6) ◽  
pp. 1020-1023 ◽  
Author(s):  
Xianping Qu ◽  
Jiang Lu ◽  
Olusola Lamikanra
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Rapd Analysis ◽  
The United States ◽  
Average Genetic Distance ◽  
Separate Study ◽  
Randomly Amplified Polymorphic Dna ◽  
And Cluster Analysis ◽  
Grape Cultivars

Two morphologically distinct types of grapes belonging to the subgenera Euvitis and Muscadinia in the genus Vitis are cultivated in the United States. The former is commonly called bunch grapes while the latter is usually called muscadine. Genetic diversity among these grapes was investigated using RAPD markers. Sixteen grape cultivars, with parentage including V. rotundifolia Michx., V. vinifera L., and several American Vitis species, were used for the RAPD analysis. A total of 156 RAPD markers was produced from 19 random primers, over 90% of which was polymorphic among the muscadine and the bunch grapes. Polymorphisms were lower within each subgenus. Relationships between these two subgenera were estimated based on band-sharing and cluster analysis. The average genetic distance between the bunch and the muscadine grape cultivars was 0.45. The results based on DNA analysis agree with isozyme data obtained from a separate study, which demonstrated that muscadine grapes share very few common alleles with American bunch grapes and European grapes.

scholarly journals Comparison of Ribotyping, Randomly Amplified Polymorphic DNA Analysis, and Pulsed-Field Gel Electrophoresis in Typing ofLactobacillus rhamnosus and L. caseiStrains

1999 ◽  
Vol 65 (9) ◽  
pp. 3908-3914 ◽  
Author(s):  
Soile Tynkkynen ◽  
Reetta Satokari ◽  
Maria Saarela ◽  
Tiina Mattila-Sandholm ◽  
Maija Saxelin
Keyword(s):  
Gel Electrophoresis ◽  
Type Strain ◽  
Dna Analysis ◽  
Rapd Analysis ◽  
Pulsed Field Gel Electrophoresis ◽  
Strain Atcc ◽  
Randomly Amplified Polymorphic Dna ◽  
Specific Primers ◽  
Pulsed Field ◽  
Species Specific

ABSTRACT A total of 24 strains, biochemically identified as members of theLactobacillus casei group, were identified by PCR with species-specific primers. The same set of strains was typed by randomly amplified polymorphic DNA (RAPD) analysis, ribotyping, and pulsed-field gel electrophoresis (PFGE) in order to compare the discriminatory power of the methods. Species-specific primers for L. rhamnosusand L. casei identified the type strain L. rhamnosus ATCC 7469 and the neotype strain L. caseiATCC 334, respectively, but did not give any signal with the recently revived species L. zeae, which contains the type strain ATCC 15820 and the strain ATCC 393, which was previously classified asL. casei. Our results are in accordance with the suggested new classification of the L. casei group. Altogether, 21 of the 24 strains studied were identified with the species-specific primers. In strain typing, PFGE was the most discriminatory method, revealing 17 genotypes for the 24 strains studied. Ribotyping and RAPD analysis yielded 15 and 12 genotypes, respectively.

scholarly journals Assessment of the Genetic Diversity among Strains of Xanthomonas cynarae by Randomly Amplified Polymorphic DNA Analysis and Development of Specific Characterized Amplified Regions for the Rapid Identification of X. cynarae

2001 ◽  
Vol 67 (8) ◽  
pp. 3379-3384 ◽  
Author(s):  
Gaëlle Trébaol ◽  
Charles Manceau ◽  
Yves Tirilly ◽  
Stéphane Boury
Keyword(s):  
Genetic Diversity ◽  
Genetic Background ◽  
Genomic Dna ◽  
Dna Polymorphism ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Rapd Analysis ◽  
Rapid Identification ◽  
Randomly Amplified Polymorphic Dna ◽  
Pcr Markers

ABSTRACT The randomly amplified polymorphic DNA (RAPD) method was used to investigate the genetic diversity in Xanthomonas cynarae, which causes bacterial bract spot disease of artichoke. This RAPD analysis was also intended to identify molecular markers characteristic of this species, in order to develop PCR-based markers which can be used to detect this pathogenic bacterium in artichoke fields. Among the 340 RAPD primers tested, 40 were selected on their ability to produce reproducible and reliable fingerprints in our genetic background. These 40 primers produced almost similar patterns for the 37 X. cynarae strains studied, different from the fingerprints obtained for other Xanthomonas species and other xanthomonad-like bacteria isolated from artichoke leaves. Therefore, X. cynarae strains form a homogeneous genetic group. However, a little DNA polymorphism within this species was observed and the collection of X. cynarae isolates was divided into two groups (one containing three strains, the second one including all other strains). Out of seven RAPD markers characteristic of X. cynarae that were cloned, four did not hybridize to the genomic DNA of strains belonging to other Xanthomonas species. These four RAPD markers were converted into PCR markers (specific characterized amplified regions [SCARs]); they were sequenced, and a PCR primer pair was designed for each of them. Three derived SCARs are good candidates to develop PCR-based tests to detectX. cynarae in artichoke fields.

scholarly journals Identification of Pecan Cultivars and Their Genetic Relatedness as Determined by Randomly Amplified Polymorphic DNA Analysis

2001 ◽  
Vol 126 (4) ◽  
pp. 474-480 ◽  
Author(s):  
Patrick J. Conner ◽  
Bruce W. Wood
Keyword(s):  
Genetic Similarity ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Genetic Distances ◽  
Similarity Coefficient ◽  
Carya Illinoinensis ◽  
Randomly Amplified Polymorphic Dna ◽  
Average Value

Genetic variation among pecan [Carya illinoinensis (Wangenh.) C. Koch] cultivars was studied using randomly amplified polymorphic DNA (RAPD) markers. Using a combination of primers, a unique fingerprint is presented for each of the pecan genotypes studied. The genetic relatedness between 43 cultivars was estimated using 100 RAPD markers. Genetic distances, based on the similarity coefficient of Nei & Li, varied from 0.91 to 0.46, with an average value of 0.66 among all cultivars. The phenetic dendrogram developed from cluster analysis showed relatively weak grouping association. However, cultivars with known pedigrees usually grouped with at least one of the parents and genetic similarity estimates appear to agree with known genetic relationships.

scholarly journals Osmotic Stress-Induced Genetic Rearrangements inEscherichia coli H10407 Detected by Randomly Amplified Polymorphic DNA Analysis

2000 ◽  
Vol 66 (12) ◽  
pp. 5484-5487 ◽  
Author(s):  
Anne Jolivet-Gougeon ◽  
Sandrine David-Jobert ◽  
Zohreh Tamanai-Shacoori ◽  
Christian M�nard ◽  
Michel Cormier
Keyword(s):  
Osmotic Stress ◽  
Dna Analysis ◽  
Rapd Analysis ◽  
Agarose Gel Electrophoresis ◽  
Randomly Amplified Polymorphic Dna ◽  
Reaction Conditions ◽  
Banding Patterns ◽  
Dna Modifications ◽  
As Stress ◽  
Genetic Rearrangements

ABSTRACT Randomly amplified polymorphic DNA (RAPD) analysis is a DNA polymorphism assay commonly used for fingerprinting genomes. After optimizing the reaction conditions, samples of Escherichia coli H10407 DNA were assayed to determine the influence of osmotic and/or oligotrophic stress on variations in RAPD banding patterns. Genetic rearrangements or DNA topology variations could be detected as changes in agarose gel electrophoresis banding profiles. A new amplicon generated using DNA extracted from bacteria prestarved by an osmotic stress and resuscitated in rich medium was observed. Enrichment improved recovery of mutator cells and allowed them to be detected in samples, suggesting that DNA modifications, such as stress-induced alterations and supercoiling phenomena, should be taken into consideration before beginning RAPD analyses.

scholarly journals 090 Identification and Genetic Relatedness among Pecan Cultivars Detected by Randomly Amplified Polymorphic DNA (RAPD) Analysis

HortScience ◽  
2000 ◽  
Vol 35 (3) ◽  
pp. 404B-404
Author(s):  
Patrick J. Conner ◽  
Bruce W. Wood
Keyword(s):  
Cluster Analysis ◽  
Genetic Variation ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Genetic Relatedness ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Genetic Distances ◽  
Carya Illinoinensis ◽  
Randomly Amplified Polymorphic Dna

Genetic variation among pecan [Carya illinoinensis (Wangenh.) K. Koch] cultivars was studied using randomly amplified polymorphic DNA (RAPD) markers. Using a combination of primers, a unique fingerprint was produced for each of the pecan genotypes studied. The genetic relatedness between 44 cultivars was estimated using more than 100 RAPD markers. Genetic distances based on the simple matching coefficient varied from 0.91 to 0.59. The phenetic dendogram developed from cluster analysis showed relatively weak grouping association. However, cultivars with known pedigrees usually grouped with at least one of the parents and genetic similarity estimates appear to agree with known genetic relationships. Using RAPD information in determining genetic relationships among pecan cultivars with unknown or questionable pedigrees and the integration of that knowledge into the breeding program is discussed.

scholarly journals Strain Typing of Trichosporon asahii Clinical Isolates by Random Amplification of Polymorphic DNA (RAPD) Analysis

2021 ◽  
Author(s):  
Thayanidhi Premamalini ◽  
Vijayaraman Rajyoganandh ◽  
Ramaraj Vijayakumar ◽  
Hemanth Veena ◽  
Anupma Jyoti Kindo ◽  
...  
Keyword(s):  
Genetic Relatedness ◽  
Rapd Analysis ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Strain Typing ◽  
Trichosporon Asahii ◽  
Pcr Fingerprinting ◽  
Specific Pcr ◽  
Rapd Primer ◽  
Random Amplification

Abstract Objective The aim of this study was to identify and isolate Trichosporon asahii (T. asahii) from clinical samples and to assess the genetic relatedness of the most frequently isolated strains of T. asahii using random amplification of polymorphic DNA (RAPD) primers GAC-1 and M13. Methods All the clinical samples that grew Trichosporon species, identified and confirmed by polymerase chain reaction (PCR) using Trichosporon genus-specific primers, were considered for the study. Confirmation of the species T. asahii was carried out by T. asahii-specific PCR. Fingerprinting of the most frequently isolated T. asahii isolates was carried out by RAPD using random primers GAC-1 and M13. Results Among the 72 clinical isolates of Trichosporon sp. confirmed by Trichosporon-specific PCR, 65 were found to be T. asahii as identified by T. asahii-specific PCR. Fingerprinting of the 65 isolates confirmed as T. asahii using GAC-1 RAPD primer yielded 11 different patterns, whereas that of M13 primer produced only 5 patterns. The pattern I was found to be the most predominant type (29.2%) followed by pattern III (16.9%) by GAC-1 primer. Conclusions This study being the first of its kind in India on strain typing of T. asahii isolates by adopting RAPD analysis throws light on genetic diversity among the T. asahii isolates from clinical samples. Fingerprinting by RAPD primer GAC-1 identified more heterogeneity among the T. asahii isolates than M13.

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