scholarly journals Complementary Randomly Amplified Polymorphic DNA (RAPD) Analysis Patterns and Primer Sets to DifferentiateMycoplasma GallisepticumStrains

1999 ◽  
Vol 11 (2) ◽  
pp. 158-161 ◽  
Author(s):  
B. R. Charlton ◽  
A. A. Bickford ◽  
R. L. Walker ◽  
R. Yamamoto
Keyword(s):  
Rapd Analysis ◽  
Randomly Amplified Polymorphic Dna ◽  
Primer Sets

Genetic variability within isolates of Colletotrichum lindemuthianum belonging to race 65 from the state of Minas Gerais, Brazil

Biologia ◽  
2008 ◽  
Vol 63 (2) ◽  
Author(s):  
Francine Ishikawa ◽  
Elaine Souza ◽  
Livia Davide
Keyword(s):  
Rapd Analysis ◽  
Anastomosis Group ◽  
Minas Gerais ◽  
Great Variability ◽  
The State ◽  
Colletotrichum Lindemuthianum ◽  
Randomly Amplified Polymorphic Dna ◽  
Dice Coefficient ◽  
The Common ◽  
Pathogenic Variability

AbstractColletotrichum lindemuthianum, the causal agent of anthracnose in the common bean (Phaseolus vulgaris), presents a wide genetic and pathogenic variability that gives rise to complications in the development of resistant bean cultivars. The aim of this study was to identify the variability within race 65 of C. lindemuthianum, the race most commonly encountered in Brazil, through randomly amplified polymorphic DNA (RAPD) and anastomosis analyses. Thirteen isolates of race 65, collected in different years and from various host cultivars located in diverse areas of the state of Minas Gerais, Brazil, were investigated. Twenty-four RAPD primers were employed and 83 polymorphic bands amplified. Genetic similarities were estimated from the Sorensen-Dice coefficient and ranged from 0.54 to 0.82. The dendrogram obtained by cluster analysis classified the isolates into 11 separate groups. For the purposes of the analysis of anastomosis, isolates were considered to be compatible when the fusion of hyphae from different isolates could be observed. The proportion of compatible reactions for each isolate was estimated and similarity estimates, based on the Russel & Rao coefficient, ranged from 0.28 to 0.85. Isolates were classified into 11 anastomosis groups, 10 of which were formed by only one isolate. Although isolates LV61, LV73 and LV58 were classified in the same anastomosis group, they were genetically distinct according to RAPD analysis. Results from both RAPD and anastomosis analyses revealed great variability within C. lindemuthianum race 65.

scholarly journals Differentiation of Strains of Xylella fastidiosa by a Variable Number of Tandem Repeat Analysis

2001 ◽  
Vol 67 (9) ◽  
pp. 4091-4095 ◽  
Author(s):  
Helvécio Della Coletta-Filho ◽  
Marco Aurélio Takita ◽  
Alessandra Alves de Souza ◽  
Carlos Ivan Aguilar-Vildoso ◽  
Marcos Antonio Machado
Keyword(s):  
Tandem Repeat ◽  
Rapd Analysis ◽  
Xylella Fastidiosa ◽  
Variable Number ◽  
Randomly Amplified Polymorphic Dna ◽  
Dinucleotide Repeats ◽  
Ecological Analysis ◽  
Repeat Analysis ◽  
Maximum Value ◽  
Nucleotide Repeats

ABSTRACT Short sequence repeats (SSRs) with a potential variable number of tandem repeat (VNTR) loci were identified in the genome of the citrus pathogen Xylella fastidiosa and used for typing studies. Although mono- and dinucleotide repeats were absent, we found several intermediate-length 7-, 8-, and 9-nucleotide repeats, which we examined for allelic polymorphisms using PCR. Five genuine VNTR loci were highly polymorphic within a set of 27 X. fastidiosa strains from different hosts. The highest average Nei's measure of genetic diversity (H) estimated for VNTR loci was 0.51, compared to 0.17 derived from randomly amplified polymorphic DNA (RAPD) analysis. For citrus X. fastidiosa strains, some specific VNTR loci had a Hvalue of 0.83, while the maximum value given by specific RAPD loci was 0.12. Our approach using VNTR markers provides a high-resolution tool for epidemiological, genetic, and ecological analysis of citrus-specific X. fastidiosa strains.

A stydy of Rhizobium leguminosarum biovar trifolii populations from soil extracts using randomly amplified polymorphic DNA profiles

1995 ◽  
Vol 41 (4-5) ◽  
pp. 336-344 ◽  
Author(s):  
Malcolm Dye ◽  
Leif Sket ◽  
Lance R. Mytton ◽  
Ann Cresswell ◽  
Stephen P. Harrison ◽  
...  
Keyword(s):  
Rhizobium Leguminosarum ◽  
Rapd Analysis ◽  
Dna Amplification ◽  
Differential Centrifugation ◽  
Randomly Amplified Polymorphic Dna ◽  
Phenotypic Characteristics ◽  
Soil Extracts ◽  
Dna Profiles ◽  
Rapd Fragment ◽  
Rhizobium Leguminosarum Biovar Trifolii

This study has shown that isolates of Rhizobium leguminosarum biovar trifolii can be grouped on the basis of their randomly amplified polymorphic DNA (RAPD) fragment patterns. Evidence is presented that these groups are not entirely arbitrary but are consistent with other genetic and phenotypic characteristics. RAPD analysis has been used to assess the efficiency of a dispersion and differential centrifugation procedure used to extract bacteria from soil. Whilst the major groups of Rhizobium isolates in soils were also found in the extracts, some of the others were missing. This is also reflected in the finding, made by measuring abundance of organisms, that as many Rhizobium isolates are left in the residue as appear in the supernatant; more dispersion steps, possibly with different dispersants, are needed to maximize extraction. The technique has also demonstrated that dispersing soil by simply shaking it in water not only underestimates the numbers of Rhizobium isolates present but also masks much of their diversity.Key words: Rhizobium, DNA amplification, random primers, bacterial extraction.

scholarly journals Reduction of campylobacter infections in broiler flocks by application of hygiene measures

1998 ◽  
Vol 121 (1) ◽  
pp. 57-66 ◽  
Author(s):  
A. W. VAN DE GIESSEN ◽  
J. J. H. C. TILBURG ◽  
W. S. RITMEESTER ◽  
J. VAN DER PLAS
Keyword(s):  
Rapd Analysis ◽  
Randomly Amplified Polymorphic Dna ◽  
Hygiene Measures ◽  
Prevention Of Infections ◽  
Cleaning And Disinfection ◽  
Broiler House ◽  
Campylobacter Infections

Transmission routes of Campylobacter spp. in broilers and possibilities for prevention of infections were studied on two Dutch broiler farms. The occurrence of Campylobacter spp. was studied in successive broiler flocks, in the environment of the farms and in some of the parent flocks involved. Isolates of Campylobacter spp. were typed by using randomly amplified polymorphic DNA (RAPD) analysis. The results indicate that broiler flocks become infected from environmental sources. The typing results suggest that on one farm transmission of Campylobacter spp. occurred from cattle to broilers via the farmer's footwear. After several campylobacter positive broiler cycles hygiene measures, including thorough cleaning and disinfection procedures, change of footwear at the entrance of each broiler house, control of vermin and other hygienic precautions, were introduced on both farms in order to prevent transmission of Campylobacter spp. from the farm environment to the broilers. The results indicate that the application of hygiene measures significantly reduced campylobacter infections of broiler flocks on both farms.

scholarly journals Isozyme, Randomly Amplified Polymorphic DNA (RAPD), and Restriction Fragment-length Polymorphism (RFLP) Markers Used to Deduce a Putative Parent for the `Braeburn' Apple

1996 ◽  
Vol 121 (6) ◽  
pp. 996-1001 ◽  
Author(s):  
S.E. Gardiner ◽  
H.C.M. Bassett ◽  
C. Madie ◽  
D.A.M. Noiton
Keyword(s):  
New Zealand ◽  
Fragment Length Polymorphism ◽  
Rapd Analysis ◽  
Rflp Analysis ◽  
Rare Allele ◽  
Genetic Distances ◽  
Rflp Markers ◽  
High Likelihood ◽  
Randomly Amplified Polymorphic Dna ◽  
Restriction Fragment Length

Information about a rare allele of phosphoglucomutase (PGM) that is shared by `Braeburn' and 16% of cultivars in the New Zealand Cultivar Collection was combined with historical information about cultivar distribution to select a set of 15 cultivars for a more detailed genetic analysis of their relatedness to the key New Zealand apple (Malus domestica Borkh.) `Braeburn'. DNA from all 16 cultivars was examined by RFLP analysis using 41 probe-enzyme combinations and also by RAPD analysis with 39 selected primers. The RFLP and RAPD data excluded a proposal that `Lady Hamilton' and `Braeburn' are genetically identical. All cultivars except `Lady Hamilton' were excluded as potential parents for `Braeburn' based on incompatible RFLP banding. Assessment of genetic distances between `Braeburn' and the other 15 cultivars from RFLP and RAPD data demonstrated that `Lady Hamilton' was more closely related to `Braeburn' than all others. We conclude that there is a high likelihood that `Lady Hamilton' is one of the parents of `Braeburn'.

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 Production of Reliable Randomly Amplified Polymorphic DNA (RAPD) Markers from DNA of Woody Plants

HortScience ◽  
1993 ◽  
Vol 28 (12) ◽  
pp. 1188-1190 ◽  
Author(s):  
Amnon Levi ◽  
Lisa J. Rowland ◽  
John S. Hartung
Keyword(s):  
Woody Plants ◽  
Rapd Markers ◽  
Woody Plant ◽  
Rapd Analysis ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
23S Rrna ◽  
Randomly Amplified Polymorphic Dna ◽  
Polymerase Chain ◽  
Triton X

A procedure for identifying reproducible RAPD markers from woody plant DNA is presented. The procedure relies on using a PCR buffer that contains 1% Triton-X-100 and 0.1 % gelatin [previously described for successful polymerase chain reaction (PCR) amplification of 16S/23S rRNA intergenic spacer regions from eubacteria], and amplification conditions of 50 cycles: 30 sec at 94C, 70 sec at 48C, and 120 sec at 72C. The combination of this buffer and these conditions amplified consistent fragments in higher amounts, as compared to other standard PCR buffers and conditions generally used for RAPD analysis. This procedure resulted in reliable RAPD patterns for all organisms tested. Chemical name used: α-[4-(1,1,3,3,-tetramethylbutyl)phenyl]-cohydroxypoly(oxy-l,2-ethanediyl) (Triton-X-l00).

scholarly journals Genetic Relationships of Pyrus Species and Cultivars Native to East Asia Revealed by Randomly Amplified Polymorphic DNA Markers

2002 ◽  
Vol 127 (2) ◽  
pp. 262-270 ◽  
Author(s):  
Yuanwen Teng ◽  
Kenji Tanabe ◽  
Fumio Tamura ◽  
Akihiro Itai
Keyword(s):  
East Asia ◽  
Clustering Analysis ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Randomly Amplified Polymorphic Dna ◽  
Pyrus Calleryana ◽  
Chinese White ◽  
Species Specific ◽  
Kochi Prefecture

A total of 118 Pyrus sp. (pear) and cultivars native mainly to east Asia were subjected to randomly amplified polymorphic DNA (RAPD) analysis to evaluate genetic variation and relationships among the accessions. Two hundred fifty RAPD markers were scored from 20 decamer primers. RAPD markers specific to species were identified. Clustering analysis revealed two divisions: one comprising cultivars of P. communis L., and the other including all accessions of Pyrus native to east Asia. The grouping of the species and cultivars by RAPD data largely agrees with morphological pear taxonomy. However, some noted incongruence existed between two classification methods. Pyrus calleryana Dcne. clustered together with P. koehnei Schneid., P. fauriei Schneid. and P. dimorphophylla Makino. Pyrus betulaefolia Bge. clustered with P. ×hopeiensis Yu and P. ×phaeocarpa Rehd. A noncultivated clone of P. aromatica Kikuchi et Nakai grouped with P. aromatica cultivars. Pyrus hondoensis Nakai et Kikuchi and cultivars of P. ussuriensis Max. formed a single group. Some accessions from Korea (named Korean pear) had species-specific RAPD markers and comprised an independent group. Most of the Chinese white pears clustered together with most of the Chinese sand pears. Based on the present results, the new nomenclature P. pyrifolia var. sinensis (Lindley) Teng et Tanabe for Chinese white pear was suggested. Most accessions of Japanese pears fell into one main group, whereas pear cultivars from Kochi Prefecture of Japan subclustered with some Chinese sand pears and one accession from Korea. Our results infer that some local Japanese pear cultivar populations may have been derived from cultivars native to Kochi Prefecture in Shikoku region, and that the latter may have been introduced from ancient China and/or Korea.

scholarly journals Characterization of Alstroemeria Species using Random Amplified Polymorphic DNA (RAPD) Analysis

HortScience ◽  
1997 ◽  
Vol 32 (3) ◽  
pp. 482F-482 ◽  
Author(s):  
Deric D. Picton ◽  
Harrison G. Hughes
Keyword(s):  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Randomly Amplified Polymorphic Dna ◽  
Banding Patterns ◽  
Extraction Buffer ◽  
Rapd Pcr ◽  
High Degree ◽  
Species Hybrids ◽  
Color Variants

In this study, 11 species, hybrids, and color variants were characterized using randomly amplified polymorphic DNA (RAPD) analysis. Total genomic DNA was extracted using a 2% CTAB extraction buffer using fresh or frozen leaf material. The DNA was amplified using standard RAPD-PCR protocols utilizing 10-mer primers. All primers utilized exhibited a high degree of polymorphism in their banding patterns among the species and hybrids studied. The primers used produced ≈40 reproducible bands. It was possible to identify and uniquely distinguish all species and hybrids investigated using these bands.

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