scholarly journals Identification of the Edible Fig `Bianco del Cilento' by Random Amplified Polymorphic DNA Analysis

HortScience ◽  
1999 ◽  
Vol 34 (7) ◽  
pp. 1263-1265 ◽  
Author(s):  
U. Galderisi ◽  
M. Cipollaro ◽  
G. Di Bernardo ◽  
L. De Masi ◽  
G. Galano ◽  
...  
Keyword(s):  
Dna Analysis ◽  
Southern Italy ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Accurate Identification ◽  
Banding Patterns ◽  
Campania Region ◽  
Quality Of Products

Random amplified polymorphic DNA (RAPD) analysis is currently used to estimate genetic relationships in plants. We have used RAPD analysis to distinguish six different cultivars of Ficus carica, and several of their clones, that are widespread in the Campania Region of Southern Italy. Among these cultivars, `Bianco del Cilento' has unique characteristics, and is particularly useful for drying and for the manufacture of syrups. The protection of this cultivar is important to the Campania Region. We have utilized molecular markers to allow accurate identification of this cultivar, making it possible to control the quality of products and prevent fraudulent commerce. DNA was extracted from leaves and amplified by PCR using random oligonucleotide primers. The amplification patterns obtained with five decamer primers were useful for distinguishing all six cultivars analyzed. `Bianco del Cilento' was identified by two primers. The banding patterns were scored and used in similarity value calculations to estimate genetic relationships.

scholarly journals Isolates of Uromyces appendiculatus with Specific Virulence to Landraces of Phaseolus vulgaris of Andean Origin

Plant Disease ◽  
1999 ◽  
Vol 83 (2) ◽  
pp. 108-113 ◽  
Author(s):  
Craig M. Sandlin ◽  
James R. Steadman ◽  
Carlos M. Araya ◽  
Dermot P. Coyne
Keyword(s):  
Phaseolus Vulgaris ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Rust Fungus ◽  
Distinct Group ◽  
Uromyces Appendiculatus ◽  
Bean Rust ◽  
Banding Patterns ◽  
Highly Virulent ◽  
Specific Virulence

Five isolates of the bean rust fungus Uromyces appendiculatus were shown to be specifically virulent on bean genotypes of Andean origin. This specificity was demonstrated by the virulence of five pairs of isolates on a differential set of 30 Phaseolus vulgaris landraces. Each isolate pair was from a different country in the Americas and consisted of one Andean-specific isolate and one nonspecific isolate. Of the differential P. vulgaris landraces, 15 were of Middle American origin and 15 were of Andean origin. The Andean-specific rust isolates were highly virulent on Andean landraces but not on landraces of Middle American origin. Rust isolates with virulence to Middle American landraces were also generally virulent on Andean material; no truly Middle American-specific isolates were found. Random amplified polymorphic DNA (RAPD) analysis of the rust isolates also distinguished the two groups. Four of the Andean-specific rust isolates formed a distinct group compared to four of the nonspecific isolates. Two of the isolates, one from each of the two virulence groups, had intermediate RAPD banding patterns, suggesting that plasmagomy but not karyogamy occurred between isolates of the two groups.

Phylogenetic relationships of five morphological groups of hexaploid wheat (Triticum aestivum L. em Thell.) based on RAPD analysis

Genome ◽  
2000 ◽  
Vol 43 (4) ◽  
pp. 724-727 ◽  
Author(s):  
Wenguang Cao ◽  
G Scoles ◽  
P Hucl ◽  
R N Chibbar
Keyword(s):  
Hexaploid Wheat ◽  
Phylogenetic Relationships ◽  
Genetic Similarity ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Triticum Aestivum L ◽  
Similarity Coefficients ◽  
Morphological Classification ◽  
Wild Wheat

The genetic relationships among the five groups of hexaploid wheat: common, spelta, macha, vavilovii, and semi-wild wheat (SWW) are not clear. Random amplified polymorphic DNA (RAPD) analysis was used to assess phylogenetic relationships among these five morphological groups of hexaploid wheat. RAPD data were analyzed using the NTSYS-PC computer program to generate Jaccard genetic similarity coefficients. A dendrogram based on RAPD analysis grouped 15 accessions into five distinct clusters. These results are in agreement with those based on morphological classification, suggesting that common wheat is most closely related to SWW, followed by spelta, vavilovii, and macha.Key words: RAPD, macha, spelta, vavilovii, semi-wild wheat, phylogenetic relationships.

Comparison of repetitive-sequence-based polymerase chain reaction with random amplified polymorphic DNA analysis for rapid genotyping of nontuberculosis mycobacteria

2012 ◽  
Vol 58 (8) ◽  
pp. 953-964 ◽  
Author(s):  
Sara Christianson ◽  
Joyce Wolfe ◽  
Hafid Soualhine ◽  
Meenu K. Sharma
Keyword(s):  
Repetitive Sequence ◽  
Dna Analysis ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Gene Sequencing ◽  
Variable Number ◽  
Outbreak Investigations ◽  
Hsp65 Gene ◽  
Polymerase Chain ◽  
Clinically Significant

Nontuberculosis mycobacteria (NTM) are an important cause of human disease and infections. Though less notorious than tuberculosis, these infections are clinically significant and have been associated with outbreaks in various settings. To accommodate outbreak investigations for the numerous species of NTM, we evaluated a DiversiLab repetitive-sequence-based PCR (rep-PCR) kit for genotyping of mycobacteria. This kit was used to genotype both rapidly and slowly growing mycobacteria and was compared with other PCR-based genotyping methods, including random amplified polymorphic DNA (RAPD) analysis, hsp65 gene sequencing, and mycobacterial interspersed repetitive unit – variable number of tandem repeat (MIRU–VNTR) analysis. Compared with RAPD analysis, rep-PCR achieved better reproducibility in testing. When compared with hsp65 gene sequencing and MIRU–VNTR for Mycobacterium avium , rep-PCR provided results that agreed with these less discriminatory genotyping methods but provided a higher level of discrimination for situations such as outbreak investigations. We also evaluated the kit for its ability to identify closely related rapidly growing NTM. While rep-PCR was informative in some cases, a much larger library of isolates would be necessary to truly evaluate it as an identification tool. Overall, rep-PCR was able to provide improved reproducibility over RAPD and a discriminatory genotyping method for the isolates evaluated in this study.

Isolation of Genotype- and Chromosome-specific DNA Markers in a Biotype of Colletotrichum gloeosporioides Using Random Amplified Polymorphic DNA Analysis

1998 ◽  
Vol 46 (1) ◽  
pp. 143
Author(s):  
Agnieszka M. Poplawski ◽  
John A. G. Irwin ◽  
John M. Manners
Keyword(s):  
Dna Sequences ◽  
Fungal Pathogen ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Colletotrichum Gloeosporioides ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Dna Probes ◽  
Race 2 ◽  
Biotype B

Genetic markers that distinguish fungal genotypes are important tools for genetic analysis of heterokaryosis and parasexual recombination in fungi. Random amplified polymorphic DNA (RAPD) markers that distinguish two races of biotype B of Colletotrichum gloeosporioides infecting the legume Stylosanthes guianensis were sought. Eighty-five arbitrary oligonucleotide primers were used to generate 895 RAPD bands but only two bands were found to be specifically amplified from DNA of the race 3 isolate. These two RAPD bands were used as DNA probes and hybridised only to DNA of the race 3 isolate. Both RAPD bands hybridised to a dispensable 1.2 Mb chromosome of the race 3 isolate. No other genotype-specific chromosomes or DNA sequences were identified in either the race 2 or race 3 isolates. The RAPD markers hybridised to a 2 Mb chromosome in all races of the genetically distinct biotype A pathogen which infects other species of Stylosanthes as well as S. guianensis. The experiments indicate that RAPD analysis is a potentially useful tool for obtaining genotype- and chromosome-specific DNA probes in closely related isolates of one biotype of this fungal pathogen.

scholarly journals Polymorphism and Discrimination Capacity of Randomly Amplified Polymorphic Markers in an Olive Germplasm Bank

2001 ◽  
Vol 126 (1) ◽  
pp. 64-71 ◽  
Author(s):  
A. Belaj ◽  
I. Trujillo ◽  
R. de la Rosa ◽  
L. Rallo ◽  
M.J. Giménez
Keyword(s):  
Gel Electrophoresis ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Origin ◽  
Group Method ◽  
Polymorphic Markers ◽  
Germplasm Bank ◽  
Banding Patterns ◽  
Olive Cultivars

Random amplified polymorphic DNA (RAPD) analysis was performed on the main Mediterranean cultivars of olive (Olea europaea L.) from the Germplasm Bank of the Centro de Investigación y Formación Agraria “Alameda del Obispo” in Cordoba, Spain. One hundred and ninety reproducible amplification fragments were identified using 46 random primers followed by agarose gel electrophoresis. Some 63.2% of the amplification products were polymorphic, with an average of 2.6 RAPD markers obtained for each primer. The combination of polymorphic markers resulted in 244 banding patterns. The high degree of polymorphism detected made identification of all the cultivars (51) possible by combining the RAPD banding patterns of just only four primers: OPA-01, OPK-08, OPX-01, and OPX-03. Cultivar-specific RAPD markers and banding patterns were also found. A dendrogram based on unweighted pair-group method cluster analysis was constructed using a similarity matrix derived from the RAPD amplification products generated by the 46 primers. Three major groups of cultivars could be distinguished by RAPD analysis: 1) cultivars from east and northeast Spain, 2) Turkish, Syrian, and Tunisian cultivars, and 3) the majority of common olive cultivars in Spain. The dendrogram thus showed a good correlation between the banding patterns of olive cultivars and their geographic origin. A higher level of polymorphism was observed when polyacrylamide gel electrophoresis was used to separate the amplification products. Thus, adequate use of RAPD technology offers a valuable tool to distinguish between olive cultivars.

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.

scholarly journals Sources of Potential Errors in the Application of Random Amplified Polymorphic DNAs in Cucumber

HortScience ◽  
1996 ◽  
Vol 31 (2) ◽  
pp. 262-266 ◽  
Author(s):  
Jack Staub ◽  
Jeffery Bacher ◽  
Karl Poetter
Keyword(s):  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Inbred Lines ◽  
Sphaerotheca Fuliginea ◽  
Chain Reaction ◽  
Banding Patterns ◽  
Taq Dna Polymerase ◽  
Polymerase Chain ◽  
Stock Solutions ◽  
Pcr Conditions

The influence of tissue age, pathogen infestation, intrapopulation contamination, and polymerase chain reaction (PCR) conditions were assessed as sources of error in random amplified polymorphic DNA (RAPD) analysis. DNA from young, uninfected tissue provided the most consistent results. Plants infected with Sphaerotheca fuliginea Schl. (ex Fr.) Poll. showed variation in RAPD banding patterns compared to those of uninfected plants. Differences in banding patterns were detectable when DNA from two inbred lines were mixed at dilution ratios of ≤20:1 but not ≥50:1. Differing lots of commercially available 10× reaction buffer, MgCl2 stock solutions, and Taq DNA polymerase affected RAPD banding patterns and overall yield. For reproducibility of RAPD assays, it may be necessary to optimize reactions for specific lots of PCR reagents from either commercial or in-house sources.

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