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.

Inheritance of random amplified polymorphic DNA markers in an interspecific cross in the genus Stylosanthes

Genome ◽  
1993 ◽  
Vol 36 (1) ◽  
pp. 50-56 ◽  
Author(s):  
Kemal Kazan ◽  
John M. Manners ◽  
Don F. Cameron
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequences ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Interspecific Cross ◽  
Parental Origin ◽  
Chain Reaction ◽  
Stylosanthes Hamata ◽  
Polymerase Chain

The inheritance of random amplified polymorphic DNA (RAPD) markers generated via the polymerase chain reaction amplification of genomic DNA sequences in an F2 family of an interspecific cross between Stylosanthes hamata and S. scabra was investigated. An initial comparison between the parental species, S. hamata cv. Verano and S. scabra cv. Fitzroy, demonstrated that 34% of detected RAPD bands were polymorphic. Of 90 primers tested, 35 showed relatively simple and reliably scorable polymorphisms and were used for segregation analysis. Sixty F2 individuals were scored for the segregation of 73 RAPD markers and 55 of these markers fit a 3:1 ratio. Segregation of eight other RAPD markers deviated significantly from a 3:1 ratio. There was no bias in the inheritance of RAPD markers regarding parental origin of the segregating RAPD markers. Linkage analysis revealed 10 linkage groups containing a total of 44 RAPD loci. Another 10 RAPD markers (7 of maternal origin) that were polymorphic between the parents did not segregate in the F2 population. One of the maternally inherited RAPD bands hybridized to chloroplast DNA. Analysis of RAPD loci by DNA hybridization indicated that mainly repeated sequences were amplified. These data indicate that RAPDs are useful genetic markers in Stylosanthes spp. and they may be suitable for genetic mapping.Key words: genetic mapping, molecular markers, polymerase chain reaction, Stylosanthes hamata, Stylosanthes scabra.

Genetic-Relationships as Assessed by Molecular Markers and Cross-Infection Among Strains of Colletotrichum gloeosporioides

1994 ◽  
Vol 42 (1) ◽  
pp. 9 ◽  
Author(s):  
HL Hayden ◽  
KG Pegg ◽  
EAB Aitken ◽  
JAG Irwin
Keyword(s):  
Rapd Markers ◽  
Colletotrichum Gloeosporioides ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Colletotrichum Acutatum ◽  
Fruit Species ◽  
Pathogenicity Tests ◽  
Colletotrichum Musae ◽  
Highly Virulent

Morphological characterisation allows isolates of Colletotrichum gloeosporioides, Colletotrichum musae and Colletotrichum acutatum to be identified only to species level. Pathogenicity tests and random amplified polymorphic DNA (RAPD) markers distinguished a mango biotype of C. gloeosporioides from eight other isolates of C gloeosporioides obtained from five different fruit species. Using these procedures, it was also possible to distinguish C. acutatum and C. musae both from each other, and from the C. gloeosporioides isolates. In cross-infectivity studies, isolates of C. gloeosporioides displayed a wide host range with the exception of isolates from mango, which were highly virulent on mango only. Teleomorphic isolates of C. gloeosporioides were clustered together by RAPD analysis. This work has demonstrated the existence of a biotype of C. gloeosporioides which shows specialisation to mango.

scholarly journals Loss of Avirulence and Reduced Pathogenicity of a Gamma-Irradiated Mutant of Fusarium oxysporum f. sp. lycopersici

1999 ◽  
Vol 89 (12) ◽  
pp. 1131-1137 ◽  
Author(s):  
Jurriaan J. Mes ◽  
Robbert Wit ◽  
Christa S. Testerink ◽  
Francis de Groot ◽  
Michel A. Haring ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Dna Sequences ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Marker Gene ◽  
Gene Interaction ◽  
Polymorphism Analysis ◽  
Genomic Changes ◽  
Race 2 ◽  
Gamma Irradiated

The tomato Fusarium resistance gene I-2 confers resistance to F. oxy-sporum f. sp. lycopersici race 2, which expresses the corresponding aviru-lence gene avrI-2. To elucidate the molecular basis of this gene-for-gene interaction, we initiated a search for the avrI-2 gene. Gamma irradiation mutagenesis, using 137Cs, was performed to generate an avrI-2 mutant of F. oxysporum f. sp. lycopersici. To this end, a race 2 isolate was first transformed with a phleomycine resistance gene and a GUS marker gene in order to distinguish mutants from contaminating isolates. A total of 21,712 mutagenized colonies was tested for loss of avirulence on I-2-containing tomato seedlings. One mutant was selected that showed the expected loss of avirulence but, surprisingly, also showed reduced pathogenicity toward susceptible tomato plants. DNA analysis was subsequently used to visualize genomic changes in the mutant. Southern analysis on contour-clamped homogeneous electrophoretic field blots demonstrated a translocation of a 3.75-Mb chromosome in the mutant. Random amplified polymorphic DNA and amplified fragment length polymorphism analysis identified at least nine polymorphisms between the wild-type and mutant isolates. Most of these polymorphisms appeared as extra fragments in the mutant and contained repetitive DNA sequences.

Detection of genetic diversity in tea (Camellia sinensis) using RAPD markers

Genome ◽  
1995 ◽  
Vol 38 (2) ◽  
pp. 201-210 ◽  
Author(s):  
F. N. Wachira ◽  
R. Waugh ◽  
W. Powell ◽  
C. A. Hackett
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Southeast Asia ◽  
Camellia Sinensis ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Systematic Assessment ◽  
Tree Crop ◽  
Taxonomic Relationships

Camellia sinensis is a beverage tree crop native to Southeast Asia and introductions have been made into several nonindigenous countries. No systematic assessment of genetic variability in tea has been done anywhere. In this study, random amplified polymorphic DNA (RAPD) analysis was used to estimate genetic diversity and taxonomic relationships in 38 clones belonging to the three tea varieties, assamica, sinensis, and assamica ssp. lasiocalyx. Extensive genetic variability was detected between species, which was partitioned into between and within population components. Seventy percent of the variation was detected within populations. Analyses based on band sharing separated the three populations in a manner consistent with both the present taxonomy of tea and with the known pedigrees of some clones. RAPD analysis also discriminated all of the 38 commercial clones, even those which cannot be distinguished on the basis of morphological and phenotypic traits.Key words: genetic diversity, RAPDs, Camellia sinensis.

scholarly journals Random Amplification of Polymorphic DNA Analysis for Genetic Characterization of Two Breeds of Dogs, German Shepherd and Japanese Spitz

2013 ◽  
Vol 13 (2) ◽  
pp. 73-78
Author(s):  
Jarina Joshsi ◽  
Lumanti Manandhar ◽  
Patima Shrestha ◽  
Rani Gupta ◽  
Rojlina Manadhar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Genetic Characterization ◽  
Random Amplified Polymorphic Dna ◽  
Neighbor Joining ◽  
German Shepherd ◽  
Polymorphic Loci ◽  
Random Amplification

Random amplified polymorphic DNA (RAPD) markers were used to study genetic diversity in dog samples belonging to populations of German Shepherd and Japanese Spitz. A total of twelve samples were typed using eight RAPD primers. Out of eight primers, three primers gave result in six individuals of dogs. The phylogenetic tree constructed by the neighbor joining method based on Nei. Original measures revealed highest genetic identity found in German Shepherd as 0.9444 and highest genetic distance as 1.2809. The analysis predicts the number of polymorphic loci as 15 and the percentage of polymorphic loci as 83.3. Nepal Journal of Science and Technology Vol. 13, No. 2 (2012) 73-78 DOI: http://dx.doi.org/10.3126/njst.v13i2.7717

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.

Identification of RAPD markers linked to a gene governing cadmium uptake in durum wheat

Genome ◽  
1995 ◽  
Vol 38 (3) ◽  
pp. 543-547 ◽  
Author(s):  
Greg A. Penner ◽  
Leslie J. Bezte ◽  
Dave Leisle ◽  
John Clarke
Keyword(s):  
Durum Wheat ◽  
Gel Electrophoresis ◽  
Marker Assisted Selection ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Cadmium Uptake ◽  
Cadmium Content ◽  
Diverse Range ◽  
Selection For

Temperature sweep gel electrophoresis in combination with random amplified polymorphic DNA analysis was employed to detect two markers for a single gene governing low cadmium uptake in western Canadian durum wheat (Triticum turgidum L. var. durum). Analysis of progeny derived from a cross of the high cadmium accumulating cultivar Kyle by the low cadmium accumulating cultivar Nile resulted in linkage estimates of 4.6 (OPC-20) and 21.2 (UBC-180) cM. The closest marker (OPC-20) was shown to be useful for making low cadmium uptake selections from two other sources of low cadmium, 'Biodur' and 'Hercules'. The marker was further used to determine the genetic basis of resistance in 20 introduced durum wheat lines. Within this diverse range of germplasm the marker was correlated with cadmium contents as expected in all but two cases. Plant breeding selection for low cadmium genotypes is hindered by the high cost of chemical determination of cadmium content. Marker assisted selection for a low cadmium uptake gene offers an effective alternative.Key words: cadmium, durum wheat, RAPD markers, marker assisted selection, temperature sweep gel electrophoresis.

scholarly journals Morphological, Chemical, and Genetic Characteristics of Korean Native Thyme Bak-Ri-Hyang (Thymus quinquecostatus Celak.)

Antibiotics ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 289
Author(s):  
Minju Kim ◽  
Jun-Cheol Moon ◽  
Songmun Kim ◽  
Kandhasamy Sowndhararajan
Keyword(s):  
Essential Oil ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Essential Oil Composition ◽  
Similarity Coefficient ◽  
Gas Chromatography Mass Spectrometry ◽  
Aromatic Plant ◽  
Oil Composition ◽  
Genetic Characteristics

Bak-ri-hyang (Thymus quinquecostatus Celak.) is an important medicinal and aromatic plant in Korea. T. quinquecostatus population and is always mixed with other thyme cultivars during cultivation and marketing. Hence, this study aimed to determine the genetic variability and the essential oil composition of three Korean native thyme, T. quinquecostatus cultivars collected from the Wolchul, Jiri, and Odae mountains, in comparison with six commercial thyme cultivars (T. vulgaris), to distinguish Bak-ri-hyang from other thyme cultivars. The composition of essential oils obtained from nine individuals was analyzed by gas chromatography–mass spectrometry (GC–MS). The random amplified polymorphic DNA (RAPD) analysis was accomplished using 16 different primers. The GC–MS analysis revealed that Wolchul, creeping, golden, and orange cultivars belong to the geraniol chemotype. Whereas the Odae, lemon, and silver cultivars belong to the thymol chemotype. Further, linalool was the most abundant component in carpet and Jiri cultivars. The RAPD analysis demonstrated that all thyme cultivars showed characteristic RAPD patterns that allowed their identification. In total, 133 bands were obtained using 16 primers, and 124 bands were polymorphic, corresponding to 93.2% polymorphism. Cluster analysis of RAPD markers established the presence of clear separation from nine thyme cultivars. The highest dissimilarity and similarity coefficient of the RAPD markers were 0.58 and 0.98, respectively. According to the RAPD patterns, the nine thyme cultivars could be divided into two major clusters. Among three Korean cultivars, the Wolchul and Odae cultivars were placed into the same cluster, but they did not show identical clustering with their essential oil compositions. The findings of the present study suggest that RAPD analysis can be a useful tool for marker-assisted identification of T. quinquecostatus from other Thymus species.

Comparative analysis of diversity based on morpho-metric and molecular markers in chickpea over different environments

2018 ◽  
Author(s):  
Indu Rialch ◽  
Rama Kalia ◽  
H. K. Chaudhary ◽  
B. Kumar ◽  
J. C. Bhandari ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Rapd Markers ◽  
Agronomic Traits ◽  
Rapd Analysis ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Coefficient ◽  
Breeding Programme ◽  
Metric Traits

Ten morpho-agronomic traits and 80 random amplified polymorphic DNA (RAPD) molecular markers were used to survey genetic diversity in 25 chickpea genotypes. Analysis of variance revealed significant variability among different genotypes for morpho-metric traits. The cluster analysis done using morpho-metric traits grouped 25 genotypes into seven and six clusters in Environment I (Env. I) and Environment II (Env. II), respectively. Three genotypes viz., ICCV-96904, HPG-17, ICCV-95503 and L-HR-1 belonging to diverse clusters were identified divergent and may use in heterosis breeding programme. Of 80 random RAPD markers, 25 were found polymorphic. Three major clusters were identified using 25 polymorphic RAPD markers. The genetic similarity coefficient among genotypes ranged from 0.57 to 0.91. The average polymorphic information content (PIC) for 25 RAPD markers ranges from 0.12 to 0.40. D2-statistic, RAPD analysis and study of genotypes performance revealed sufficient genetic diversity among chickpea genotypes which would be useful in future breeding programme.

scholarly journals 676 PB 160 IDENTIFICATION AND CLASSIFICATION OF PISTACHIO (Pistacia vera L.) CULTIVARS WITH RAPD MARKERS

HortScience ◽  
1994 ◽  
Vol 29 (5) ◽  
pp. 529f-529
Author(s):  
J.I. Hormaza ◽  
L. Dollo ◽  
V.S. Polito
Keyword(s):  
Rapd Markers ◽  
Geographical Origin ◽  
Cultivar Identification ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Pistacia Vera ◽  
Polymorphic Markers ◽  
Molecular Phenotype ◽  
And Cluster Analysis

The Random Amplified Polymorphic DNA (RAPD) technique was used to characterize 15 cultivars of pistachio (Pistacia vera L.). A total of 37 polymorphic markers were considered in this study. Each cultivar exhibited a unique molecular phenotype and, as a consequence, can be uniquely fingerprinted. A similarity and cluster analysis based on the amplified fragments produced two distinct groups which are consistent with the known geographical origin of the cultivars. Our results suggest that RAPD analysis can provide a new alternative for cultivar identification and classification of pistachio.

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