Characterization of Botrytis cinerea from Table Grapes in Chile Using RAPD-PCR

Random amplified polymorphic DNA (RAPD) analysis was performed on 29 isolates of Botrytis cinerea Pers. ex Fr. isolated from table grapes (Vitis vinifera L.) and other crops in Chile with 29 decaprimers. No single primer was found to differentiate either the host or the geographical origin of each of the B. cinerea isolates tested. The DNA profiles obtained, particularly with primers OPA4 and OPA11, distinguished isolates of B. cinerea from other epiphyte fungi found on table grapes, including Alternaria alternata, Aspergillus niger, Cladosporium herbarum, Epiccocum nigrum, Rhizopus stolonifer, a Penicillium sp., and yeasts (Cryptococcus laurentii, Rhodotorula glutinis, and Saccharomyces cerevisiae). Regardless of host origin, primers OPA4 and OPA11 amplified a strong fragment of 1.2 kilobases (kb) and two fragments of 1.10 and 0.7 kb, respectively. These DNA fragments were obtained even when only one conidium of B. cinerea was in the test sample. Three main groups were clearly defined based on the genetic similarities found in additional RAPD analysis with 19 arbitrary decaprimers and 15 selected isolates of B. cinerea. The overall similarity coefficients (SC) between the groups obtained ranged from 0.326 to 0.891. Interestingly, all isolates from table grapes were included in group I (SC: 0.761 to 0.826), isolates from apple and tomato were in group II (SC: 0.739 to 0.848), while isolates from blueberry were either in group I (SC: 0.804) or III (SC: 0.673). Consequently, the genetic variability determined by RAPD analysis among these B. cinerea isolates suggested a possible host:pathogen relationship. However, further research is needed to clarify its pathological significance.

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

Genome ◽

10.1139/g00-030 ◽

2000 ◽

Vol 43 (4) ◽

pp. 724-727 ◽

Cited By ~ 16

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.

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Occurrence and genetic variability of Candida parapsilosis sensu lato in Hungary

Journal of Medical Microbiology ◽

10.1099/jmm.0.46838-0 ◽

2007 ◽

Vol 56 (2) ◽

pp. 190-195 ◽

Cited By ~ 36

Author(s):

Sándor Kocsubé ◽

Mónika Tóth ◽

Csaba Vágvölgyi ◽

Ilona Dóczi ◽

Miklós Pesti ◽

...

Keyword(s):

Genetic Variability ◽

Candida Parapsilosis ◽

Sequence Data ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Its Region ◽

Molecular Data ◽

Rrna Gene ◽

Phenotypic Data ◽

Group I

The occurrence and genetic variability of Candida parapsilosis isolates in two Hungarian hospitals, located in Debrecen and Pécs, were examined. Among the 209 Candida isolates examined, 20 were found to belong to C. parapsilosis sensu lato, based on morphological, physiological and molecular data. The frequency of occurrence of C. parapsilosis isolates (9.6 %) was lower than that observed in Europe but higher than that observed previously in Hungary. The genetic variability of C. parapsilosis sensu lato isolates was also examined using random amplified polymorphic DNA (RAPD) analysis and sequence analysis of the intergenic transcribed spacer (ITS) region of the rRNA gene cluster. The genetic variability of the isolates was relatively high, as revealed by RAPD analysis. Two isolates were found to belong to the recently described Candida metapsilosis species (C. parapsilosis group III), based on ITS sequence data, RAPD analysis and phenotypic data. These two isolates could also be distinguished from C. parapsilosis sensu stricto isolates using a primer pair developed for the detection of C. parapsilosis group I isolates. To the best of the authors' knowledge, this is the first report on the identification of C. metapsilosis from bloodstream infection.

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678 PB 186 RAPD GENETIC MARKERS FOR CHARACTERIZATION OF MUSA GENETIC RESOURCES

HortScience ◽

10.21273/hortsci.29.5.530a ◽

1994 ◽

Vol 29 (5) ◽

pp. 530a-530

Author(s):

R.L. Jarret ◽

K.V. Bhat

Keyword(s):

Genetic Markers ◽

Size Range ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Dna Amplification ◽

Principal Coordinate Analysis ◽

Phenetic Analysis ◽

Similarity Coefficients ◽

Primer Sequence

Fifty-seven accessions of Musa including cultivated clones Of 6 genomic groups (AA, AB, AAA, AAB, ABB, ABBB), M. balbisiana (BB), M. acuminata ssp. banksii (AA), M. acuminata ssp. malaccensis (AA) and M. velutina were examined for random amplified polymorphic DNA (RAPD) genetic markers using PCR with sixty 10-mer random primers. Forty-nine of 60 tested primers gave reproducible DNA amplification patterns. The number of bands resolved per amplification was primer dependent and varied from 1 to a maximum of 24. The size range of the amolification products also differed with the select& primer sequence/genotype and ranged from 0.29 to 3.0 kb. RAPD data were used to generate Jaccard's similarity coefficients which were analyzed phenetically. Phenetic analysis separated clones into distinct groupings that were in agreement with clusterings revealed when data were subsequently analyzed by principal coordinate analysis (PCO). In both the phenetic and the PCO analyses, previously unclassified cultivars grouped with cultivars previously classified for their genomic group based on morphological keys. The implications of RAPD analysis for Musa germplasm classification, clonal identification, and management are discussed.

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In vitro attachment of phylloplane yeasts to Botrytis cinerea, Rhizoctonia solani, and Sclerotinia homoeocarpa

Canadian Journal of Microbiology ◽

10.1139/w04-100 ◽

2004 ◽

Vol 50 (12) ◽

pp. 1041-1048 ◽

Cited By ~ 13

Author(s):

Tom W Allen ◽

Leon L Burpee ◽

James W Buck

Keyword(s):

Rhizoctonia Solani ◽

Botrytis Cinerea ◽

Rhodotorula Glutinis ◽

Extracellular Polysaccharide ◽

Phytopathogenic Fungi ◽

Yeast Cells ◽

Cryptococcus Laurentii ◽

Sclerotinia Homoeocarpa ◽

Phylloplane Yeasts

The ability of yeasts to attach to hyphae or conidia of phytopathogenic fungi has been speculated to contribute to biocontrol activity on plant surfaces. Attachment of phylloplane yeasts to Botrytis cinerea, Rhizoctonia solani, and Sclerotinia homoeocarpa was determined using in vitro attachment assays. Yeasts were incubated for 2 d on potato dextrose agar (PDA) prior to experimentation. A total of 292 yeasts cultured on PDA were screened for their ability to attach to conidia of B. cinerea; 260 isolates (89.1%) attached to conidia forming large aggregates of cells, and 22 isolates (7.5%) weakly attached to conidia with 1 or 2 yeast cells attached to a few conidia. Ten yeasts (3.4%), including 8 isolates of Cryptococcus laurentii, 1 isolate of Cryptococcus flavescens, and an unidentified species of Cryptococcus, failed to attach to conidia. All non-attaching yeasts produced copious extracellular polysaccharide (EPS) on PDA. Seventeen yeast isolates did not attach to hyphal fragments of B. cinerea, R. solani, and S. homoeocarpa after a 1 h incubation, but attachment was observed after 24 h. Culture medium, but not culture age, significantly affected the attachment of yeast cells to conidia of B. cinerea. The 10 yeast isolates that did not attach to conidia when grown on agar did attach to conidia (20%–57% of conidia with attached yeast cells) when cultured in liquid medium. Attachment of the biocontrol yeast Rhodotorula glutinis PM4 to conidia of B. cinerea was significantly greater at 1 × 107 yeast cells·mL–1 than at lower concentrations of yeast cells. The ability of yeast cells to attach to fungal conidia or hyphae appears to be a common phenotype among phylloplane yeasts.Key words: adhesion, biological control, Cryptococcus laurentii, Rhodotorula glutinis.

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Variation in Pathogenicity and DNA Polymorphism Among Botrytis cinerea Isolates Sampled Inside and Outside a Glasshouse

Plant Disease ◽

10.1094/pdis.1997.81.7.781 ◽

1997 ◽

Vol 81 (7) ◽

pp. 781-786 ◽

Cited By ~ 44

Author(s):

A. Kerssies ◽

A. I. Bosker-van Zessen ◽

C. A. M. Wagemakers ◽

J. A. L. van Kan

Keyword(s):

Botrytis Cinerea ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Germination Rate ◽

Sampling Time ◽

Reference Isolate ◽

Pure Cultures ◽

Rose Petals ◽

Almost All ◽

Different Sources

Colonies of Botrytis cinerea were obtained from spore samplers placed inside and outside a glasshouse with a rose crop. Pure cultures were made from five colonies collected on one sampling date every month throughout the year. These isolates were tested for germination on water agar and for pathogenicity on gerbera and rose petals. The germination rate of the conidia on water agar varied between 60 and 99%. Pathogenicity of the isolates on gerbera and rose flowers ranged from 14 to 166% relative to reference isolate Bc16 and varied among isolates collected on the same day as much as among isolates collected in different months. The pathogenicity of the isolates on rose flowers was overall higher than on gerbera flowers. Random amplified polymorphic DNA (RAPD) analysis was performed on 30 selected isolates with different relative pathogenicity, collected both inside and outside the glasshouse. Almost all of the isolates were genetically different. No correlation was found among pathogenicity, sampling time, sampling place, and RAPD patterns. Results are further evidence for the statement that B. cinerea inoculum in glasshouses continuously originates from many different sources in their vicinity.

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Genetic Variability in Bangladeshi Aromatic Rice through RAPD Analysis

Turkish Journal of Agriculture - Food Science and Technology ◽

10.24925/turjaf.v3i3.107-111.210 ◽

2014 ◽

Vol 3 (3) ◽

pp. 107 ◽

Cited By ~ 1

Author(s):

Mehfuz Hasan ◽

Mohammad Sharif Raihan

Keyword(s):

Genetic Diversity ◽

Rapd Analysis ◽

Oryza Sativa L ◽

Random Amplified Polymorphic Dna ◽

Group Method ◽

Aromatic Rice ◽

Similarity Coefficients ◽

Rice Varieties ◽

Pair Group ◽

Minimum Number

Genetic polymorphism and relationships among 30 commercial varieties of Bangladeshi aromatic rice (Oryza sativa L.) were established using random amplified polymorphic DNA (RAPD) primers. Out of fifty 10-mer RAPD primers screened initially, four were chosen and used in a comparative analysis of different varieties of indigenous Bangladeshi aromatic rice. Of the 33 total RAPD fragments amplified, 7 (21.21%) were found to be shared by individuals of all eight varieties. The remaining 26 fragments were found to be polymorphic (78.79%). Pair-wise estimates of similarity ranged from 0.101 to 0.911. Highest genetic diversity was determined between Radhunipagol and Dubsail varieties (0.911). The amount of genetic diversity within aromatic rice germplasm was quite high as determined by the genetic similarity coefficients between varieties. Genetic similarities obtained from RAPD data were also used to create a cluster diagram. Cluster analysis using an un-weighted pair-group method with arithmetic averages (UPGMA) was used to group the varieties and the 30 aromatic rice varieties were grouped into 6 clusters where cluster I includes the maximum number of varieties (9). Cluster VI includes minimum number of varieties (2). This Study offered a rapid and reliable method for the estimation of variability between different varieties which could be utilized by the breeders for further improvement of the local aromatic rice varieties.

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Characterization of Botrytis cinerea Isolates Present in Thompson Seedless Table Grapes in the Central Valley of Chile

Plant Disease ◽

10.1094/pdis-04-10-0298 ◽

2011 ◽

Vol 95 (6) ◽

pp. 683-690 ◽

Cited By ~ 26

Author(s):

Marcela Esterio ◽

Gastón Muñoz ◽

Cecilia Ramos ◽

Gonzalo Cofré ◽

Rodrigo Estévez ◽

...

Keyword(s):

Genetic Differentiation ◽

Botrytis Cinerea ◽

Random Amplified Polymorphic Dna ◽

Central Valley ◽

Control Program ◽

Control Treatment ◽

Thompson Seedless ◽

Phenological Stages ◽

Table Grapes ◽

Wide Range

Botrytis cinerea isolates from flowers and berries of Vitis vinifera ‘Thompson seedless’ (grapevine) were characterized in terms of two transposable elements (TEs) Boty and Flipper, random amplified polymorphic DNA (RAPD), infection levels, and resistance to iprodione. The isolates were collected from grapevines under fungicide programs of variable numbers of iprodione applications, and replicated in three Chilean Central Valley locations. Recovery was repeated from clusters collected at four phenological stages. Highest infection levels were found at bloom. Fungicide programs including one iprodione application or a combination of other fungicides were most effective for reducing gray mold symptoms. A total of 457 isolates collected from fungicide programs including only one iprodione application, and the control program, were tested for the presence of TEs. In all locations and during all phenological stages, transposa isolates (containing both TEs) were most common, followed by Boty. Vacuma isolates (containing neither TE) were identified at very low levels in two locations and only in the control treatment, and isolates with only Flipper were not detected at any time or location. Vacuma and Boty isolates were all sensitive to iprodione, while transposa isolates showed a wide range of resistance. Based on response to iprodione, the presence of TEs, and presence of vegetative-incompatibility alleles (Bc-hch), the isolates studied belong to B. cinerea Group II, a phylogenetic species within B. cinerea. Hierarchical analysis of molecular variance and genetic diversity analyses of the RAPD genotypes showed a genetic differentiation linked to location, but it was not related to geographic distance. Moreover, a genetic differentiation related to the phenological stage of grapes was also detected.

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Taxonomic variation among Schinus molle L. plants associated with a slight change in elevation

Bangladesh Journal of Plant Taxonomy ◽

10.3329/bjpt.v24i2.35116 ◽

2017 ◽

Vol 24 (2) ◽

pp. 205-214

Author(s):

Abeer Al-Andal ◽

Mahmoud Moustafa ◽

Suliman Alruman

Keyword(s):

Genetic Similarity ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Dna Fingerprints ◽

Similarity Coefficients ◽

Tree Analysis ◽

Schinus Molle ◽

Plant Taxon ◽

Maximum Similarity ◽

Rapd And Issr

This study examined the degree of variations in DNA fingerprints associated with slight altitudinal change of Schinus molle grown in Abha region, Saudi Arabia. Seven populations from Schinus molle plants located at 2193.0, 2246.0, 2197.7, 2441.0, 2372.0, 2250.6 and 2175.0 meters had been investigated. The degree of genetic variability was evaluated using random amplified polymorphic DNA (RAPD), mixed RAPD and intersimple sequence repeat markers (ISSR). The genetic similarity coefficients from RAPD analysis revealed the maximum similarity value (89.9%) was between population at 2250.6 m and population at 2175.0 m. The genetic similarity coefficients from mixed RAPD primers displayed the highest similarity value (87.6%) between population at 2246.0 m and population at 2197.7 m. Similarity coefficients from ISSR analysis revealed the highest similarity value (86.2%) among populations at 2193.0 m, 2246.0 m, 2441.0 m and at 2250.6 m. Super tree analysis (RAPD + mixed RAPD + ISSR) showed the highest similarity value (85.5%) between population at 2441.0 m and population at 2250.6 m. In conclusion, marker systems including RAPD, mixed RAPD and ISSR, alone or combined can be effectively used in determining the genetic relationship among Schinus molle plants even at very close populations.Bangladesh J. Plant Taxon. 24(2): 205–214.

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SNP and SCAR Markers for Specific Discrimination of Antler-Shaped Ganoderma lucidum

Microorganisms ◽

10.3390/microorganisms7010012 ◽

2019 ◽

Vol 7 (1) ◽

pp. 12 ◽

Cited By ~ 2

Author(s):

O-Chul Kwon ◽

Chang-Soo Lee ◽

Young-Jin Park

Keyword(s):

Ganoderma Lucidum ◽

Gene Sequence ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Morphological Characteristics ◽

Pcr Analysis ◽

Scar Markers ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Specific Fragment

In this study we identified single nucleotide polymorphism (SNP) and sequence characteristic amplification region (SCAR) markers for specific identification of antler-shaped Ganoderma lucidum strains. When the partial mitochondrial SSU rDNA gene sequence of various antler- and kidney-shaped G. lucidum strains were analyzed and aligned, an SNP was found only in the antler-shaped G. lucidum strain at position 456 bp. In addition, this SNP of antler-shaped strains was digested by HinfI restriction enzyme. We further analyzed the polymorphism of various G. lucidum strains by random amplified polymorphic DNA (RAPD) analysis. In RAPD analysis, we isolated and sequenced a fragment, specific for antler-shaped G. lucidum strains. Based on this specific fragment sequence, two sets of specific primer pairs for antler-shaped G. lucidum strains were designed. PCR analysis revealed that two specific bands were observed only from antler-shaped strains. These two molecular markers will be helpful for identification of morphological characteristics of G. lucidum.

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