scholarly journals Diversity of Phytophthora capsici in Northwest Spain: Analysis of Virulence, Metalaxyl Response, and Molecular Characterization

Plant Disease ◽  
2006 ◽  
Vol 90 (9) ◽  
pp. 1135-1142 ◽  
Author(s):  
C. Silvar ◽  
F. Merino ◽  
J. Díaz
Keyword(s):  
Mating Type ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Phytophthora Capsici ◽  
Crown Rot ◽  
Group Method ◽  
Pair Group ◽  
Highly Sensitive ◽  
Virulence Assay ◽  
Pepper Cultivar

Phytophthora crown rot, caused by Phytophthora capsici, is potentially the most destructive disease of pepper in Spain. Phenotypic and genetic diversity of 16 P. capsici isolates collected from 11 farms in northwest Spain was characterized based on virulence, mating type, sensitivity to metalaxyl, and genetic analysis using random amplified polymorphic DNA (RAPD) methods. Low variability was observed among the isolates in their metalaxyl response, with 87.5% being highly sensitive. No isolates of the A2 mating type were detected. More variability was found in the virulence assay, and isolates were classified into two groups according to their pathogenicity on a set of four pepper cultivar differentials. Genetic variation examined with eight RAPD primers generated 92 polymorphic bands and revealed the existence of different patterns among isolates. Cluster analysis using the unweighted pair-group method with arithmetic averages (UPGMA) separated the Spanish isolates into three RAPD groups and established a relationship between the Spanish population and a representative worldwide group of isolates. No correlation was found between groups obtained by RAPD analysis and groups defined by virulence or metalaxyl response.

scholarly journals Assessment of Genetic Diversity in Cultivated Tomato (Solanum Lycopersicum L.) Genotypes Using Rapd Primers

2013 ◽  
Vol 21 (1) ◽  
pp. 83-89 ◽  
Author(s):  
Saida Sharifova ◽  
Sabina Mehdiyeva ◽  
Konstantinos Theodorikas ◽  
Konstantinos Roubos
Keyword(s):  
Genetic Diversity ◽  
Rapd Analysis ◽  
Diversity Index ◽  
Random Amplified Polymorphic Dna ◽  
Arithmetic Mean ◽  
Similarity Coefficient ◽  
Group Method ◽  
Solanum Lycopersicum L ◽  
Pair Group ◽  
Upgma Cluster Analysis

Abstract Random Amplified Polymorphic DNA (RAPD) analysis was carried out on 19 Azerbaijan tomato genotypes, both cultivars and local populations. A total of 26 amplified products were revealed by 6 primers. The genetic similarity among evaluated genotypes ranged from 0.188 to 1.000. The lowest similarity was observed between cultivars ‘Azerbaijan’ and ‘Shakar’ (0.188), while the highest between ‘Elnur’ and ‘Garatag’ (1.000). The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster analysis based on Jaccard’s similarity coefficient divided genotypes into four main groups. The first group was the largest and consisted of 12 genotypes, while the fourth group was the smallest consisted of 1 genotype only. The most polymorphic primer was OPB-18 that presented a genetic diversity index of 0.823, while the least informative was primer OPG-17 with an index of 0.349. The average genetic diversity calculated from RAPD data was 0.665.

scholarly journals Characterization of Phytophthora capsici Isolates from Processing Pumpkin in Illinois

Plant Disease ◽  
2005 ◽  
Vol 89 (2) ◽  
pp. 191-197 ◽  
Author(s):  
S. Z. Islam ◽  
M. Babadoost ◽  
K. N. Lambert ◽  
A. Ndeme ◽  
H. M. Fouly
Keyword(s):  
Mating Type ◽  
Random Amplified Polymorphic Dna ◽  
Phytophthora Capsici ◽  
Group Analysis ◽  
Genetic Distances ◽  
Growth Patterns ◽  
Pair Group ◽  
Genetic Groups ◽  
The Mean

This study was conducted to investigate pathogenic, morphologic, and genetic variations among Phytophthora capsici isolates from processing pumpkin (Cucurbita moschata) fields in Illinois. Random amplified polymorphic DNA (RAPD) markers were employed to assess genetic variation among 24 isolates of P. capsici from 10 individual fields at six locations. Unweighted mean pair group analysis clustered isolates into six groups. The genetic distances ranged from 0.03 to 0.45. Inoculation of pumpkin seedlings in the greenhouse revealed that the isolates belonged to six distinct genetic groups differing significantly (P = 0.05) in virulence. Isolates tested exhibited four growth patterns in culture: cottony, rosaceous, petaloid, and stellate. P. capsici isolates, including an ATCC isolate (ATCC-15427), with cottony growth pattern did not grow at 36°C. The mean oospore diameter of A1 mating type isolates was greater than that of A2 mating type isolates. Nine of 24 isolates tested produced chlamydospores in V8-CaCO3 liquid medium.

RAPD analysis of cultivated and wild yellow nutsedge (Cyperus esculentusL.)

Weed Science ◽  
1998 ◽  
Vol 46 (3) ◽  
pp. 318-321 ◽  
Author(s):  
Paloma Abad ◽  
Bernardo Pascual ◽  
José V. Maroto ◽  
Salvador López-Galarza ◽  
María J. Vicente ◽  
...  
Keyword(s):  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Wild Populations ◽  
Arithmetic Average ◽  
Yellow Nutsedge ◽  
Pair Group ◽  
High Level ◽  
Unweighted Pair Group Method

Cultivated and weedy clones of yellow nutsedge were analyzed using random amplified polymorphic DNA (RAPD) markers to assess the polymorphism within the species and determine if this approach was suitable for identification of cultivar and wild populations. The RAPD markers unambiguously identified all studied clones. Nei-Li similarities were computed and used in an unweighted pair group method using arithmetic average (UPGMA) cluster analyses. Cultivated and weedy clones were clustered in two groups, but two cultivated clones were more closely related to weedy clones than to cultivated clones. The results showed a high level of genetic variability among the clones tested, particularly among the cultivated ones. Identification of yellow nutsedge cultivars and analysis of genetic diversity within and among weedy populations is possible by using only a small number of primers. In this study, seven selected primers discriminated among the 10 tested clones.

scholarly journals Genetic Variability in Bangladeshi Aromatic Rice through RAPD Analysis

2014 ◽  
Vol 3 (3) ◽  
pp. 107 ◽  
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.

scholarly journals Analysis of Genetic Variability Amongst Polyploid Genotypes of Pteris vittata L. From Various Geographic Locales of India

2021 ◽  
Vol 9 ◽  
Author(s):  
Jyoti Mathur ◽  
P. B. Khare ◽  
Apurva Panwar ◽  
S. A. Ranade
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Genomic Structure ◽  
Inter Simple Sequence Repeat ◽  
Pteris Vittata ◽  
Group Method ◽  
Bootstrap Analysis ◽  
Pair Group ◽  
Fern Species ◽  
Outgroup Taxon ◽  
Effective Multiplex Ratio

Pteris vittata L. is very common and a widely distributed species belongs to the family Pteridaceae. Various cytotypes from diploid to octaploid is available in this fern species. The present work has been carried out for genetic diversity in this fern both within and between the cytotypes. The molecular analysis at inter- as well as intra-species has been carried out with 57 accessions of P. vittata as well as of other species of Pteris with Microsorium punctatum considered as an out group taxon. For the present study 48 P. vittata (36 tetraploid and 12 pentaploid) and five of other species (four P. cretica, one P. pellucida, one P. tremula, one P. quadriaurita, and two P. ensiformis) accessions were used. The UPGMA (unweighted pair group method with arithmetic mean) dendrograms were generated for each method separately, as well as for all methods cumulatively, after a 1000 replicate bootstrap analysis. In order to determine the utility of each of the method, a comparative statistical assessment was done and marker index (MI), expected average heterozygosity, fraction of polymorphic loci and effective multiplex ratio (EMR) were calculated in case of each of the methods used in the present study. At the level of individual methods highest MI was obtained for directed amplification of minisatellites DNA (DAMD) method. Our findings of the present study concluded that out of the three methods Random Amplified Polymorphic DNA (RAPD), Inter-Simple Sequence Repeat (ISSR), and Directed Amplification of Minisatellite DNA (DAMD), DAMD was the best in term of polymorphism and heterozygosity as scores exhibited highest MI. The different accessions of P. vittata collected from different phytogeographical regions falls into six groups. Out of six clusters, one cluster is of pentaploid cytotype, four clusters are of tetraploid cytotype and one for outgroup taxon (M. punctatum). The result thus showed that within tetraploid, heterozygosity with variable genomic structure exists.

Molecular Diversity Analysis of Lentil (Lens culinaris Medik.) through RAPD Markers

2012 ◽  
Vol 22 (1) ◽  
pp. 51-58 ◽  
Author(s):  
M.E. Hoque ◽  
M.M. Hasan
Keyword(s):  
Genetic Distance ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Group Method ◽  
Diversity Analysis ◽  
Pair Group ◽  
Molecular Genetic Diversity

Random Amplified Polymorphic DNA (RAPD) markers were used to study the molecular genetic diversity analysis among six BARI released lentil varieties viz. BARI masur-1, BARI masur-2, BARI masur-3, BARI masur-4, BARI masur-5 and BARI masur-6. PCR amplified products were visualized on 1.0% agarose gel and the band for each primer were scored. Ten RAPD markers were used in this study. Out of them 7 primers showed amplification of 53 DNA fragments with 60.37% of them being polymorphic. The highest number of polymorphic loci was noticed in the variety BARI masur-3. The same variety also showed maximum Nei’s gene diversity value (0.0552). The highest Nei’s genetic distance (0.5002) was observed in BARI masur-1 vs. BARI masur-5 whereas, the lowest genetic distance (0.0692) was found in BARI masur-1 vs. BARI masur-2. The unweighted pair group method of arithmetic mean (UPGMA) dendrogram based on Nei’s genetic distance grouped the six cultivars into two main clusters. BARI masur-1, BARI masur-2 and BARI masur-3 were in cluster I and BARI masur-4, BARI masur-5 and BARI masur-6 were in cluster II. The cultivar BARI masur-4 was closest to the cultivar BARI masur-6 with the lowest genetic distance (0.0972) and the highest genetic distance (0.5002) was found between BARI masur-1 and BARI masur-5. The RAPD markers were found to be useful in molecular characterization of lentil varieties which could be utilized by the breeders for the improvement of lentil cultivars. DOI: http://dx.doi.org/10.3329/ptcb.v22i1.11260 Plant Tissue Cult. & Biotech. 22(1): 51-58, 2012 (June)

Development of DNA fingerprinting keys for the identification of radish cultivars

2004 ◽  
Vol 44 (1) ◽  
pp. 95 ◽  
Author(s):  
A. Pradhan ◽  
G. Yan ◽  
J. A. Plummer
Keyword(s):  
Dna Fingerprinting ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Morphological Characteristics ◽  
Group Method ◽  
Base Pairs ◽  
Difference Matrix ◽  
Pair Group ◽  
Young Leaves ◽  
Polymerase Chain

Identification of cultivars is extremely important both for cultivation and breeding of crop plants. Cultivar identification based on morphological characteristics can be difficult and complicated. Polymerase chain reaction technologies, such as random amplified polymorphic DNA (RAPD) analysis, can readily and quickly identify cultivars using seeds and young leaves. Sixty individuals representing 7 radish cultivars were examined for RAPD marker polymorphism. Based on the polymorphism generated, 5 primers were selected, out of the 14��examined, to fingerprint the cultivars. The 5 primers produced a total of 52 fragments, 6 monomorphic and 46�polymorphic fragments, ranging in size from 206 to 2258 base pairs. A total and mean character difference matrix was calculated based on the RAPD data and a dendrogram was constructed using the unweighted pair-group method with arithmetic averages (UPGMA). Three DNA fingerprinting keys were developed for the 7 cultivars and 5 markers derived from 3 primers was the minimum required to distinguish cultivars. Results demonstrated that RAPD markers could be effectively used for the identification of radish cultivars.

scholarly journals Investigating the Spatiotemporal Genetic Structure of Phytophthora capsici in Michigan

2001 ◽  
Vol 91 (10) ◽  
pp. 973-980 ◽  
Author(s):  
K. H. Lamour ◽  
M. K. Hausbeck
Keyword(s):  
Fragment Length Polymorphism ◽  
Aflp Marker ◽  
Phytophthora Capsici ◽  
Group Method ◽  
Analysis Of Molecular Variance ◽  
Arithmetic Average ◽  
Pair Group ◽  
Average Cluster ◽  
Over Time ◽  
F Statistics

Phytophthora capsici isolates were recovered from pepper and cucurbit hosts at seven locations in Michigan from 1998 to 2000. Isolates were characterized for compatibility type (CT), mefenoxam sensitivity (MS), and amplified fragment length polymorphism (AFLP) marker profiles. In total, 94 AFLP bands were resolved. Individual populations were highly variable. Within populations, 39 to 49% of the AFLP bands were polymorphic and estimated heterozygosities ranged from 0.16 to 0.19. Of the 646 isolates fingerprinted, 70% (454) had unique AFLP profiles. No clones were recovered between years or locations. Pairwise F statistics (ΦST) between populations from different locations ranged from 0.18 to 0.40. A tree based on unweighted pair-group method with arithmetic average cluster analysis indicates discrete clusters based on location. Isolates from the same location showed no clustering based on the year of sampling. Analysis of molecular variance partitioned variability among (40%) and within populations (60%). The overall estimated ΦST was 0.34 (SD = 0.03). A1/A2 CT ratios were ≈1:1, and MS frequencies were similar between years for the two locations sampled over time. These data suggest that P. capsici persists in discrete outcrossing populations and that gene flow among locations in Michigan is infrequent.

scholarly journals Blueberry Cultivar Identification Using Random Amplified Polymorphic DNA and Sequence-characterized Amplified Region Markers

HortScience ◽  
2017 ◽  
Vol 52 (11) ◽  
pp. 1483-1489 ◽  
Author(s):  
Kang Hee Cho ◽  
Seo Jun Park ◽  
Su Jin Kim ◽  
Se Hee Kim ◽  
Han Chan Lee ◽  
...  
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
The United States ◽  
Morphological Characters ◽  
Polymorphic Band ◽  
Group Method ◽  
Highbush Blueberry ◽  
United States Department ◽  
Scar Markers ◽  
Sequence Characterized Amplified Region ◽  
Pair Group

Blueberry cultivars have traditionally been identified based on the evaluation of sets of morphological characters; however, distinguishing closely related cultivars remains difficult. In the present study, we developed DNA markers for the genetic fingerprinting of 45 blueberry cultivars, including 31 cultivars introduced from the United States Department of Agriculture. We obtained 210 random amplified of polymorphic DNA (RAPD) markers using 43 different primers. The number of polymorphic bands ranged from three (OPG-10 and OPQ-04) to eight (OPR-16), with an average of five. A cluster analysis performed with the unweighted pair group method using arithmetic averages produced genetic similarity values among the blueberry cultivars ranging from 0.53 to 0.85, with an average similarity of 0.68. A dendrogram clustered the 45 blueberry cultivars into two main clusters, with a similarity value of 0.65. Cluster I consisted of four rabbiteye cultivars (Pink Lemonade, Alapaha, Titan, and Vernon) and the Ashworth northern highbush cultivar. Cluster II consisted of 31 northern highbush cultivars, eight southern highbush blueberry cultivars, and Northland half-highbush blueberry cultivar. Fifty five RAPD fragments selected were sequenced to develop sequence-characterized amplified region (SCAR) markers, resulting in the successful conversion of 16 of 55 fragments into SCAR markers. An amplified polymorphic band has the same size as the RAPD fragment or smaller according to the primer combinations in the 16 SCAR markers. Among these markers, a combination of 11 SCAR markers provided sufficient polymorphisms to distinguish the blueberry cultivars investigated in this study. These newly developed markers could be a fast and reliable tool to identify blueberry cultivars.

The use of RAPD markers to distinguish among juniper and cedar cultivars

2000 ◽  
Vol 78 (5) ◽  
pp. 655-659 ◽  
Author(s):  
Tom Hsiang ◽  
Junbin Huang
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Unknown Origin ◽  
Genetic Distances ◽  
Group Method ◽  
Pair Group ◽  
Juniperus Chinensis ◽  
Juniperus Scopulorum ◽  
Close Relatives

Two species of Chamaecyparis and six cultivars each of Juniperus chinensis L. and Juniperus scopulorum Sarg. (Cupressaceae) were subjected to random amplified polymorphic DNA (RAPD) analysis using seven primers. Unweighted pair group method with averages (UPGMA) and principal component analyses of genetic distances between cultivars showed that 42 polymorphic RAPD bands could distinguish among all cultivars and properly group them by species and genera. Where the origin of a specific juniper cultivar is uncertain, analysis of genetic distance can pinpoint close relatives. For example, we were unable to trace the origin of J. chinensis 'Alps', and we initially thought it was a mislabeled J. chinensis 'Blue Alps'. However, we found 'Alps' to be closer to J. chinensis 'Fairview' and 'Mountbatten' than to 'Blue Alps'. Similarly, 'Wichita Blue' has an unknown origin, but it had the highest genetic similarity with 'Medora'.Key words: juniper, cedar, RAPD, cultivars, phylogenetics.

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