An Assessment of Genetic Relationships between Members of the Phytophthora megasperma Complex and Phytophthora vignae using Molecular Markers

1993 ◽  
Vol 6 (4) ◽  
pp. 295 ◽  
Author(s):  
SC Whisson ◽  
BJ Howlett ◽  
ECY Liew ◽  
DJ Maclean ◽  
JM Manners ◽  
...  
Keyword(s):  
Nuclear Dna ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Intergenic Spacer ◽  
Rflp Analysis ◽  
Protein Patterns ◽  
Separate Species ◽  
Phytophthora Megasperma ◽  
Polymerase Chain ◽  
Mitochondrial Rflps

Genetic relationships between Phytophora megasperma f. sp. glycinea (Pmg) and morphologically similar taxa, P. megasperma f. sp. medicaginis (Pmm), P. megasperma f. sp. trifolii (Pmt), P. megasperma from Douglas Fir (PmDF) and asparagus (PmAS) and Phytophthora vignae, were explored by restriction fragment length polymorphism (RFLP) analysis of nuclear DNA using random genomic multi-copy, cDNA, and ribosomal DNA probes as well as random amplified polymorphic DNA (RAPDs) and RFLP analysis of ribosomal intergenic spacer regions amplified by the polymerase chain reaction (PCR). Each method detected large differences between these taxa and P. megasperma f. sp. glycinea. P. vignae was more closely related to P. megasperma f. sp. glycinea than the other taxa on the basis of the cDNA RFLPs and RFLPs of PCR amplified rDNA intergenic spacer regions. We conclude that each of the taxa examined represent separate species. This supports the most recent reclassification based on mitochondrial RFLPs and electrophoretic protein patterns of the host-specific taxa to P. sojae (Pmg), P. trifolii (Pmt) and P. medicaginis (Pmm).

scholarly journals Population Structure of Cercospora kikuchii, the Causal Agent of Cercospora Leaf Blight and Purple Seed Stain in Soybean

2008 ◽  
Vol 98 (7) ◽  
pp. 823-829 ◽  
Author(s):  
G. Cai ◽  
R. W. Schneider
Keyword(s):  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Intergenic Spacer ◽  
Chain Reaction ◽  
Cercospora Kikuchii ◽  
Vegetative Compatibility Groups ◽  
Intergenic Spacer Region ◽  
Group I ◽  
Polymerase Chain ◽  
Purple Seed Stain

Random amplified polymorphic DNA (RAPD) and microsatellite-primed polymerase chain reaction (MP-PCR) were used to characterize 164 isolates of Cercospora kikuchii, most of which were collected from Louisiana. Plant tissue (seeds versus leaves), but not host cultivar, had a significant impact on pathogen population differentiation. Cluster analysis showed that the Louisiana population was dominated by a primary lineage (group I) with only a few Louisiana isolates belonging to the minor lineage that also included the non-Louisiana isolates (group II). A previous study showed that isolates could be differentiated according to vegetative compatibility groups (VCGs). However, RAPD and MP-PCR data demonstrated that isolates of C. kikuchii were not generally clustered according to these VCGs. Furthermore, genetic relationships within and between VCGs were examined using sequences of the intergenic spacer region of rDNA. These analyses showed that VCG is not an indicator of evolutionary lineage in this fungus. Our results suggest the likely existence of a cryptically functioning sexual stage in some portion of the C. kikuchii population.

RFLP analysis of rRNA intergenic spacer regions of 23 isolates of the entomopathogenPaecilomyces farinosus

1997 ◽  
Vol 75 (12) ◽  
pp. 2038-2044 ◽  
Author(s):  
J. S. K. Chew ◽  
D. B. Strongman ◽  
R. M. MacKay
Keyword(s):  
Ribosomal Rna ◽  
Population Biology ◽  
Genetic Relationships ◽  
Intergenic Spacer ◽  
Rflp Analysis ◽  
Restriction Enzyme Digestion ◽  
Paecilomyces Fumosoroseus ◽  
Chain Reaction ◽  
Ecological Requirements ◽  
Polymerase Chain

Genetic relationships between 23 eastern Canadian isolates of the entomopathogen Paecilomyces farinosus (Holm ex S.F. Gray) Brown & Smith were investigated by comparison of DNA fragments produced by restriction enzyme digestion of polymerase chain reaction amplified ribosomal RNA intergenic spacer regions. The variation observed was limited to 40% or less of these regions. All P. farinosus isolates were very dissimilar to isolates of the entomopathogens Beauveria bassiana (Bals.) Vuill. and Paecilomyces fumosoroseus (Wize) Brown & Smith. Seventeen P. farinosus isolates from six different hosts and diverse habitats yielded identical or nearly identical results. Two groups, each with three isolates from two different hosts, were distinct from the main group of isolates. Each of the three P. farinosus groups included some isolates that produced synnemata and some that did not, indicating multiple evolutionary losses of the ability to produce this sporulation structure. We conclude that eastern Canadian P. farinosus, while genetically and phenotypically variable, is not composed largely of strains with strict ecological requirements. Key words: entomopathogenic fungus, population biology, RFLP, ribosomal RNA intergenic spacer.

Genetic relationships and variation in the Stylosanthes guianensis species complex assessed by random amplified polymorphic DNA

Genome ◽  
1993 ◽  
Vol 36 (1) ◽  
pp. 43-49 ◽  
Author(s):  
Kemal Kazan ◽  
John M. Manners ◽  
Don F. Cameron
Keyword(s):  
Species Complex ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Random Sequence ◽  
Distinct Species ◽  
Similar Species ◽  
Protein Patterns ◽  
Stylosanthes Guianensis ◽  
Taxonomic Groups

Genetic variation in the five taxonomic groups of the Stylosanthes guianensis (Aubl.) Sw. complex was investigated using random amplified polymorphic DNA markers (RAPDs). DNA samples from four plants of each of 45 accessions within the S. guianensis species complex were analyzed using 20 oligonucleotides of random sequence. Little variation was found within each of the 18 accessions (1–7% of total RAPD bands in pairwise comparisons) and none within each of the other 27 accessions. However, higher levels of polymorphisms were observed both within (index of genetic distance = 1 − F = 0.16–0.248) and between (1 − F = 0.254–0.408) the five taxa. This level of differentiation at the DNA level supported an earlier classification of the taxa as distinct species. A phenogram based on band sharing was constructed to show genetic relationships among the taxa studied. This phenogram corroborated the description of relationships based on morphological–agronomic characteristics, seed protein patterns, rhizobial affinities, crossability, and pollen stainability of the hybrids. In this phenogram, the most similar species were S. grandiflora and S. hippocampoides (1 − F = 0.264), with S. acuminata also showing closest similarity to these two species (1 − F = 0.277 and 0.283, respectively). Stylosanthes gracilis accessions showed the closest similarity (1 − F = 0.296) to S. guianensis ssp. guianensis accessions. Lowest similarity values (1 − F = 0.335–0.411) were found between these two species and S. grandiflora, S. acuminata, and S. hippocampoides.Key words: polymerase chain reaction, random amplified polymorphic DNA, Stylosanthes guianensis species complex.

Identification and characterization of RAPD markers inferring genetic relationships among Pine species

Genome ◽  
2002 ◽  
Vol 45 (1) ◽  
pp. 51-58 ◽  
Author(s):  
K K Nkongolo ◽  
P Michael ◽  
W S Gratton
Keyword(s):  
Pinus Banksiana ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characteristics ◽  
Rflp Analysis ◽  
Pinus Monticola ◽  
Species Specific ◽  
Specific Sequences ◽  
Pine Species

Total genomic DNAs were extracted from several populations of pine species and amplified using oligonucleotides of random sequences. Polymorphism in random amplified polymorphic DNA (RAPD) markers was high and sufficient in distinguishing each of the species. Genetic relationships among eight pine species (Pinus sylvestris, Pinus strobus, Pinus rigida, Pinus resinosa, Pinus nigra, Pinus contorta, Pinus monticola, and Pinus banksiana) from different provenances were analyzed. The degree of band sharing was used to evaluate genetic distance between species and to construct a phylogenetic tree. In general, the dendrogram corroborated the description of relationships based on morphological characteristics and crossability, but also provided new insights into pine taxonomy. RAPD markers specific to some pine species were cloned and sequenced. PCR amplifications using pairs of designed specific primers revealed that all the cloned sequences were likely genus specific because they were not found in spruce or larch. True species-specific sequences were identified using designed primers flanking cloned RAPD fragments. The analysis of RAPD fragment sequences confirmed the genetic relationships among species. A 2281-bp RAPD band called PI-Mt-Stb-23 from P. strobus was used as a probe in restriction fragment length polymorphism (RFLP) analysis and produced distinct banding patterns for each species examined, consistent with the highly polymorphic character of DNA-fingerprinting probes.Key words: Pine, RAPD, RFLP, cloning, species-specific sequences.

scholarly journals RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD™) MARKERS FOR ESTIMATING GENETIC RELATIONSHIPS IN MANGIFERA INDICA L.

HortScience ◽  
1992 ◽  
Vol 27 (6) ◽  
pp. 574c-574
Author(s):  
Raymond J. Schnell ◽  
Robert J. Knight
Keyword(s):  
Family Relationships ◽  
Linkage Mapping ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Mangifera Indica ◽  
Germplasm Collection ◽  
Chain Reaction ◽  
Mapping Analysis ◽  
Polymerase Chain ◽  
Nei's Genetic Distance

Genetic relationships between commercial mango cultivars are often speculative and only the maternal parent is generally known. RAPD™ primers were used with the polymerase chain reaction (PCR) to provide markers useful in determining individual identity, family relationships, and linkage mapping analysis. In mango, 53 RAPD primers were screened for markers and 27 proved useful. Genomic DNA was isolated from 70 clones of mango maintained in the USDA germplasm collection. DNA from these clones was amplified with each of the 27 primers. Data were scored as the presence or absence of bands. Groupings of the clones using UPGMA based on Nei's genetic distance gave distinct clusters. RAPD clusters vs. clusters based on isozyme analysis are compared.

scholarly journals Phylogenetic Relationships of Xylella fastidiosa Strains Isolated from Landscape Ornamentals in Southern California

2007 ◽  
Vol 97 (7) ◽  
pp. 857-864 ◽  
Author(s):  
Rufina Hernandez-Martinez ◽  
Karla A. de la Cerda ◽  
Heather S. Costa ◽  
Donald A. Cooksey ◽  
Francis P. Wong
Keyword(s):  
Southern California ◽  
Genetic Characterization ◽  
Xylella Fastidiosa ◽  
Random Amplified Polymorphic Dna ◽  
Intergenic Spacer ◽  
Disease Symptoms ◽  
Intergenic Spacer Region ◽  
Rapd Pcr ◽  
Polymerase Chain ◽  
Maidenhair Tree

Xylella fastidiosa is an insect-borne, xylem-limited pathogenic bacterium that has been associated with a rise in incidence of diseased landscape ornamentals in southern California. The objective of this study was to genetically characterize strains isolated from ornamental hosts to understand their distribution and identity. Strains of X. fastidiosa isolated from ornamentals were characterized using a multiprimer polymerase chain reaction (PCR) system, random amplified polymorphic DNA (RAPD)-PCR, and sequence analysis of the 16S-23S rDNA intergenic spacer region (ISR). Based on RAPD-PCR and 16S-23S rDNA ISR, strains isolated from daylily, jacaranda, and magnolia clustered with members of X. fastidiosa subsp. sandyi and caused oleander leaf scorch but not Pierce's disease symptoms in glasshouse assays on oleander and grape, respectively. This demonstrated both that our groupings based on genetic characterization were valid and that strains of X. fastidiosa subsp. sandyi are present in hosts other than oleander. Strains isolated from Spanish broom, cherry, and one strain isolated from western redbud clustered with X. fastidiosa subsp. fastidiosa members. Strains isolated from purple-leafed plum, olive, peach, plum, sweetgum, maidenhair tree, crape myrtle, and another western redbud strain clustered with members of X. fastidiosa subsp. multiplex. All strains isolated from mulberry and one from heavenly bamboo formed a separate cluster that has not yet been defined as a subspecies.

scholarly journals Corn with Symptoms of Reddening: New Host of Stolbur Phytoplasma

Plant Disease ◽  
2006 ◽  
Vol 90 (10) ◽  
pp. 1313-1319 ◽  
Author(s):  
B. Duduk ◽  
A. Bertaccini
Keyword(s):  
16S Rdna ◽  
Intergenic Spacer ◽  
Rflp Analysis ◽  
Gene Sequences ◽  
New Host ◽  
Intergenic Spacer Region ◽  
New Finding ◽  
Polymerase Chain ◽  
Stolbur Phytoplasma ◽  
Uncertain Etiology

Recurrent epiphytotic outbreaks of a disease of uncertain etiology known as reddening of corn (Zea mays) have occurred in some areas of Serbia during the last 50 years. Affected plants show early and abnormal ripening, dry precociously, and have poor, shriveled grains. Using molecular tools, phytoplasmas were detected in diseased plants and their identity was subsequently deduced as a subgroup 16SrXII-A strain by a variety of supporting assays involving restriction fragment length polymorphism (RFLP) analysis of polymerase chain reaction (PCR)-amplified 16S rDNA and tuf gene sequences, selective amplification of phytoplasma DNA using primer pair G35p/m, similarity of 16-23S intergenic spacer region (SR) sequences, and similarity and phylogenetic analysis of 16S rDNA gene sequences. Presence of stolbur phytoplasmas in corn with reddening symptoms is a new finding not only for Serbia: it is the first report of stolbur phytoplasma in this species worldwide.

Genetic characterization ofToxoplasma gondiistrains by random amplified polymorphic DNA polymerase chain reaction

Parasitology ◽  
1995 ◽  
Vol 111 (2) ◽  
pp. 127-132 ◽  
Author(s):  
Z. G. Guo ◽  
A. M. Johnson
Keyword(s):  
Genetic Characterization ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Dna Polymorphisms ◽  
Chain Reaction ◽  
Initial Separation ◽  
Virulent Strains ◽  
Rapd Pcr ◽  
Genomic Dnas ◽  
Polymerase Chain

SUMMARYThe technique of Random Amplified Polymorphic DNA (RAPD) PCR has been used to detect DNA polymorphisms amongToxoplasma gondiistrains. Seven arbitrary oligonucleotides (10-mer) were used as primers to amplify total genomic DNAs and significant genetic heterogeneity was detected among 11T gondiistrains with different virulence for mice. The polymorphisms observed allowed relationship dendrograms ofT. gondiistrains to be constructed by PHYLIP and PAUP analyses. The genetic relationships of theT. gondiistrains generated by 2 analyses using completely different assumptions were similar. Both analyses revealed 2 groups ofT. gondiistrains, one formed by the 6 virulent strains and the other formed by the 5 avirulent strains. This suggests that the genus Toxoplasma may actually contain 2 groups, correlated with their virulence, which have probably evolved independently following their initial separation. Significant polymorphisms were also detected between 2 different laboratory stocks of theT. gondiiRH strain.

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