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.

Species-diagnostic and species-specific DNA sequences evenly distributed throughout pine and spruce chromosomes

Genome ◽  
2010 ◽  
Vol 53 (10) ◽  
pp. 769-777 ◽  
Author(s):  
Melanie Mehes-Smith ◽  
Paul Michael ◽  
Kabwe Nkongolo
Keyword(s):  
Dna Sequences ◽  
Random Amplified Polymorphic Dna ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Pinus Monticola ◽  
The Family ◽  
Species Specific ◽  
Rapd And Issr ◽  
Specific Sequences

Genome organization in the family Pinaceae is complex and largely unknown. The main purpose of the present study was to develop and physically map species-diagnostic and species-specific molecular markers in pine and spruce. Five RAPD (random amplified polymorphic DNA) and one ISSR (inter-simple sequence repeat) species-diagnostic or species-specific markers for Picea mariana , Picea rubens , Pinus strobus , or Pinus monticola were identified, cloned, and sequenced. In situ hybridization of these sequences to spruce and pine chromosomes showed the sequences to be present in high copy number and evenly distributed throughout the genome. The analysis of centromeric and telomeric regions revealed the absence of significant clustering of species-diagnostic and species-specific sequences in all the chromosomes of the four species studied. Both RAPD and ISSR markers showed similar patterns.

scholarly journals Genetic and Pathogenic Analyses of Colletotrichum gloeosporioides Isolates from Strawberry and Noncultivated Hosts

2004 ◽  
Vol 94 (5) ◽  
pp. 446-453 ◽  
Author(s):  
C. L. Xiao ◽  
S. J. MacKenzie ◽  
D. E. Legard
Keyword(s):  
Rapd Markers ◽  
Colletotrichum Gloeosporioides ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Crown Rot ◽  
Inoculum Sources ◽  
Marker Data ◽  
Colletotrichum Spp ◽  
Species Specific

Colletotrichum crown rot of strawberry in Florida is caused primarily by Colletotrichum gloeosporioides. To determine potential inoculum sources, isolates of Colletotrichum spp. from strawberry and various noncultivated plants growing in the areas adjacent to strawberry fields were collected from different sites. Species-specific internal transcribed spacer primers for C. gloeosporioides and C. acutatum were used to identify isolates to species. Random amplified polymorphic DNA (RAPD) markers were used to determine genetic relationships among isolates recovered from noncultivated hosts and diseased strawberry plants. Selected isolates also were tested for pathogenicity on strawberry plants in the greenhouse. In all, 39 C. gloeosporioides and 3 C. acutatum isolates were recovered from diseased strawberry crowns, and 52 C. gloeosporioides and 1 C. acutatum isolate were recovered from noncultivated hosts. In crown inoculation tests, 18 of the 52 C. gloeosporioides isolates recovered from noncultivated hosts were pathogenic to strawberry. Phylogenetic analysis using RAPD marker data divided isolates of C. gloeosporioides from noncultivated hosts into two separate clusters. One cluster contained 50 of the 52 isolates and a second cluster contained 2 isolates that were homothallic in culture. Isolates from strawberry were interspersed within the cluster containing the 50 isolates that were recovered from noncultivated hosts. The results are not inconsistent with the hypothesis that C. gloeosporioides isolates obtained from strawberry and noncultivated hosts adjacent to strawberry fields are from the same population and that noncultivated hosts can serve as potential inoculum sources for Colletotrichum crown rot of strawberry.

scholarly journals Ascochyta fabae and A. lentis: Host Specificity, Teleomorphs (Didymella), Hybrid Analysis, and Taxonomic Status

Plant Disease ◽  
1997 ◽  
Vol 81 (7) ◽  
pp. 809-816 ◽  
Author(s):  
W. J. Kaiser ◽  
B.-C. Wang ◽  
J. D. Rogers
Keyword(s):  
Faba Bean ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characteristics ◽  
Taxonomic Status ◽  
Fungal Species ◽  
Hybrid Progeny ◽  
Banding Patterns ◽  
Pathogenicity Tests ◽  
Ascochyta Fabae

Isolates of Ascochyta fabae from faba bean (Vicia faba) and A. lentis from lentil (Lens culinaris) collected from different countries were used in this study. The Didymella teleomorph (sexual state) of each fungus was induced to develop and mature on inoculated sterile lentil stems. Both fungi were heterothallic, with two mating types, designated MAT1-1 and MAT1-2. When certain isolates of A. fabae and A. lentis were crossed, hybrid pseudothecia developed. Growth, sporulation, colony appearance, morphology, and pathogenicity of the hybrid progeny frequently differed greatly from the parent isolates. Inoculations with single-ascospore progeny from matings among compatible isolates of A. fabae caused disease in faba bean but not in lentil; inoculations with single-ascospore progeny from matings among compatible isolates of A. lentis incited disease in lentil but not in faba bean. Inoculations with single-ascospore progeny from crosses between faba bean and lentil isolates did not induce disease in either host. Asci from crosses between A. fabae and A. lentis mostly contained fewer than eight ascospores that were, on average, larger than those from eight-spored asci. Matings among certain isolates of A. fabae resulted in production of pseudothecia with ascospores considerably larger than is typical for D. fabae. Random amplified polymorphic DNA (RAPD) banding patterns of Ascochyta isolates from faba bean and lentil are clearly different, and banding patterns from hybrid progeny from crosses between A. fabae and A. lentis confirmed hybridity. RAPD markers proved useful in supporting identifications of ascospore isolates from faba bean to known Ascochyta species. Dendrogram analysis indicated similarity between the two fungal species was low. The pathogenicity tests, morphological characteristics, and RAPD markers indicate that A. fabae and A. lentis represent distinct taxa. D. lentis, with its anamorph, A. lentis, is proposed as a new species that is distinct from D. fabae, with its anamorph, A. fabae.

scholarly journals Genetic Relationships of Pyrus Species and Cultivars Native to East Asia Revealed by Randomly Amplified Polymorphic DNA Markers

2002 ◽  
Vol 127 (2) ◽  
pp. 262-270 ◽  
Author(s):  
Yuanwen Teng ◽  
Kenji Tanabe ◽  
Fumio Tamura ◽  
Akihiro Itai
Keyword(s):  
East Asia ◽  
Clustering Analysis ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Randomly Amplified Polymorphic Dna ◽  
Pyrus Calleryana ◽  
Chinese White ◽  
Species Specific ◽  
Kochi Prefecture

A total of 118 Pyrus sp. (pear) and cultivars native mainly to east Asia were subjected to randomly amplified polymorphic DNA (RAPD) analysis to evaluate genetic variation and relationships among the accessions. Two hundred fifty RAPD markers were scored from 20 decamer primers. RAPD markers specific to species were identified. Clustering analysis revealed two divisions: one comprising cultivars of P. communis L., and the other including all accessions of Pyrus native to east Asia. The grouping of the species and cultivars by RAPD data largely agrees with morphological pear taxonomy. However, some noted incongruence existed between two classification methods. Pyrus calleryana Dcne. clustered together with P. koehnei Schneid., P. fauriei Schneid. and P. dimorphophylla Makino. Pyrus betulaefolia Bge. clustered with P. ×hopeiensis Yu and P. ×phaeocarpa Rehd. A noncultivated clone of P. aromatica Kikuchi et Nakai grouped with P. aromatica cultivars. Pyrus hondoensis Nakai et Kikuchi and cultivars of P. ussuriensis Max. formed a single group. Some accessions from Korea (named Korean pear) had species-specific RAPD markers and comprised an independent group. Most of the Chinese white pears clustered together with most of the Chinese sand pears. Based on the present results, the new nomenclature P. pyrifolia var. sinensis (Lindley) Teng et Tanabe for Chinese white pear was suggested. Most accessions of Japanese pears fell into one main group, whereas pear cultivars from Kochi Prefecture of Japan subclustered with some Chinese sand pears and one accession from Korea. Our results infer that some local Japanese pear cultivar populations may have been derived from cultivars native to Kochi Prefecture in Shikoku region, and that the latter may have been introduced from ancient China and/or Korea.

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).

Single juveniles of the potato cyst nematodes Globodera rostochiensis and G. pallida differentiated by randomly amplified polymorphic DNA

Parasitology ◽  
1993 ◽  
Vol 107 (5) ◽  
pp. 567-572 ◽  
Author(s):  
J. Roosien ◽  
P. M. Van Zandvoort ◽  
R. T. Folkertsma ◽  
J. N. A. M. Rouppe Van Der Voort ◽  
A. Goverse ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Nematode Species ◽  
Globodera Rostochiensis ◽  
Cyst Nematodes ◽  
Wide Range ◽  
Potential Basis ◽  
Polymerase Chain ◽  
Species Specific

SUMMARYRandom amplified polymorphic DNA (RAPD) offers a potential basis for the development of a diagnostic assay to differentiate the potato cyst nematode species Globodera rostochiensis and G. pallida. Nine decamer primers have been tested for their ability to amplify species-specific DNA sequences. Primer OPG-05 produced 2 discrete DNA fragments, which were consistently present in 5 G. rostochiensis populations and absent in 5 G. pallida populations. These fragments were detectable in single females as well as in single 2nd-stage juveniles. Their amplification is extremely efficient, and reproducible over a wide range of template concentrations. One-fifth of a single juvenile is sufficient to generate reproducible RAPD markers. The amplification from single juveniles requires no DNA isolation. The use of a crude homogenate does not impair the polymerase chain reaction.

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.

Genetic relationships and variation among ecotypes of seashore paspalum (Paspalum vaginatum) determined by random amplified polymorphic DNA markers

Genome ◽  
1994 ◽  
Vol 37 (6) ◽  
pp. 1011-1017 ◽  
Author(s):  
Zhao-Wei Liu ◽  
Robert L. Jarret ◽  
Ronny R. Duncan ◽  
Stephen Kresovich
Keyword(s):  
Rapd Markers ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
The United States ◽  
Principal Coordinates Analysis ◽  
Data Set ◽  
Seashore Paspalum ◽  
Principal Coordinates ◽  
Paspalum Vaginatum ◽  
High Level

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic relationships and variation among ecotypes of the turfgrass seashore paspalum (Paspalum vaginatum Swartz). Vegetative tissues or seeds of 46 seashore paspalum ecotypes were obtained from various locations in the United States, Argentina, and South Africa. Leaf DNA extracts were screened for RAPD markers using 34 10-mer random primers. A total of 195 reproducible RAPD fragments were observed, with an average of six fragments per primer. One hundred and sixty-nine fragments (87% of the total observed) were polymorphic, among which 27 fragments (16%) were present in three or less ecotypes, indicating the occurrence of a high level of genetic variation among the examined accessions of this species. Cluster analysis (UPGMA) and principal coordinates analysis were performed on the RAPD data set. The results illustrate genetic relationships among the 46 ecotypes, and between ecotypes and their geographical origins. Ecotypes from southern Africa could be differentiated from the U.S. and most of the Argentinean ecotypes. With a few exceptions, ecotypes collected from Argentina, Hawaii, Florida, and Texas were separated into distinct clusters.Key words: RAPDs, polymerase chain reaction, genetic diversity, phenetic analysis.

RFLP and Rapd Analyses in the Identification and Differentiation of Isolates of the Leaf Spot Fungus Corynespora cassiicola

1995 ◽  
Vol 43 (6) ◽  
pp. 609 ◽  
Author(s):  
WPK Silva ◽  
DS Multani ◽  
BJ Deverall ◽  
BR Lyon
Keyword(s):  
Fragment Size ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characteristics ◽  
Rflp Analysis ◽  
Molecular Techniques ◽  
Arbitrary Sequence ◽  
Corynespora Cassiicola ◽  
Its Regions ◽  
Digestion Pattern ◽  
Leaf Spot Fungus

Genetic variabilty in isolates of the fungal plant pathogen Corynespora cassiicola cultured from pawpaw, mimosa and thyme hosts was assessed using restriction fragment length polymorphism (RFLP) analysis of internal transcribed spacer (ITS) regions of ribosomal DNA and random amplified polymorphic DNA (RAPD) analysis of total fungal DNA. Strains of Corynespora could be distinguished from a member of the closely-related genus Helminthosporium on the basis of amplified ITS fragment size, but could not be typed individually as the ITS regions of all isolates exhibited identical size and restriction endonuclease digestion pattern. However, RAPD profiles generated by 14 decamer primers of arbitrary sequence did reveal significant differences between some of the C. cassiicola isolates and succeeded in differentiating all but two of the strains. Cluster analysis of 218 amplified DNA fragments showed that the five isolates could be placed into three groups that correspond with their host origin and morphological characteristics. The use of these molecular techniques will be extended to assess intra-specific variation in C. cassiicola isolates from rubber trees in Sri Lanka, where highly pathogenic strains present a serious threat to the natural rubber industry.

Characterization of Spanish Trichinella isolates by random amplified polymorphic DNA (RAPD)

1996 ◽  
Vol 70 (4) ◽  
pp. 335-343 ◽  
Author(s):  
E. Rodríguez ◽  
J. Nieto ◽  
J.A. Castillo ◽  
T. Gárate
Keyword(s):  
Copy Number ◽  
Rapd Markers ◽  
Trichinella Spiralis ◽  
Random Amplified Polymorphic Dna ◽  
Arbitrary Primers ◽  
Cross Hybridization ◽  
Muscle Larvae ◽  
Genetic Clusters ◽  
Species Specific

AbstractThe random amplified polymorphic DNA (RAPD) assay was used to find molecular markers able to distinguish Trichinella spiralis from T. britovi, the two recognized Spanish Trichinella species. Fourteen Spanish Trichinella isolates, as well as reference Trichinella isolates representing the five species T. spiralis (T1), T. nativa (T2), T. britovi (T3), T. pseudospiralis (T4) and T. nelsoni (T7) and the three other taxa Trichinella T5, Trichinella T6 and Trichinella T8 of the genus, were characterized by RAPD using both purified and crude DNAs from infective muscle larvae (ML) and seven arbitrary primers. Three primers yielded diagnostic RAPD markers for the Spanish T. spiralis and T. britovi isolates as well as for the Trichinella reference isolates analysed, and in the case of crude DNAs the results were obtained in few hours. In addition, the species-specificity of the diagnostic RAPD markers from Spanish Trichinella isolates was studied by cross-hybridization assays. These assays confirmed that the selected diagnostic DNA fragments were not species-specific, but showed potential differences in the copy number among the examined Trichinella genetic clusters.

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