Genome- and species-specific markers and genome relationships of diploid perennial species in Triticeae based on RAPD analyses

Genome ◽  
1995 ◽  
Vol 38 (6) ◽  
pp. 1230-1236 ◽  
Author(s):  
Jun-Zhi Wei ◽  
Richard R.-C. Wang
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Diploid Species ◽  
Perennial Species ◽  
Genome Composition ◽  
Sequence Analyses ◽  
Evolution Analysis ◽  
Close Relationship ◽  
Species Specific ◽  
Tribe Triticeae

Eight different genomes (E, H, I, P, R, St, W, and Ns) represented by 22 diploid species of the tribe Triticeae were analyzed using the random amplified polymorphic DNA (RAPD) technique. The genome relationships were obtained based on 371 RAPD fragments produced with 30 primers. The four species of the genus Psathyrostachys (having various Ns genomes) were closely related. The genomes Ee and Eb had a similarly close relationship and were distinct from all other genomes analyzed. Genomes P, R, and St were grouped in one cluster and genomes H and I in another. Genome W had a distant relationship with all other genomes. These results agree with the conclusions from studies of chromosome pairing and isozyme and DNA sequence analyses. Twenty-nine and 11 RAPD fragments are considered to be genome- and species-specific markers, respectively. One to six genome-specific markers were identified for each genome. These RAPD markers are useful in studies of genome evolution, analysis of genome composition, and genome identification.Key words: Triticeae, perennial, diploid, genome, RAPD, genome-specific markers.

scholarly journals Identification of RAPD markers linked to A and B genome sequences in Musa L.

Genome ◽  
2000 ◽  
Vol 43 (5) ◽  
pp. 763-767 ◽  
Author(s):  
M Pillay ◽  
D C Nwakanma ◽  
A Tenkouano
Keyword(s):  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Diploid Species ◽  
Morphological Characteristics ◽  
Genome Composition ◽  
Reliable System ◽  
B Genome ◽  
Wild Diploid Species

Plantains and bananas (Musa spp. sect. eumusa) originated from intra- and interspecific hybridization between two wild diploid species, M. acuminata Colla. and M. balbisiana Colla., which contributed the A and B genomes, respectively. Polyploidy and hybridization have given rise to a number of diploid, triploid, and tetraploid clones with different permutations of the A and B genomes. Thus, dessert and highland bananas are classified mainly as AAA, plantains are AAB, and cooking bananas are ABB. Classification of Musa into genomic groups has been based on morphological characteristics. This study aimed to identify RAPD (random amplified polymorphic DNA) markers for the A and B genomes. Eighty 10-mer Operon primers were used to amplify DNA from M. acuminata subsp. burmannicoides clone 'Calcutta 4' (AA genomes) and M. balbisiana clone 'Honduras' (BB genomes). Three primers (A17, A18, and D10) that produced unique genome-specific fragments in the two species were identified. These primers were tested in a sample of 40 genotypes representing various genome combinations. The RAPD markers were able to elucidate the genome composition of all the genotypes. The results showed that RAPD analysis can provide a quick and reliable system for genome identification in Musa that could facilitate genome characterization and manipulations in breeding lines.Key words: banana and plantain, A and B genomes, genomic groups, RAPD markers.

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.

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.

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.

scholarly journals Assessment of genetic diversity in sea buckthorn (Hippophae rhamnoides L.) accessions from Mongolia based on RAPD markers

2021 ◽  
pp. 1-9
Author(s):  
Zolzaya Sandag ◽  
Dorjderem Balchin ◽  
Ariya Enkhtuya ◽  
Nomin Myagmar ◽  
Nomuun Oyunbat ◽  
...  
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Sea Buckthorn ◽  
Hippophae Rhamnoides ◽  
Germplasm Collections ◽  
Hippophaë Rhamnoides ◽  
Geographical Regions ◽  
Close Relationship ◽  
Agricultural Industries ◽  
Hippophae Rhamnoïdes L

Hippophae rhamnoides L., which belongs to the Elaegnaceae family, is one of the medically and environmentally valuable berry crops with its high nutritious and bioactive compounds. Despite its high demand in the food, medicinal and agricultural industries, this species has been less studied molecularly. In view of this, an effort has been made in the present study to characterize 24 accessions of H. rhamnoides collected from different geographical regions of Mongoliaa through random amplified polymorphic DNA (RAPD) markers. A total of 10 RAPD primers were used in the present study for their ability to produce clear, scorable amplicons. The RAPD analysis totally generated 87 bands, of which 84 (96.34%) were polymorphic, pointing to a high degree of genetic variation. The similarity coefficient ranged from 0.4-1 with the mean of 0.78. The UPGMA dendrogram was generated using these data grouped accessions into two main clusters. Cluster analysis reflected a relatively close relationship between accessions grown at the same or neighbouring areas. Thus, our data could be informative for further selection and management of germplasm collections and crossing strategies for sea buckthorn.

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 RANDOM AMPLIFIED POLYMORPHIC DNA VARIATION IN THE CULTIVATED SPECIES OF PRUNUS

HortScience ◽  
1992 ◽  
Vol 27 (6) ◽  
pp. 574a-574
Author(s):  
S. Arulsekar ◽  
F. A. Bliss
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Crop Species ◽  
Gene Markers ◽  
Dna Variation ◽  
Efficient Gene ◽  
Tree Fruit ◽  
Germplasm Diversity ◽  
Cultivated Species ◽  
Species Specific

Studies of genetic variation at the DNA level in the tree fruit and nut crop species of Prunus have been very limited. Recently molecular markers based on random amplified polymorphic DNA (RAPD) markers have been shown to be highly useful and efficient gene markers in other plant and animal species. We have used a total of 50 primers (10-mers) with arbitrary nucleotide sequence to identify cultivars of cherry, plum, apricot, peach and almond. A total of 120 accessions of different cultivars were assayed. The variation revealed by RAPD markers was highly species specific in the five Prunus species examined. High levels of polymorphism were observed for almond cultivars whereas sweet cherry revealed the lowest levels of polymorphism for the RAPD primers examined. The implications of these results in the germplasm diversity in the cultivated species of Prunus will be discussed.

EVALUATION OF PTYCHOBOTHRIDEAN CESTODES USING RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) MARKERS FROM FRESH WATER FISHES IN GODAVARI BASIN (M.S.) INDIA

2017 ◽  
Vol 23 (2) ◽  
Author(s):  
SUNITA BORDE ◽  
ASAWARI FARTADE ◽  
AMOL THOSAR ◽  
RAHUL KHAWAL
Keyword(s):  
Fresh Water ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Band Pattern ◽  
Genomic Variation ◽  
Polymorphic Band ◽  
Rapd Profile ◽  
Band Size ◽  
Pcr Product ◽  
The Common

Ptychobothridean genera like Senga and Circumoncobothrium are the common parasites of fresh water fishes. The genotypic study of these parasites was taken by RAPD. The RAPD profile of these two parasites were not similar to each other as depicted by the band pattern in picture. These results suggest the presence of inter-specific polymorphism among cestode parasites of two different genera for RAPD analysis. The present study demonstrated that genetic differentiation of cestode parasites could be accomplished on the basis of genomic variation with polymorphic band pattern using RAPD. All the detected bands (PCR product) were polymorphic and band size ranged from 500-5000 bp in length. The RAPD of profiles using GBO-31, GBO-32, GBO-33, GBO-34, GBO-35 and GBO-36. Primers were able to characterize inter-specific polymorphism among the two genus ( Senga and Circumoncobothrium ). Genetic analysis suggests that Senga and Circumoncobothrium show genetic diversity with respect to RAPD patterns using all the six primers used for the present study. The genetic distance between the analyzed genuses ranged from 0.14 to 0.80. The differentiation of the two parasites on the basis of genetic markers could greatly facilitate study on the biology of these parasites.

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.

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