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.

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 A comparative analysis of genetic diversity in Portuguese grape germplasm from ampelographic collections fit for quality wine production

2016 ◽  
Vol 14 (4) ◽  
pp. e0712 ◽  
Author(s):  
Isaura Castro ◽  
Olinda Pinto-Carnide ◽  
Jesús M. Ortiz ◽  
Vanessa Ferreira ◽  
Juan P. Martín
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characters ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Molecular Techniques ◽  
Wine Production ◽  
Rapd And Issr ◽  
Simple Sequence

Grapevine cultivars diversity is vast and full of synonyms and homonyms. Up to few decades ago characterization of grapevine was based on morphological characters. In the last decades, molecular markers were developed and have been used as tools to study genetic diversity in a range of different plant species. Fifty-six Portuguese accessions representative of ‘Vinhos Verdes’ and ‘Douro’ Controlled Designations of Origin (DOC) were analysed through DNA fingerprints generated by Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR). The study aimed to compare the effectiveness of RAPD and ISSR molecular techniques in the detection of synonyms, homonyms and misnames. RAPD and ISSR analysis enabled the detection of 36 different band patterns, reducing in about 36% the initial material. Several accessions grown under different names, between and within collections, were confirmed as the same genotype, namely Gouveio/Verdelho, Sousão Douro/Vinhão and Arinto Oeste/Pedernã. Similarly, some homonyms/misnames were also identified, namely within Azal Tinto and Rabigato accessions. RAPD and ISSR markers revealed to be adequate molecular techniques for grapevine varieties fingerprinting with advantages over other molecular procedures, contributing for a good management of grapevine collections.

scholarly journals Genetic Variation in the Qinghai-Tibetan Plateau Endemic and Endangered Conifer Cupressus gigantea, Detected Using RAPD and ISSR Markers

2008 ◽  
Vol 57 (1-6) ◽  
pp. 85-92 ◽  
Author(s):  
T. Xia ◽  
L. Meng ◽  
K. Mao ◽  
B. Tian ◽  
G. Miehe ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Tibetan Plateau ◽  
Population Differentiation ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Conservation Strategies ◽  
High Degree ◽  
Rapd And Issr

Abstract Assessing the level and distribution of genetic diversity of rare tree species is essential for their management and the development of effective conservation strategies. Cupressus gigantea is a long-lived endemic cypress of the west Qinghai-Tibetan Plateau and the tallest tree in its genus. The current populations of this species are fragmented and highly disturbed. We used RAPD (Random Amplified Polymorphic DNA) and ISSR (Inter-Simple Sequence Repeat amplification) markers to assess the genetic variation and population structure of this endangered cypress. The 15 RAPD primers used in this study amplified 108 reproducible bands, 49 (45.4%) of which were polymorphic, while the 12 ISSR primers amplified 94 bands, 65 (69.2%) of which were polymorphic. Analysis of Molecular Variance (AMOVA) indicated that 49.7% and 38.3% of the variation was attributable to differences between populations for the RAPD and ISSR markers, respectively; relatively high compared to values reported for other conifer species. These estimates were also similar to Gst values obtained from Nei’s gene diversity analyses (RAPD = 0.41 and ISSR = 0.36), and suggest that there is a high degree of population differentiation in this narrowly-distributed conifer. The genetic structure of this species has probably been shaped by its long life cycle and climatic changes during the Quaternary. The high degree of population differentiation in this species highlights the need for additional conservation measures, including measures to protect of all of the remaining populations. The substantial similarities between the results of the RAPD and ISSR analyses of samples from the same individuals indicate that they can be interpreted with high levels of confidence.

scholarly journals Retention of relict satellite DNA sequences in Anemone (Ranunculaceae)

2013 ◽  
Vol 72 (1) ◽  
pp. 1-133 ◽  
Author(s):  
Višnja Besendorfer ◽  
Jelena Mlinarec
Keyword(s):  
Dna Sequences ◽  
Southern Hybridization ◽  
Repeat Unit ◽  
Similar Species ◽  
Genomic Component ◽  
Library Hypothesis ◽  
Species Specific ◽  
Eukaryotic Organisms ◽  
Fish Signal

Abstract Satellite DNAis a genomic component present in virtually all eukaryotic organisms. The turnover of highly repetitive satellite DNAis an important element in genome organization and evolution in plants. Here we study the presence, physical distribution and abundance of the satellite DNAfamily AhTR1 in Anemone. Twenty-two Anemone accessions were analyzed by PCR to assess the presence of AhTR1, while fluorescence in situ hybridization and Southern hybridization were used to determine the abundance and genomic distribution of AhTR1. The AhTR1 repeat unit was PCR-amplified only in eight phylogenetically related European Anemone taxa of the Anemone section. FISH signal with AhTR1 probe was visible only in A. hortensis and A. pavonina, showing localization of AhTR1 in the regions of interstitial heterochromatin in both species. The absence of a FISH signal in the six other taxa as well as weak signal after Southern hybridization suggest that in these species AhTR1 family appears as relict sequences. Thus, the data presented here support the »library hypothesis« for AhTR1 satellite evolution in Anemone. Similar species-specific satellite DNAprofiles in A. hortensis and A. pavonina support the treatment of A. hortensis and A. pavonina as one species, i.e. A. hortensis s.l.

scholarly journals Karyotype Characterization of Nine Periwinkle Species (Gastropoda, Littorinidae)

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 517 ◽  
Author(s):  
Daniel García-Souto ◽  
Sandra Alonso-Rubido ◽  
Diana Costa ◽  
José Eirín-López ◽  
Emilio Rolán-Álvarez ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Chromosome Numbers ◽  
Gene Clusters ◽  
Chromosomal Mapping ◽  
Closely Related Species ◽  
Submetacentric Chromosome ◽  
The Family ◽  
Littorina Arcana

Periwinkles of the family Littorinidae (Children, 1834) are common members of seashore littoral communities worldwide. Although the family is composed of more than 200 species belonging to 18 genera, chromosome numbers have been described in only eleven of them. A molecular cytogenetic analysis of nine periwinkle species, the rough periwinkles Littorina arcana, L. saxatilis, and L. compressa, the flat periwinkles L. obtusata and L. fabalis, the common periwinkle L. littorea, the mangrove periwinkle Littoraria angulifera, the beaded periwinkle Cenchritis muricatus, and the small periwinkle Melarhaphe neritoides was performed. All species showed diploid chromosome numbers of 2n = 34, and karyotypes were mostly composed of metacentric and submetacentric chromosome pairs. None of the periwinkle species showed chromosomal differences between male and female specimens. The chromosomal mapping of major and minor rDNA and H3 histone gene clusters by fluorescent in situ hybridization demonstrated that the patterns of distribution of these DNA sequences were conserved among closely related species and differed among less related ones. All signals occupied separated loci on different chromosome pairs without any evidence of co-localization in any of the species.

An intergeneric hybrid in the family Phocoenidae

1998 ◽  
Vol 76 (1) ◽  
pp. 198-204 ◽  
Author(s):  
Robin W Baird ◽  
Pamela M Willis ◽  
Tamara J Guenther ◽  
Paul J Wilson ◽  
Bradley N White
Keyword(s):  
Dna Sequences ◽  
Parental Species ◽  
Intergeneric Hybrid ◽  
Harbour Porpoise ◽  
Colour Pattern ◽  
Phocoena Phocoena ◽  
Female Fetus ◽  
The Family ◽  
In The Wild ◽  
Species Specific

A 60-cm female fetus recovered from a Dall's porpoise (Phocoenoides dalli) found dead in southern British Columbia was fathered by a harbour porpoise (Phocoena phocoena). This is the first report of a hybrid within the family Phocoenidae and one of the first well-documented cases of cetacean hybridization in the wild. In several morphological features, the hybrid was either intermediate between the parental species (e.g., vertebral count) or more similar to the harbour porpoise than to the Dall's porpoise (e.g., colour pattern, relative position of the flipper, dorsal fin height). The fetal colour pattern (with a clear mouth-to-flipper stripe, as is found in the harbour porpoise) is similar to that reported for a fetus recovered from a Dall's porpoise to off California. Hybrid status was confirmed through genetic analysis, with species-specific repetitive DNA sequences of both the harbour and Dall's porpoise being found in the fetus. Atypically pigmented porpoises (usually traveling with and behaving like Dall's porpoises) are regularly observed in the area around southern Vancouver Island. We suggest that these abnormally pigmented animals, as well as the previously noted fetus from California, may also represent hybridization events.

scholarly journals Rapid Plant Regeneration and Molecular Assessment of Genetic Stability Using ISSR and RAPD Markers in Commercial Banana Cv. Grand Naine (G-9)

2014 ◽  
Vol 4 (3) ◽  
pp. 393-403
Author(s):  
J. S. DUHAN ◽  
S. Kajla ◽  
D. Choudhary ◽  
A. K. Poonia
Keyword(s):  
Tissue Culture ◽  
Genetic Stability ◽  
Random Amplified Polymorphic Dna ◽  
Issr Markers ◽  
Ms Medium ◽  
Inter Simple Sequence Repeats ◽  
Rapd Primer ◽  
Molecular Assessment ◽  
Rapd And Issr ◽  
Issr Primers

The investigation was carried out to assess the genetic stability in   tissue culture raised plants of banana cv. G-9 using random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) markers.Aims:  Molecular assessment of genetic stability of tissue culture raised plants of banana cv. G-9 using molecular markers.Material and Results: Apical shoots were established on medium EM4 (MS + BAP 4.0 mg L-1) with maximum of 3.8 buds/explant in 2.6 days. The maximum bud multiplication with 16.5±0.06 shoots was observed on medium Ma3 (MS medium+ 5.0 mg L-1 BAP + 0.25 mg L-1 NAA of + 30 mg L-1 AdSO4). The maximum rooting response (100%) was observed on 1/2 MS medium supplemented with 2.0 mg L-1 NAA in 12.2 days. After acclimatization the hardened plants were examined for genetic stability using RAPD and ISSR primers. Total forty six (twenty six RAPD and twenty ISSR) markers were used. RAPD primers produced 87 distinct and scorable bands, with an average of 3.34 bands per primer and the amplification products range was from 100-1200 bps. The number of scorable bands for RAPD primer varied from 2 to 5 with an average of 3.34 bands per primer. ISSR primers produced 71 distinct and scorable bands in the range of 100-1000 bps and the number of scorable bands for each primer varied from 2 to 6 with an average of 3.55 bands per primer.Conclusion: Similar profile with monomorphic bands was observed for all the tissue culture raised plants when compared to mother plant in both types of markers used. The results corroborate the fact that plant tissue culture technology has immense importance for production of true to type of planting material. 

scholarly journals Fingerprinting of Vaccinium corymbosum cultivars using DNA of fruits

2014 ◽  
Vol 41 (No. 4) ◽  
pp. 175-184 ◽  
Author(s):  
M. Carvalho ◽  
M. Matos ◽  
V. Carnide
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Vaccinium Corymbosum ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Highbush Blueberry ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Production And Consumption ◽  
Simple Sequence

  In recent years the production and consumption Vaccinium corymbosum has increased. Highbush blueberry cultivars are divided into three types, northern, intermediate and southern. The traditional methods for classification of highbush blueberry cultivars using morphological and flavour traits are largely unsuccessful, due to environmental influences. The genetic similarity of ten highbush blueberry cultivars was evaluated using random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers from fruits and leaves. The DNA concentrations obtained in fruits and leaves were very similar and the band profiles observed in the two tissues were analogous with both molecular markers. RAPD analysis generated 144 bands, of which 112 were polymorphic (77.8%) in fruits and 141 bands of which 118 were polymorphic (83.7%) in leaves. In fruits, ISSR analysis produced 151 bands of which 127 were polymorphic (84.1%) and in leaves it produced 148 bands with 127 being polymorphic (85.8%). Dendrogram and principal coordinates analysis (PCO) analysis using the both markers results were concordant and a clear division of the types of highbush blueberry cultivars (northern and southern) into two distinct groups was verified.    

Assessment of Somaclonal Variations in Embryo-derived Axillary Shoots of Chickpea using Molecular Markers

2020 ◽  
Author(s):  
S.S. Alghamdi ◽  
H.M. Migdadi ◽  
M.A. Khan ◽  
E.H. El-Harty ◽  
Y.H. Dewir
Keyword(s):  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Crop Improvement ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Mother Plant ◽  
Clonal Variation ◽  
Axillary Shoots ◽  
Somaclonal Variations ◽  
Issr Primers

Background: Somaclonal variation is considered as a source of genetic variation for crop improvement. It has been investigated using cytological, biochemical and molecular techniques.Methods: Genetic stability in the embryo-derived axillary shoots of 4 chickpea genotypes was assessed using eight inter-simple sequence repeat (ISSR) and 19 random amplified polymorphic DNA (RAPD) primers. Result: RAPD primers produced 94 and ISSR primers produced 38 distinct and scorable alleles, with an average of 4.9 alleles for RAPD and 4.75 for ISSR primers. The polymorphic information content (PIC) ranged from 0.36 to 0.90 for RAPD and from 0.50 to 0.87 for ISSR. ISSR recognized a 90%, but RAPD recognized 82% similarity value. No absolute similarity value was between the mother plant and the regenerated shoots for the overall genotypes. At a 90% similarity value, 15 out of the 20 regenerated shoots from ‘Giza 88’ group with their mother plant using ISSR markers; however, 11 regenerated shoots grouped with their mother plant in one central cluster for ‘Giza 4’ using RAPD markers. The observed variations in the total number of polymorphic RAPD and ISSR bands and the number of bands specific to the mother and regenerated shoots, detected intra-clonal variation and genetic instability seem to be genotype-dependent.

RAPD markers encoding retrotransposable elements are linked to the male sex in Cannabis sativa L.

Genome ◽  
2005 ◽  
Vol 48 (5) ◽  
pp. 931-936 ◽  
Author(s):  
Koichi Sakamoto ◽  
Tomoko Abe ◽  
Tomoki Matsuyama ◽  
Shigeo Yoshida ◽  
Nobuko Ohmido ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Y Chromosome ◽  
Dna Sequences ◽  
Blot Analysis ◽  
Cannabis Sativa ◽  
Random Amplified Polymorphic Dna ◽  
Male And Female ◽  
Retrotransposable Elements

Male-associated DNA sequences were analyzed in Cannabis sativa L. (hemp), a dioecious plant with heteromorphic sex chromosomes. DNA was isolated from male and female plants and subjected to random amplified polymorphic DNA analysis. Of 120 primers, 17 yielded 400 to 1500-bp fragments detectable in male, but not female, plants. These fragments were cloned and used as probes in gel-blot analysis of genomic DNA. When male and female DNA was hybridized with 2 of these male-specific fragments, MADC(male-associated DNA sequences in C. sativa)3 and MADC4, particularly intense bands specific to male plants were detected in addition to bands common to both sexes. The MADC3 and MADC4 sequences were shown to encode gag/pol polyproteins of copia-like retrotransposons. Fluorescence in situ hybridization with MADC3 and MADC4 as probes revealed a number of intense signals on the Y chromosome as well as dispersed signals on all chromosomes. The gel-blot analysis and fluorescence in situ hybridization results presented here support the hypothesis that accumulation of retrotransposable elements on the Y chromosome might be 1 cause of heteromorphism of sex chromosomes.Key words: Cannabis sativa, FISH, RAPD, retrotransposon, sex chromosome.

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