Molecular phylogeny of mangroves VI. Intraspecific genetic variation in mangrove species Excoecaria agallocha L. (Euphorbiaceae)

Genome ◽  
2000 ◽  
Vol 43 (1) ◽  
pp. 110-115 ◽  
Author(s):  
M Lakshmi ◽  
M Parani ◽  
Nivedita Ram ◽  
Ajay Parida
Keyword(s):  
Genetic Variation ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
The West ◽  
Mangrove Species ◽  
Excoecaria Agallocha ◽  
Polymorphic Restriction ◽  
High Level ◽  
Key Words Mangroves ◽  
Mean Similarity

Genomic DNA from 84 individuals of Excoecaria agallocha from seven mangrove populations were analysed for random amplified polymorphic DNAs (RAPDs) using 16 random 10-mer primers. Polymorphism within populations varied from 20% to 31%. At the interpopulation level, 111/149 (74%) of RAPDs were polymorphic. Restriction fragment length polymorphism (RFLP) analysis of 21 individuals (3 individuals randomly selected from the 7 populations) using 30 probe-enzyme combinations revealed a high level of interpopulation polymorphism (62.2%) indicating interpopulation genetic divergence. The polymorphic RAPDs and RFLPs were pooled, and clustering was carried out based on mean similarity for individual populations. The dendrogram showed groupings of populations from the West and East Coasts of India into separate clusters, at 60% similarity level. Further, RAPD and RFLP analysis of male and female plants showed approximately the same level of variation in both sexes, and no sex-linked markers were found. These results demonstrate that considerable intrapopulation and interpopulation genetic variations exist in E. agallocha, and that lack of genetic variation is not the reason for the morphological uniformity observed across the range of the species. Key words: mangroves, Excoecaria agallocha, molecular markers, RAPD, RFLP, genetic variation.

scholarly journals Characterization of the Mycobacterium bovis Restriction Fragment Length Polymorphism DNA Probe pUCD and Performance Comparison with Standard Methods

2000 ◽  
Vol 38 (9) ◽  
pp. 3362-3369 ◽  
Author(s):  
Rory O'Brien ◽  
Bret S. Danilowicz ◽  
Louise Bailey ◽  
Orla Flynn ◽  
Eamon Costello ◽  
...  
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Mycobacterium Bovis ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Performance Comparison ◽  
High Level ◽  
Restriction Fragment Length

In this study, the newly described Mycobacterium bovisrestriction fragment length polymorphism (RFLP) typing probe pUCD was characterized by sequence analysis and the previously observed polymorphic banding pattern was reproduced with a combination of three oligonucleotide probes in a single, mixed hybridization. In addition, the ability of pUCD to distinguish between 299 M. bovisisolates from the Republic of Ireland was assessed in relation to established methods and a statistical function for objective comparison of RFLP probes was derived. It was found that typing with pUCD alone produced greater discrimination between M. bovis isolates than typing with the commonly used mycobacterial DNA probes IS6110, PGRS, and DR and also by the spoligotyping technique. pUCD and DR in combination produced the highest level of discrimination while maintaining a high level of concordance with known epidemiological data relating to the samples. The reduction of pUCD to the level of oligonucleotides should in future allow pUCD and DR to be included together in a mixed hybridization, thus producing a high level of M. bovis strain type discrimination from a single round of RFLP analysis.

scholarly journals Genetic variation of Chilo suppressalis Walker (Lepidoptera: Pyralidae) populations in Guilan and west of Mazandaran provinces analysed with RAPD markers 

2014 ◽  
Vol 50 (No. 1) ◽  
pp. 26-35 ◽  
Author(s):  
A. Farahpour Haghani ◽  
R. Hosseini ◽  
A.A. Ebadi ◽  
A. Aalami
Keyword(s):  
Genetic Variation ◽  
Rapd Markers ◽  
Population Group ◽  
Stem Borer ◽  
Pcr Analysis ◽  
Chilo Suppressalis ◽  
Mazandaran Province ◽  
The West ◽  
Population Genetic Variation ◽  
High Level

Genetic variation of striped stem borer Chilo suppressalis populations in Guilan and Mazandaran provinces in Iran was studied in 2010 by means of RAPD markers. Collected 45 samples from 19 locations (representing 17 counties in Guilan province and 2 counties in Mazandaran province) were classified into four groups of populations: three population groups corresponding to the west, centre, and east of Guilan and one population group from the west of Mazandaran. RAPD PCR analysis showed that Chilo suppressalis populations in Mazandaran are genetically different from the Guilan populations while the western populations of Guilan are genetically separated from the two other populations. The central and the eastern populations of Guilan exhibit some similarities with those of Mazandaran and the similarities are more obvious between the eastern populations of Guilan and the western population of Mazandaran. The population from the centre of Guilan showed the highest level of intra-population genetic variation possibly due to wider rice cultivated area and/or due to higher sample size. The results showed a high level of genetic variation in Chilo suppressalis populations in the two provinces in Iran. In spite of the model species is a widely distributed pest, the study indicated that the samples originated in populations with a different genetic make-up.

Molecular characterization of trypanosome species and subgroups within subgenus Nannomonas

Parasitology ◽  
1995 ◽  
Vol 111 (3) ◽  
pp. 301-312 ◽  
Author(s):  
L. H. Garside ◽  
W. C. Gibson
Keyword(s):  
Fragment Length Polymorphism ◽  
Genomic Library ◽  
Molecular Level ◽  
Pcr Amplification ◽  
Rflp Analysis ◽  
Rdna Locus ◽  
Kinetoplast Dna ◽  
Banding Patterns ◽  
High Level

SUMMARYRestriction fragment length polymorphism (RFLP) analysis of both genomic and kinetoplast DNA from representative stocks from 3 Trypanosoma congolense subgroups (Savannah, Forest, and Kilifi), T. simiae and T. godfreyi, was used to investigate the relatedness of the different groups within subgenus Nannomonas, DNA probes for β-tubulin and the ribosomal DNA (rDNA) locus were isolated from a T. congolense Savannah genomic library; additional probes were generated by PCR amplification of mini-exon and glutamate and alanine rich protein (GARP) gene sequences. Our results provide evidence that at the molecular level the T. congolense Savannah and Forest groups are the most closely related groups within the subgenus Nannomonas: the Savannah and the Forest groups had mini-exon gene repeats of identical size, which shared homology, had mini-circles of the same size and had a high level of similarity (63%) when the banding patterns produced with a tubulin and rDNA probe were subjected to numerical analysis. All other pairwise combinations of groups have very low percentage similarities of < 10%, suggesting that the Kilifi group trypanosomes, are as distantly related to the T. congolense Savannah and Forest groups as they are to T. simiae or T. godfreyi. The conservation of the GARP gene between the Savannah, Forest and Kilifi groups provides the only evidence linking the Kilifi trypanosomes to the other groups in T. congolense. We find no evidence for the presence of the GARP gene in the T. simiae or T. godfreyi group trypanosomes.

scholarly journals Genetic Similarities among Wine Grape Cultivars Revealed by Restriction Fragment-length Polymorphism (RFLP) Analysis

1996 ◽  
Vol 121 (4) ◽  
pp. 620-624 ◽  
Author(s):  
John E. Bowers ◽  
Carole P. Meredith
Keyword(s):  
Fragment Length Polymorphism ◽  
Similarity Index ◽  
Rflp Analysis ◽  
Cabernet Franc ◽  
Geographic Origins ◽  
The Mean ◽  
And Cluster Analysis ◽  
Chenin Blanc ◽  
Mean Similarity ◽  
Grape Cultivars

RFLP data were used to assess genetic similarity among 33 Vitis vinifera L. cultivars and one interspecific cultivar. A similarity matrix was constructed on the basis of the presence or absence of 49 bands generated by eight RFLP probes and cluster analysis was performed. The mean similarity index for all pairwise comparisons was 0.696 and ranged from 0.444 between `St. Emilion' and the interspecific hybrid `Salvador' to 0.952 between `Chenin blanc' and `Semillon'. Mean similarity among all V. vinifera cultivars was 0.705. Several groupings of similar cultivars are consistent with historical reports and presumed geographic origins: `Chardonnay' and `Melon', `Colombard' and `Folle blanche', `Gewürztraminer' and `Trousseau', `Cabernet franc' and `Cabernet Sauvignon', `Mission' and `Palomino'. The similarity between `Mission' and `Palomino' is the first genetic evidence to support the putative Spanish origin of `Mission'. Some groupings are unexpected (`Sauvignon blanc' and `Gewürztraminer', `Chenin blanc' and `Semillon') because the cultivars are not thought to have originated in the same regions. While some relationships suggested by this study may be artifacts of RFLP analysis or of the statistical method, they raise questions for further genetic inquiry into the origins of grape cultivars.

Localization of the Br Polymorphism on a 144 bp Exon of the GPIa Gene and Its Application in Platelet DNA Typing

1994 ◽  
Vol 71 (05) ◽  
pp. 651-654 ◽  
Author(s):  
Rainer Kalb ◽  
Sentot Santoso ◽  
Katja Unkelbach ◽  
Volker Kiefel ◽  
Christian Mueller-Eckhardt
Keyword(s):  
Genomic Organization ◽  
Fragment Length Polymorphism ◽  
Human Platelet ◽  
Dna Typing ◽  
Rflp Analysis ◽  
Serological Typing ◽  
Allele Specific ◽  
Polymerase Chain ◽  
Alloimmune Thrombocytopenia ◽  
Rflp Typing

SummaryAlloimmunization against the human platelet alloantigen system Br (HPA-5) is the second most common cause of neonatal alloimmune thrombocytopenia (NAIT) in Caucasian populations. We have recently shown that a single base polymorphism at position 1648 on platelet mRNA coding for GPIa results in an aminoacid substitution at position 505 on the mature GPIa which is associated with the two serological defined Br phenotypes.Since DNA-typing of platelet alloantigens offers possibilities for useful clinical applications, we designed genomic DNA-based restriction fragment length polymorphism (RFLP) typing for Br alloantigens. To establish this technique we analyzed the genomic organization of GPIa adjacent to the polymorphic base. Using the polymerase chain reaction (PCR) of blood cell DNA we have identified two introns (approximately 1.7 and 1.9 kb) flanking a 144 bp coding sequence of the GPIa gene encompassing the polymorphic base 1648. Based on the in- tron sequence, a PCR primer was constructed to amplify a 274 bp fragment which was used for allele-specific RFLP to determine the Br genotypes. The results of RFLP analysis using Mnll endonuclease obtained from 15 donors (2 Br37*, 2 Br^ and 11 Brb/b) correlate perfectly with serological typing by monoclonal antibody-specific immobilization of platelet antigens (MAIPA) assay.

scholarly journals POPULATION GENETICS OF ALLOZYME VARIATION IN NEUROSPORA INTERMEDIA

Genetics ◽  
1975 ◽  
Vol 80 (4) ◽  
pp. 785-805
Author(s):  
P T Spieth
Keyword(s):  
Genetic Variation ◽  
Vegetative Reproduction ◽  
Vascular Plant ◽  
Natural Populations ◽  
Allozyme Variation ◽  
Regular Feature ◽  
Local Populations ◽  
Neurospora Intermedia ◽  
Pattern Of Variation ◽  
High Level

ABSTRACT Electrophoretically detectable variation in the fungus Neurospora intermedia has been surveyed among isolates from natural populations in Malaya, Papua, Australia and Florida. The principal result is a pattern of genetic variation within and between populations that is qualitatively no different than the well documented patterns for Drosophila and humans. In particular, there is a high level of genetic variation, the majority of which occurs at the level of local populations. Evidence is presented which argues that N. intermedia has a population structure analogous to that of an annual vascular plant with a high level of vegetative reproduction. Sexual reproduction appears to be a regular feature in the biology of the species. Substantial heterokaryon function seems unlikely in natural populations of N. intermedia. Theoretical considerations concerning the mechanisms underlying the observed pattern of variation most likely should be consistent with haploid selection theory. The implications of this constraint upon the theory are discussed in detail, leading to the presentation of a model based upon the concept of environmental heterogeneity. The essence of the model, which is equally applicable to haploid and diploid situations, is a shifting distribution of multiple adaptive niches among local populations such that a given population has a small net selective pressure in favor of one allele or another, depending upon its particular distribution of niches. Gene flow among neighboring populations with differing net selective pressures is postulated as the principal factor underlying intrapopulational allozyme variation.

A variable minisatellite sequence in the chloroplast genome of Sorbus L. (Rosaceae: Maloideae)

Genome ◽  
2002 ◽  
Vol 45 (3) ◽  
pp. 570-576 ◽  
Author(s):  
R Andrew King ◽  
Colin Ferris
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Chloroplast Genome ◽  
Length Polymorphism ◽  
Sequence Variation ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Chloroplast Microsatellites ◽  
Sorbus Aucuparia ◽  
Pcr Product ◽  
Restriction Fragment Length

The chloroplast genome is now known to be more variable than was once thought. Reports of RFLP (restriction fragment length polymorphism) and sequence variation, as well as variation in chloroplast microsatellites, are common. Here, data are presented on the variability of a minisatellite sequence in the chloroplast genome of Sorbus species. RFLP analysis of a PCR product comprising the region between the trnM and rbcL genes of nine Sorbus species identified seven size variants. Sequencing revealed the observed size polymorphism to be due to differences in the number of copies of an imperfect 9-bp motif. A more intensive survey of the variability of the minisatellite was undertaken in populations of Sorbus aucuparia. The potential uses of such regions in chloroplast DNA are discussed and a possible mechanism for the evolution of the minisatellite is presented.Key words: atpE, homoplasy, microsatellite, rowan, VNTR.

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