Polymorphic DNA Markers (polymorphic + dna_marker)

Distribution by Scientific Domains

Kinds of Polymorphic DNA Markers

  • amplified polymorphic dna marker
  • random amplified polymorphic dna marker


  • Selected Abstracts


    Infraspecific variation and phylogeography of the high-polyploid Iberian endemic Anthoxanthum amarum Brot. (Poaceae; Pooideae) assessed by random amplified polymorphic DNA markers (RAPDs) and morphology

    BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2007
    MANUEL PIMENTEL
    High morphological and ecological diversity has been observed in the north-west Iberian Peninsula endemic Anthoxanthum amarum Brot., for which two different morphotypes (northern and southern) have been described on the basis of qualitative traits and geographical origin. In the present study, a combined molecular and morphological method was applied to ten populations of this species with the following aims: (1) to assess whether the variation observed was taxonomically meaningful; (2) to assess the influence of the environment on the variation in the morphological characters; and (3) to track the potential phylogeographical information deduced from our random amplified polymorphic DNA marker (RAPD) data in order to draw inferences about the past history of this species in the north-west Iberian Peninsula. To achieve these aims, 26 macromorphological characters were recorded in 279 specimens, and 77 RAPD phenotypes were identified in the 79 plants studied. The association analyses performed using the morphological and molecular data showed that no clear separation existed between the morphs, and a strong correlation between qualitative characters and the environment was detected. Moreover, both the multivariate analyses and the assignment test based on RAPD data revealed that the genetic variation was hierarchically structured, and three genetically distinct groups could be identified. Two of these clusters might correspond to different expansion routes proposed in the literature for different plant species in the north-west Iberian Peninsula. 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 155, 179,192. [source]


    Using lipid profiles and genotypes for the characterization of Corsican olive oils

    EUROPEAN JOURNAL OF LIPID SCIENCE AND TECHNOLOGY, Issue 1 2008
    Virginie Bronzini de Caraffa
    Abstract In 2004, the Corsican producers of olive oils obtained a French protected designation of origin (PDO) "huile d'olive de Corse", but up to now specifications of Corsican oil production do not clearly indicate the oil attributes related to the territory of production. That is why the fatty acid and triacylglycerol (TAG) compositions of olive oils from the nine main cultivars used to produce oils under PDO were determined and related to the olive variety. The results showed (i),that the nine cultivars covered only four olive varieties, as revealed by random-amplified polymorphic DNA markers, (ii),that the lipid composition of oils is strongly dependent on the variety, and (iii),that the lipid composition of the four varieties is completely discriminated on the basis of the proportions of four TAG (OOO, OOL, PoOO, OOL) and one fatty acid (18:0). These results clearly establish the relationships between some characteristics of oils and the area of production (Corsica) for at least three varieties that are originated from Corsica. For the fourth variety, other investigations on minor compounds and on sensory attributes of oils must be undertaken to link some oil traits to the territory of production. [source]


    A genetic linkage map for Tribolium confusum based on random amplified polymorphic DNAs and recombinant inbred lines

    INSECT MOLECULAR BIOLOGY, Issue 5 2003
    A. Yezerski
    Abstract Tribolium beetles provide an excellent and easily manipulated model system for the study of genetics. However, despite significant increases in the availability of molecular markers for the study of genetics in recent years, a significant genetic linkage map for these beetles remains undeveloped. We present the first molecular genetic linkage map for Tribolium confusum using random amplified polymorphic DNA markers. The linkage map contains 137 loci mapped on to eight linkage groups totaling 968.5 cM. [source]


    A Novel Early Onset Lethal Form of Catecholaminergic Polymorphic Ventricular Tachycardia Maps to Chromosome 7p14-p22

    JOURNAL OF CARDIOVASCULAR ELECTROPHYSIOLOGY, Issue 10 2007
    Ph.D., ZAHURUL A. BHUIYAN M.D.
    Introduction: Previously, autosomal dominant catecholaminergic polymorphic ventricular tachycardia (CPVT [1]) was mapped to chromosome 1q42,43 with identification of pathogenic mutations in RYR2. Autosomal recessive CPVT (2) was mapped to chromosome 1p13,21, leading to the identification of mutations in CASQ2. In this study, we aimed to elucidate clinical phenotypes of a new variant of CPVT (3) in an inbred Arab family and also delineate the chromosomal location of the gene causing CPVT (3). Methods and Results: In a highly inbred family, clinical symptoms of CPVT appeared early in childhood (7,12 years) and in three of the four cases, the first appearance of symptoms turned into a fatal outcome. Parents of the affected children were first-degree cousins and without any symptoms. Segregation analysis suggested an autosomal recessive inheritance. A genome-wide search using polymorphic DNA markers mapped the disease locus to a 25-Mb interval on chromosome 7p14-p22. A maximal multipoint LOD score of 3.17 was obtained at marker D7S493. Sequencing of putative candidate genes, SP4, NPY, FKBP9, FKBP14, PDE1C, and TBX20, in and around this locus, did not reveal any mutation. Conclusions: We have identified a novel highly malignant autosomal recessive form of CPVT and mapped this disorder to a 25-Mb interval on chromosome 7p14-p22. [source]


    A short-cut DNA extraction from cod caviar

    JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 3 2006
    Futoshi Aranishi
    Abstract Caviars represent the most consumed form of fish roe products. Due to high demand, ingredient roes of fish are often susceptible to illegal substitution with those of related fish. This study developed a simple and inexpensive protocol enabling the rapid extraction of DNA of acceptable quality and amount to PCR amplification from both cod caviars and their ingredient pollack roes. The protocol was based on extracting total genomic DNA from eggs using urea and a Chelex 100 chelating resin, and could be completed in less than 15 min. Approximately 8 g of DNA were reproducibly obtained from single eggs of cod caviars and pollack roes in eight individual experiments, and the quality and amount of DNA were sufficient to serve as template for hundreds of PCR reactions of polymorphic DNA markers for phylogenetic analysis. Being applicable to various caviars, this protocol can be useful to detect illegal substitution among ingredient roes of related fishes in PCR-based food inspection. Copyright 2005 Society of Chemical Industry [source]


    Possible causes of morphological variation in an endemic Moroccan groundsel (Senecio leucanthemifolius var. casablancae): evidence from chloroplast DNA and random amplified polymorphic DNA markers

    MOLECULAR ECOLOGY, Issue 2 2003
    Max Coleman
    Abstract Genetic variation was assessed in Senecio leucanthemifolius var. casablancae (Compositae), a Moroccan Atlantic coast endemic, in order to examine possible causes of atypical leaf morphology in three populations south of the known range. Evidence for introgression from S. glaucus ssp. coronopifolius and/or divergence was investigated with molecular markers. Both random amplified polymorphic DNA (RAPD) and chloroplast (cp) DNA restriction fragment length polymorphism (RFLP) differentiated the species well. Some evidence that hybridization may have occurred between the two species was provided by cpDNA markers. However, biparentally inherited RAPD markers failed to provide any support for the hypothesis that intermediate leaf morphologies in atypical populations arose through hybridization. Consequently, they are most likely to have arisen via divergence caused by drift and/or selection. Genetic distances among populations of S. leucanthemifolius were significant in all but one case. Isolation by distance was indicated by a significant positive correlation between genetic and geographical distances (r = 0.68, P = 0.01, Mantel test). These results suggest that long-distance achene dispersal is rare, despite the presence of a well-developed pappus. The observed loss of pappus at achene maturity may explain this unexpected result. Due to the morphological distinction of var. casablancae from other varieties of S. leucanthemifolius, we suggest elevation to species rank and treatment of the atypical material at infraspecific rank. [source]


    On the correlation between heterozygosity and fitness in natural populations

    MOLECULAR ECOLOGY, Issue 12 2002
    Bengt Hansson
    Abstract Three primary hypotheses currently prevail for correlations between heterozygosity at a set of molecular markers and fitness in natural populations. First, multilocus heterozygosity,fitness correlations might result from selection acting directly on the scored loci, such as at particular allozyme loci. Second, significant levels of linkage disequilibrium, as in recently bottlenecked-and-expanded populations, might cause associations between the markers and fitness loci in the local chromosomal vicinity. Third, in partially inbred populations, heterozygosity at the markers might reflect variation in the inbreeding coefficient and might associate with fitness as a result of effects of homozygosity at genome-wide distributed loci. Despite years of research, the relative importance of these hypotheses remains unclear. The screening of heterozygosity at polymorphic DNA markers offers an opportunity to resolve this issue, and relevant empirical studies have now emerged. We provide an account of the recent progress on the subject, and give suggestions on how to distinguish between the three hypotheses in future studies. [source]


    Identification of RAPD markers linked to recessive genes conferring siliqua shatter resistance in Brassica rapa

    PLANT BREEDING, Issue 6 2003
    O. Mongkolporn
    Abstract Shattering of siliquae causes significant seed loss in canola (Brassica napus) production worldwide. There is little genetic variation for resistance to shatter in canola and, hence, the trait has been studied in B. rapa. Previous studies have shown two randomly segregating recessive genes to be responsible for shatter resistance. Three random amplified polymorphic DNA markers were identified as being linked to shatter resistance using bulked segregant analysis in a F3B. rapa population. The population was derived from a cross between a shatter-susceptible Canadian cultivar and a shatter-resistant Indian line. Of the three markers, RAC-3900 and RX-71000 were linked to recessive sh1 and sh2 alleles, and SAC-201300 was linked to both dominant Sh1 and Sh2 alleles. The common marker for the dominant wild-type allele for the two loci was explained to have resulted from duplication of an original locus and the associated markers through chromosome duplication and rearrangements in the process of evolution of the modern B. rapa from its progenitor that had a lower number of chromosomes. Segregation data from double heterozygous F3 families, although limited, indicated the markers were not linked to each other and provided further evidence for the duplication hypothesis. [source]


    Prenatal diagnosis of de novo t(2;18;14)(q33.1;q12.2;q31.2), dup(5)(q34q34), del(7)(p21.1p21.1), and del(10)(q25.3q25.3) and a review of the prenatally ascertained de novo apparently balanced complex and multiple chromosomal rearrangements

    PRENATAL DIAGNOSIS, Issue 2 2006
    Chih-Ping Chen
    Abstract Objectives To present the prenatal diagnosis of a de novo complex chromosomal rearrangement (CCR) associated with de novo interstitial deletions and duplication and to review the literature. Case and Methods Amniocentesis was performed at 18 weeks' gestation because of an increased risk for Down syndrome based on maternal serum ,-fetoprotein and human chorionic gonadotrophin screening. Amniocentesis revealed a karyotype of 46,XY,t(2;18;14)(q33.1;q12.2;q31.2),dup(5)(q34q34),del(7)(p21.1p21.1), del(10)(q25.3q25.3). The parental karyotypes were normal. The pregnancy was terminated. The fetus manifested facial dysmorphism, clinodactyly of both hands, and hypoplasia of the left great toe. Spectral karyotyping (SKY), cytogenetic polymorphism, and polymorphic DNA markers were used to investigate the imbalances and the origin of the de novo aberrant chromosomes. Results SKY showed a three-way CCR. Cytogenetic polymorphism investigation of the derivative chromosome 14 of the fetus and the parental chromosomes 14 determined the maternal origin of the translocation. Polymorphic DNA marker analysis confirmed the maternal origin of the de novo interstitial deletions and duplication. No cryptic imbalance at or near the breakpoints of the CCR was detected by the molecular analysis. Conclusions De novo apparently balanced CCRs may be associated with imbalances in other chromosomes. We suggest further investigation and re-evaluation of cryptic or subtle imbalances in all cases classified as de novo apparently balanced CCRs. Copyright 2006 John Wiley & Sons, Ltd. [source]


    Prenatal diagnosis and molecular cytogenetic analysis of partial monosomy 10q (10q25.3,qter) and partial trisomy 18q (18q23,qter) in a fetus associated with cystic hygroma and ambiguous genitalia

    PRENATAL DIAGNOSIS, Issue 6 2005
    Chih-Ping Chen
    Abstract Objectives To present the prenatal diagnosis and molecular cytogenetic analysis of a fetus with nuchal cystic hygroma and ambiguous genitalia. Case and Methods Amniocentesis was performed at 16 weeks' gestation because of the abnormal fetal sonographic finding of a large septated nuchal cystic hygroma. Genetic amniocentesis revealed a terminal deletion in the long arm of chromosome 10. The paternal karyotype was subsequently found to be 46,XY,t(10;18)(q25.3;q23). The maternal karyotype was normal. The pregnancy was terminated. A hydropic fetus was delivered with a septated nuchal cystic hygroma and ambiguous genitalia. Fluorescence in situ hybridization (FISH), microarray-based comparative genomic hybridization (CGH), and polymorphic DNA markers were used to investigate the involved chromosomal segments. Results FISH study showed absence of the 10q telomeric probe and presence of the 18q telomeric probe in the derivative chromosome 10. Microarray-based CGH analysis showed loss of distal 10q and gain of distal 18q. Polymorphic DNA marker analysis determined the breakpoints. The fetal karyotype was 46,XY,der(10)t(10;18)(q25.3;q23)pat. The chromosome aberration resulted in partial monosomy 10q (10q25.3,qter) and partial trisomy 18q (18q23,qter). Conclusions The present case provides evidence that partial monosomy 10q (10q25.3,qter) with partial trisomy 18q (18q23,qter) can be a genetic cause of fetal cystic hygroma and ambiguous genitalia. Cytogenetic analysis for prenatally detected structural abnormalities may detect unexpected inherited chromosome aberrations. Copyright 2005 John Wiley & Sons, Ltd. [source]


    Inheritance and reliability of random amplified polymorphic DNA-markers in two consecutive generations of common carp (Cyprinus carpio L.)

    AQUACULTURE RESEARCH, Issue 2 2010
    Noel D Novelo
    Abstract Random amplified polymorphic DNA (RAPD) markers have been used in a variety of genetic studies in fisheries and aquaculture. Most population studies are performed without preliminary data demonstrating the Mendelian inheritance and reproducibility of RAPD markers. In this study, the inheritance and reproducibility of RAPD markers was examined in two consecutive generations of common carp, Cyprinus carpio L. Variability and segregation of RAPD markers were investigated in one F1 progeny and three F2 progenies. Seventy-four RAPD markers were generated by five primers using DNA extracted from the initial ornamental (koi) common carp female and wild-type colour common carp male. Fifty-five of these RAPD markers were transmitted to the F1 progeny and the inheritance patterns were analysed. Twenty RAPD markers were fully reproducible and demonstrated dominant simple Mendelian inheritance patterns in two consecutive generations. Twenty-four RAPD markers were not reproducible in all progenies. Thirteen markers displayed inheritance ratios in the progenies that did not fit simple Mendelian inheritance patterns. Non-reproducibility of RAPD markers and distorted ratios may be caused by the absence of amplification, poor amplification or by the appearance of artefact bands. Random amplified polymorphic DNA markers with poor reproducibility and non-Mendelian inheritance can lead to misinterpretations of data in population studies, resulting in errors in the estimation of genetic diversity within and between individual populations. Therefore, it is recommended to first identify the set of reproducible RAPD markers that demonstrate Mendelian inheritance before application of the RAPD technique in population studies. [source]


    Infraspecific variation and phylogeography of the high-polyploid Iberian endemic Anthoxanthum amarum Brot. (Poaceae; Pooideae) assessed by random amplified polymorphic DNA markers (RAPDs) and morphology

    BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 2 2007
    MANUEL PIMENTEL
    High morphological and ecological diversity has been observed in the north-west Iberian Peninsula endemic Anthoxanthum amarum Brot., for which two different morphotypes (northern and southern) have been described on the basis of qualitative traits and geographical origin. In the present study, a combined molecular and morphological method was applied to ten populations of this species with the following aims: (1) to assess whether the variation observed was taxonomically meaningful; (2) to assess the influence of the environment on the variation in the morphological characters; and (3) to track the potential phylogeographical information deduced from our random amplified polymorphic DNA marker (RAPD) data in order to draw inferences about the past history of this species in the north-west Iberian Peninsula. To achieve these aims, 26 macromorphological characters were recorded in 279 specimens, and 77 RAPD phenotypes were identified in the 79 plants studied. The association analyses performed using the morphological and molecular data showed that no clear separation existed between the morphs, and a strong correlation between qualitative characters and the environment was detected. Moreover, both the multivariate analyses and the assignment test based on RAPD data revealed that the genetic variation was hierarchically structured, and three genetically distinct groups could be identified. Two of these clusters might correspond to different expansion routes proposed in the literature for different plant species in the north-west Iberian Peninsula. 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 155, 179,192. [source]