RAPD

About: RAPD is a research topic. Over the lifetime, 15960 publications have been published within this topic receiving 360391 citations.

Genetic characterization of weedy rice (Oryza sativa L.) based on morpho-physiology, isozymes and RAPD markers

Abstract: Weedy rice (Oryza sativa L.) is an important resource for breeding and for studying the evolution of rice. The present study was carried out to identify the genetic basis of the weedy rices distributed in various countries of the world. One hundred and fifty two strains of weedy rice collected from Bangladesh, Brazil, Bhutan, China, India, Japan, Korea, Nepal, Thailand and the USA were tested for variations in six morpho-physiological characteristics and in 14 isozyme loci. Twenty six weedy strains selected from the above materials were assayed for the Est-10 locus, six RAPD loci of the nuclear genome, and one chloroplast locus. From the results of multivariate analysis based on the morpho-physiological characteristics and the isozymes, weedy rice strains were classified into indica and japonica types, and each type was further divided into forms resembling cultivated and wild rice. Thus, four groups designated as I, II, III and IV were identified. Weedy strains of group I (indica-type similar to cultivars) were distributed mostly in temperate countries, group II (indica-type similar to wild rice) in tropical countries, group III (japonica-type similar to cultivars) in Bhutan and Korea, group IV ( japonica-type similar to wild rice) in China and Korea. In group I, classified as indica, several strains showed japonica-specific RAPD markers, while some others had japonica cytoplasm with indica-specific RAPD markers in a heterozygous state at several loci. One weedy strain belonging to group II showed a wild rice-specific allele at the Est-10 locus. However, in groups III and IV, no variation was ound either for the markers on Est-10 or for the RAPD loci tested. Judging from this study, weedy rice of group I might have originated at least partly from gene flow between indica and japonica, whereas that of group II most probably originated from gene flow between wild and cultivated indica rice. Weedy rice of group III is thought to have originated from old rice cultivars which had reverted to a weedy form, and that of group IV from gene flow between japonica cultivars and wild rice having japonica backgrounds.

Morphological and molecular evidence for hybridization and introgression in a willow (Salix) hybrid zone.

Abstract: Hybrid zones provide biologists with the opportunity to examine genetic and ecological interactions between differentiated populations. Accurate identification of hybrid genealogies is considered a necessary prerequisite to understanding observed patterns of hybridization‐related phenomena. We analysed molecular and morphological data from individuals in a hybrid zone between two species of willows ( Salix sericea Marshall and S. eriocephala Michaux) and report the use of randomly amplified polymorphic DNA (RAPD), chloroplast DNA (cpDNA), and ribosomal DNA (rDNA) markers, as well as vegetative morphology and foliar chemistry data to identify individuals in terms of hybrid genealogy and to infer the direction and extent of backcrossing and introgression within the hybrid zone. A novel version of a maximum likelihood estimate approach (developed for this study) was used to calculate hybrid index scores from RAPD marker data; this method produced results similar to those obtained using traditional arithmetic methods. Distribution of rDNA, cpDNA, and chemistry data were examined within the graphical context of RAPD‐based hybrid index score histograms and principal component analyses (PCA) on RAPD and morphology data. Seven of the 21 plants classified as S. eriocephala in the field were possible introgressants. Another plant presented an unequivocal example of backcrossed S. sericea chemistry and RAPD markers. Inter‐ and intraspecific chloroplast diversity found within the hybrid zone suggests both historic introgression (perhaps in a glacial refugium), and contemporary hybridization. Patterns of inheritance and expression within the hybrid zone suggest that morphological characters are often not expressed in a simple additive fashion, and problems associated with both morphological and molecular data are considered.

Similarity between Human and Chicken Escherichia coli Isolates in Relation to Ciprofloxacin Resistance Status

Abstract: Background. The food supply is suspected to be a source of fluoroquinolone-resistant Escherichia coli that cause disease in humans, but supporting molecular data are lacking. Methods. We performed a molecular-epidemiological comparison, in Barcelona, Spain (1996-1998), of 117 contemporaneous, geographically matched E. coli isolates from humans (35 blood isolates and 33 fecal) or chickens (49 fecal) that were either susceptible (n = 57) or resistant (n = 60) to ciprofloxacin and analyzed them by phylogenetic group, virulence genotype, and O antigens using random amplified polymorphic DNA (RAPD) analysis and pulsed-field gel electrophoresis (PFGE). Results. When analyzed by phylogenetic distribution, virulence profiles, and O antigens, resistant human isolates were distinct from susceptible human isolates but were largely indistinguishable from chicken isolates, whereas resistant and susceptible chicken isolates were similar. Susceptible human isolates contained more virulence-associated genes and more frequently expressed virulence-associated O antigens than did resistant human or any chicken isolates. Certain resistant human isolates closely resembled chicken isolates by RAPD and PFGE analysis. Conclusions. Ciprofloxacin-resistant E. coli may arise de novo in poultry from susceptible progenitors, be transmitted to humans via the food supply, and go on to cause potentially life-threatening infections. If confirmed, these findings would mandate efforts to eliminate this reservoir of drug-resistant pathogens and/or to block their transmission to humans.

Gene pool classification of common bean landraces from Chile based on RAPD and morphological data

Abstract: Landraces of commonb ean (Phaseolus vulgaris L) from Chile are a phenotypically diverse group whose relationship to the two major gene pools (Andeana nd Mesoamericani)s unclear The genetic composition of 69 Chileanl andraces, 15 commerciaclu itivars growni n Chile, and 11 previously characterized check accessions was examined using RAPDs (random amplified polymorphic DNA) The 25 primers used generated 106 polymorphic bands A genetic distance (GD) matrix based on simple matching of RAPD phenotypes was converted to a two dimensional plot using multidimensional scaling (MDS) Two major clusters, encompassing most of the accessions, were apparent on the resulting plot and were identified with the Andean and the Mesoamericagne ne pools No obvious signs of introgression or hybridization between gene pools were observed Clustering analysis using bootstrap samples of the RAPD bands showed that as few as 20 randomlyc hosen bands could classify the accessions into the correct gene pools nearly as well as all 106 bands In general, the Andean landraces were collected at more northerly latitudes and higher altitudes than the Mesoamerican landraces Morphological data were collected for 63 landraces for seven numerical traits and 13 categorical traits The morphological data used were to create a distance matrix and analyzed as with the RAPDd ata, but no clear separation of the groups was seen Accessions from the two groups identified by RAPDs differed significantly for 11 of the 20 traits examined It was concluded that by RAPDst, he Chilean landraces could be readily classified into the Andeana nd Mesoamericang ene pools Morphological traits were less effective at classification