RAPD

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

Genetic distances revealed by morphological characters, isozymes, proteins and RAPD markers and their relationships with hybrid performance in oilseed rape (Brassica napus L.).

Abstract: Genetic distances (GDs) based on morphological characters, isozymes and storage proteins, and random amplified polymorphic DNAs (RAPD) were used to predict the performance and heterosis of crosses in oilseed rape (Brassica napus L.). Six male-sterile lines carrying the widely used Shaan2A cytoplasm were crossed with five restorer lines to produce 30 F1 hybrids. These 30 hybrids and their parents were evaluated for seven agronomically important traits and their mid-parent heterosis (MPH) at Yangling, Shaanxi province in Northwest China for 2 years. Genetic similarity among the parents based on 34 isozyme and seven protein markers was higher than that based on 136 RAPDs and/or 48 morphological markers. No significant correlation was detected among these three sets of data. Associations between the different estimates of GDs and F1 performance for some agronomic traits were significant, but not for seed yield. In order to enhance the predicting efficiency, we selected 114 significant markers and 43 favoring markers following statistical comparison of the mean values of the yield components between the heterozygous group (where the marker is present only in one parent of each hybrid) and the homozygous group (where the marker is either present or absent in both parents of each hybrid) of the 30 hybrids. Parental GD based on total polymorphic markers (GDtotal, indicating general heterozygosity), significant markers (GDsign, indicating specific heterozygosity) and favoring markers (GDfavor, indicating favoring-marker heterozygosity) were calculated. The correlation between GDfavor or GDsign and hybrid performance was higher than the correlation between GDtotal and hybrid performance. GDsign and GDfavor significantly correlated with plant height, seeds per silique and seed yield, but not with the MPH of the other six agronomic traits with the exception of plant height. The information obtained in this study on the genetic diversity of the parental lines does not appear to be reliable for predicting F1 yield and heterosis.

Virulence and molecular polymorphism in Puccinia recondita f. sp. tritici in Canada

Abstract: Sixty-four representative single-uredinial isolates or Puccinia recondita f. sp. tritici collected from wheat in the eastern (Ontario and Quebec), prairie (Manitoba and Saskatchewan), and Pacific (Alberta and British Columbia) regions of Canada were analyzed for virulence polymorphism on 19 near-isogenic wheat differential lines and for randomly amplified polymorphic DNA (RAPD) using 10 arbitrary decamer primers. Thirty-seven phenotypes or P. r. tritici were distinguished by the 19 host differential lines. Fifteen molecular phenotypes were distinguished by the 10 primers in the RAPD analysis. Forty-five unique phenotypes or P. r. tritici were distinguished by combined virulence and RAPD data. Molecular variation was greatest between isolates or different virulence phenotypes. There was some molecular variation among isolates with identical virulences. Virulence and RAPD data were used separately and combined in cluster analyses. Two major clusters were distinguished with the combined data sets. The first cluster consisted or isolates virulent or avirulent to both resistance genes Lr2a and Lr2c, and the second cluster consisted or isolates avirulent to Lr2a and virulent to Lr2c. The molecular polymorphisms were more effective in distinguishing between the major clusters or P. r. tritici compared to the virulence polymorphisms. However, virulence polymorphisms were more effective in distinguishing between isolates within the major clusters compared to the molecular polymorphisms. There was a correlation or 0,58 between the virulence and molecular dissimilarity matrices. The cluster analyses indicated a general relationship between virulence and molecular polymorphism in P. r. tritici in Canada. There are currently two major groups or P. r. tritici in Canada. One group consists or isolates round in the prairie and eastern regions. Isolates in this group have limited molecular polymorphisms and consist or many virulence phenotypes that are either virulent or avirulent to both Lr2a and Lr2c. Isolates in the second group are round in eastern Canada and in the Pacific region. These isolates are avirulent to Lr2a and virulent to Lr2c and have molecular phenotypes distinct from isolates in the first group. The molecular data support conclusions from virulence survey data that distinct geographic populations or P. r. tritici exist in Canada and that new virulences arise and increase in the prairie population by mutations from preexisting phenotypes

Genetic diversity and safety aspects of enterococci from slightly fermented sausages

Abstract: Aims: To determine the biodiversity of enterococci from slightly fermented sausages (chorizo and fuet) at species and strain level by molecular typing, while considering their safety aspects. Methods and Results: Species-specific PCR and partial sequencing of 16S rRNA and sodA genes were used to identify enterococcal population. Enterococcus faecium was the most frequently isolated species followed by E. faecalis, E. hirae and E. durans. Randomly amplified polymorphic DNA (RAPD)-PCR revealed species-specific clusters and allowed strain typing. Sixty strains of 106 isolates exhibited different RAPD profiles indicating a high genetic variability. All the E. faecalis strains carried virulence genes (efaAfs, esp, agg and gelE) and all E. faecium isolates carried efaAfm gene. Enterococcus faecalis showed higher antibiotic resistance than the other species. Only one E. faecium strain showed vanA genotype (high-level resistance to glycopeptides) and E. gallinarum and E. casseliflavus/flavescens isolates showed vanC1 and vanC2/C3 genotypes (low-level resistance only to vancomycin) respectively. Conclusions: E. faecalis has been mainly associated with virulence factors and antimicrobial multi-resistance and, although potential risk for human health is low, the presence of this species in slightly fermented sausages should be avoided to obtain high quality products. Significance and Impact of the Study: The enterococcal population of slightly fermented sausages has been thoroughly characterized. Several relevant safety aspects have been revealed.

Random amplified hybridization microsatellites (RAHM): isolation of a new class of microsatellite-containing DNA clones

Abstract: Microsatellite repeats are widely present in eukaryotic genomes (1,2) and are interspersed throughout the genomic DNA. Microsatellite markers have been developed for a variety of organisms (3,4), including plants (5-7). The regions flanking microsatellite sequences can be amplified in a PCR reaction using microsatellite primers, thus providing codominant sequence tagged sites (STS) markers. However, efforts to develop such molecular markers are quite laborious, requiring library construction, screening, and sequencing of clones. Several groups have developed alternative methods for detection (8) and isolation of flanking sequences (9,10) using PCR. Random amplified polymorphic DNA (RAPD) markers are easy to develop and less expensive to assay, but generally are genetically dominant and have a low degree of polymorphism. We have developed a new system for microsatellite DNA detection and isolation which combines RAPD amplification and oligonucleotide screening. The method is based on a prior RAPD amplification of plant genomic DNA following standard procedures (11). After scoring the RAPD polymorphisms on an agarose gel, the amplifiedDNA is transferred onto Hybond-N+ filters (Amersham Inc.) using Southern blot procedures (12). The filters are then hybridized with oligonucleotide probes carrying simple sequence repeats (SSR) labeled with Digoxigenin-ddUTP (DIG Oligonucleotide 3'-End Labeling Kit, Boehringer Mannheim), and luminescent signals detected by autoradiography, following the manufacturer's instructions. Using random decamer primers on sugar beet (Beta vulgaris L.), olive (Olea europaea L.) and sunflower (Helianthus annuus L.) DNA (Fig. lA-), we detected several bands containing microsatellites with high efficiency and accu-

Genetic relationships among pomegranate genotypes studied by fruit characteristics and RAPD markers

Abstract: SummaryThe aim of this research was to study 24 Iranian pomegranate genotypes and thereby reveal their genetic relationships. Measurements of 28 fruit characteristics together with Randomly Amplified Polymorphic DNA (RAPD) marker data were used for this purpose. Mean values of fruit characteristics were used for factor analysis which determined seven main factors. Grouping of pomegranate genotypes by these factors was performed by Ward’s method. Among 113 random decamer primers tested, 27 showed good amplification and polymorphism, and a total of 158 RAPD markers were produced. Estimates of genetic relationships, using Jaccard’s similarity coefficient, ranged from 0.30 – 0.88 for the RAPD data. Grouping by fruit characteristics was compared with the results from RAPD analysis, but did not produce a significant correlation. This means that information based on fruit characteristics is not sufficient for genetic discrimination in pomegranate; however, RAPD markers provided a useful technique to study geneti...