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1

Development of an efficient retrotransposon-based fingerprinting method for rapid pea variety identification

100%
Smykal P.
Journal of Applied Genetics
|
2006
|
vol. 47
|
issue 3
221-230
EN
Fast and efficient DNA fingerprinting of crop cultivars and individuals is frequently used in both theoretical population genetics and in practical breeding. Numerous DNA marker technologies exist and the ratio of speed, cost and accuracy are of importance. Therefore even in species where highly accurate and polymorphic marker systems are available, such as microsatellite SSR (simple sequence repeats), also alternative methods may be of interest. Thanks to their high abundance and ubiquity, temporary mobile retrotransposable elements come into recent focus. Their properties, such as genome wide distribution and well-defined origin of individual insertions by descent, predetermine them for use as molecular markers. In this study, several Ty3-gypsy type retrotransposons have been developed and adopted for the inter-retrotransposon amplified polymorphism (IRAP) method, which is suitable for fast and efficient pea cultivar fingerprinting. The method can easily distinguish even between genetically closely related pea cultivars and provide high polymorphic information content (PIC) in a single PCR analysis.
2

Optimalization and validation of ADSRRS-fingerprinting

100%
Krawczyk B., Lewandowski K.
|
2007
|
issue 2
95-113
EN
Macrorestriction analysis of genomic DNA followed by pulsed-field gel electrophoresis (REA-PFGE) has become the 'gold standard' for molecular typing (10). In recent years, some alternative techniques have been successfully applied. However, there is still a need for a new method which may appear to be less complex, cheaper, and have a power of discrimination at least similar to that of REA-PFGE. Recently, we showed the performance and convenience of a novel assay, based on the fingerprinting of bacterial genomes by amplification of DNA fragments surrounding rare restriction sites (ADSRRS-fingerprinting), for its potential usefulness in epidemiological investigations. In this study, ADSRRS-fingerprinting method was optimized at each stage of the procedure. The modified method, named ADSRRS-fingerprinting plus, differs from the original technique in several points. The optimized method considerably shortens the time of experiment, offers good discriminatory power and also demonstrates excellent reproducibility. Next, ADSRRS-fingerprinting plus was validated. These experiments proved that the method is specific, selective and suitable for intended purpose and also confirmed its reliability, reproducibility and simplicity in the interpretation of the results. Optimized and validated procedure of ADSRRS-fingerprinting plus was used in the development of a diagnostic kit (ADSRRS-KIT) for strain differentiation of bacteria below the species level, using a simple set of ready-to-use reagents and standard equipment.
3

Random amplified polymorphic DNA fingerprinting as a marker for Paramecium jenningsi strains

100%
Skotarczak B., Przybos E., Wodecka B., Maciejewska A.
Folia Biologica
|
2004
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vol. 52
|
issue 1-2
117-124
EN
The aim of the present study is to establish a common RAPD marker for P. jenningsi using a series of Ro primers and to investigate if strains originating from distant and isolated localities (Japan, China, India, Saudi Arabia) have isolated gene pools and represent distinct species. An analysis of dendrograms constructed on the basis of RAPD-PCR fingerprints with four primers (Ro 460-04, 460-06, 460-07, and 460-10) from the first part of this project (SKOTARCZAK et al. 2004), assigns the strains to two groups consisting of the continental strains (India, Saudi Arabia, China) and Japanese strains that have been considered as a separate sibling species within P. jenningsi. The genetic similarity of the Indian and Arabian strains was ascertained, whereas the Chinese strain formed an independent branch in this sibling species. The primers Ro (460-01, 460-02, 460-03, 460-05, 460-08) also distinguish between two groups of strains, although they divide the Japanese strains into two subgroups that are not reproductively isolated. This probably indicates genetic variation within this sibling species. However, it comprises one common gene pool (successful inter-strain crosses) and is reproductively isolated from the other sibling species. The results presented in these papers confirm that the construction of ten band patterns having marker attributes is possible on the basis ofDNAamplification from 9 strains of P. jenningsi with the RAPD-PCR fingerprinting method using five primers from the Ro series. The patterns can be assigned to three marker-groups: a general species group, a group differentiating between sibling species, and accessory strain markers.
4

Polymorphism within Paramecium sexaurelia (Ciliophora, Oligohymenophorea) and description of a new stand of the species in China

100%
Przybos E., Rautian M., Greczek-Stachura M., Potekhin A.
Folia Biologica
|
2007
|
vol. 55
|
issue 3-4
121-125
EN
The presence of Paramecium sexaurelia from the Paramecium aurelia complex was recorded for the first time in China (Beijing). RAPD fingerprints (band patterns) of P. sexaurelia strains, the new strain from China and others from Asia, as well as from Europe and Puerto Rico, showed polymorphism within the species as several groups of genotypes characterized by different band patterns.
5

Genetic diversity of inbred rye lines evaluated by RAPD analysis

88%
Myskow B., Masojc P., Banek-Tabor A., Szolkowski A.
Journal of Applied Genetics
|
2001
|
vol. 42
|
issue 1
1-14
EN
This study presents an attempt to supply breeders of hybrid rye with more genetic information on inbred lines, using molecular markers. Eighteen polymorphic loci detected by means of the RAPD (Random Amplified Polymorphic DNA) technique and mapped on 2R-7R rye chromosomes, were applied to study genetic similarities among forty inbred lines of rye. The lines were grouped in four main clusters revealed on dendrogram, which was generally consistent with the pedigree data. Mapped RAPD markers were shown to be a useful tool for phenetic studies in rye. Additionally, a system of 20 polymorphic fragments, detected by three primers, was developed for fingerprinting of rye lines. The system of RAPD markers, which was developed in this study, should be helpful in characterisation of rye genetic stocks used for breeding.
6

Strains of Paramecium decaurelia (Ciliophora, Protozoa) from Russia with molecular characteristics of other known strains of the species

75%
Przybos E., Greczek-Stachura M., Potekhin A., Rautian M.
Folia Biologica
|
2007
|
vol. 55
|
issue 3-4
127-132
EN
The presence of Paramecium decaurelia from the Paramecium aurelia species complex was demonstrated in Yaroslavl, Russia, (European part, northwestern Russia) and in the Altai Mts (Asiatic part of Russia, western Siberia). RAPD-PCR fingerprints of the newly identified strains of P. decaurelia, rare throughout the world, were compared to those characteristic for the other known strains of the species. P. decaurelia strains show some polymorphism within species, strains from Russia have 60% similarity of band patterns, and strains from USA and Japan about 70% similarity of band patterns.
7

Variety discrimination in pea (Pisum sativum L.) by molecular, biochemical and morphological markers

63%
Smykal P., Horacek J., Dostalova R., Hybl M.
Journal of Applied Genetics
|
2008
|
vol. 49
|
issue 2
155-166
EN
The distinctness, uniformity and stability (DUS) requirements involve expensive, space- and time-consuming measurements of morphological traits. Moreover, for a majority of traits, interactions between genotype and environment complicate the evaluation. Molecular markers have a potential to facilitate this procedure, increase the reliability of decisions, and substantially save the time and space needed for experiments. We chose 25 varieties of pea (Pisum sativum L.) from the list of recommended varieties for cultivation in the Czech Republic, and made both a standard classification by 12 morphological descriptors and a classification by biochemical-molecular markers. Two isozyme systems, 10 microsatellite loci, 2 retrotransposons for multilocus inter-retrotransposon amplified polymorphism (IRAP), and 12 retrotransposon-based insertion polymorphism (RBIP) DNA markers were analysed. The main objective of the study was to examine the potential of each method for discrimination between pea varieties. The results demonstrate a high potential and resolving power of DNA-based methods. Superior in terms of high information content and discrimination power were SSR markers, owing to high allelic variation, which was the only biochemical-molecular method allowing clear identification of all varieties. Retrotransposon markers in RBIP format proved to be the most robust and easy to score method, while multilocus IRAP produced informative fingerprint already in a single analysis. Isozyme analysis offered a fast and less expensive alternative. The results showed that molecular identification could be used to assess distinctness and complement morphological assessment, especially in cases where the time frame plays an important role. Currently developed pea marker systems might serve also for germplasm management and genetic diversity studies.
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