Showing papers on "Genetic marker published in 1993"
TL;DR: A set of mapping markers have been designed for Arabidopsis thaliana that correspond to DNA fragments amplified by the polymerase chain reaction (PCR) that can be unambiguously mapped to one of the 10Arabidopsis chromosome arms in a single cross using a limited number of F2 progeny.
Abstract: A set of mapping markers have been designed for Arabidopsis thaliana that correspond to DNA fragments amplifed by the polymerase chain reaction (PCR). The ecotype of origin of these amplified fragments can be determined by cleavage with a restriction endo-nuclease. Specifically, 18 sets of PCR primers were synthesized, each of which amplifies a single mapped DNA sequence from the Columbia and Landsberg erecta ecotypes. Also identifed was at least one restriction endonuclease for each of these PCR products that generates ecotype-specific digestion patterns. Using these co-dominant cleaved amplified polymorphic sequences (CAPS), an Arabidopsis gene can be unambiguously mapped to one of the 10 Arabidopsis chromosome arms in a single cross using a limited number of F2 progeny.
1,650 citations
TL;DR: The objectives of this research were to calculate polymorphism information content values of 51 low-copy DNA clones and use the resulting values to choose potential mapping parents and to identify Genotype pairs that would map more highly informative DNA clones compared with a population derived from the most polymorphic potential parents.
Abstract: Genetic linkage maps based on restriction fragment length polymorphisms are useful for many purposes; however, different populations are required to fulfill different objectives. Clones from the li...
1,458 citations
TL;DR: Sequence characterized amplified regions (SCARs) were derived from eight random amplified polymorphic DNA (RAPD) markers linked to disease resistance genes in lettuce, providing information on the molecular basis of RAPD markers.
Abstract: Sequence characterized amplified regions (SCARs) were derived from eight random amplified polymorphic DNA (RAPD) markers linked to disease resistance genes in lettuce. SCARs are PCR-based markers that represent single, genetically defined loci that are identified by PCR amplification of genomic DNA with pairs of specific oligonucleotide primers; they may contain high-copy, dispersed genomic sequences within the amplified region. Amplified RAPD products were cloned and sequenced. The sequence was used to design 24-mer oligonucleotide primers for each end. All pairs of SCAR primers resulted in the amplification of single major bands the same size as the RAPD fragment cloned. Polymorphism was either retained as the presence or absence of amplification of the band or appeared as length polymorphisms that converted dominant RAPD loci into codominant SCAR markers. This study provided information on the molecular basis of RAPD markers. The amplified fragment contained no obvious repeated sequences beyond the primer sequence. Five out of eight pairs of SCAR primers amplified an alternate allele from both parents of the mapping population; therefore, the original RAPD polymorphism was likely due to mismatch at the primer sites.
1,366 citations
TL;DR: Polymerase chain reaction amplification of ( AT)n and (TAT)n microsatellites in soybean revealed that they are highly polymorphic, as a consequence of length variation, somatically stable and inherited in a co-dominant Mendelian manner.
Abstract: In order to assess the feasibility of using microsatellites as markers in plant genetics, a survey of published DNA sequence data for presence, abundance and ubiquity in higher plants of all types of dinucleotide and trinucleotide repeats with a minimum number of 10 and 7 units, respectively, was conducted. This search revealed that such microsatellites are frequent and widely distributed; they were uncovered in 34 species, with a frequency of one every 50 kb. AT repeats were by far the most frequently observed class of dinucleotide microsatellites, whereas AC/TG repeats, which are common in animals, were observed only once. TAT repeats prevailed among trinucleotides. Polymerase chain reaction amplification of (AT)n and (TAT)n microsatellites in soybean (Glycine max (L.) Merr.) revealed that they are highly polymorphic, as a consequence of length variation, somatically stable and inherited in a co-dominant Mendelian manner. The abundance and amount of information derived from such markers, together with the ease by which they can be identified, make them ideal markers for plant genetic linkage and physical mapping, population studies and varietal identification.
1,070 citations
TL;DR: Transfer of the neomycin-resistance gene into bone-marrow cells harvested from children with acute myeloid leukaemia in remission should enable the development of better marrow purging strategies.
955 citations
TL;DR: Results prove the existence of a genetically determined predisposition to colorectal cancer that has important ramifications for understanding and preventing this disease.
Abstract: Genetic linkage analysis was used to determine whether a specific chromosomal locus could be implicated in families with a history of early onset cancer but with no other unique features. Close linkage of disease to anonymous microsatellite markers on chromosome 2 was demonstrated in two large kindreds. The pairwise lod scores for linkage to marker D2S123 in these kindreds were 6.39 and 1.45 at zero recombination, and multipoint linkage with flanking markers resulted in lod scores of 6.47 and 6.01. These results prove the existence of a genetically determined predisposition to colorectal cancer that has important ramifications for understanding and preventing this disease.
918 citations
TL;DR: Many evolutionary studies, particularly kinship studies, have been limited by the availability of segregating genetic marker loci, and microsatellites promise to alleviate these problems.
Abstract: Many evolutionary studies, particularly kinship studies, have been limited by the availability of segregating genetic marker loci. Microsatellites promise to alleviate these problems. Microsatellite loci are segments of DNA with very short sequence motifs repeated in tandem; their often numerous alleles differ in the number of these repeat units. They are very common in eukaryotic DNA and can be amplified by the polymerase chain reaction, which allows the use of minute or degraded DNA samples. The alleles can be scored consistently and compared unambiguously, even across different gels.
842 citations
TL;DR: Microsatellite repeat sequences were investigated as sequenced-tagged site (STS) DNA markers to determine the potential for genetic analysis of the grapevine genome, finding high heterozygosity within individual grapevine cultivars and high genetic variation between cultivars, making it a useful marker type for plant genome mapping and genome typing.
Abstract: Microsatellite repeat sequences were investigated as sequenced-tagged site (STS) DNA markers to determine the potential for genetic analysis of the grapevine genome. The PCR-generated markers detect codominant alleles at a single locus or site in the genome. The marker type is very informative detecting high heterozygosity (69%-88%) within individual grapevine cultivars and high genetic variation between cultivars, making it a useful marker type for plant genome mapping and genome typing. For five loci a screening of 26 V. vinifera cultivars found 13, 12, 8, 5, and 4 different length alleles respectively with some alleles more common than others. The genomic DNA sequences surrounding microsatellite sequences were conserved within the genus permitting STS primers to amplify STSs from other Vitis species. These Vitis species were found to have some unique alleles not present in V. vinifera.
787 citations
741 citations
Journal Article•
TL;DR: Randomly amplified polymorphic DNA (RAPD) and arbitrarily primed PCR (AP-PCR) represent novel DNA polymorphism assays that involve the amplification of random DNA segments using PCR and oligonucleotide primers of arbitrary sequence.
Abstract: Randomly amplified polymorphic DNA (RAPD) and arbitrarily primed PCR (AP-PCR) represent novel DNA polymorphism assays that involve the amplification of random DNA segments using PCR and oligonucleotide primers of arbitrary sequence. Products defining the polymorphisms exhibit Mendelian inheritance and thus possess tremendous potential utility as genetic markers in a diverse array of scientific disciplines. Amplification profiles for specific oligonucleotide primers are highly dependent on the specific conditions of the reaction; banding patterns may thus vary extensively because of inconsistencies in a number of reaction parameters. Artifactual variation represents a potential problem in surveys of genetic variation in natural populations and must be discriminated from true polymorphism for the applications of RAPD to be both accurate and reliable.
533 citations
TL;DR: Five different genetic elements have been found to be associated with genetic rearrangements in Mycobacterium tuberculosis complex strains and the insertion sequence IS6110 is presently the most frequently used genetic marker for strain differentiation of M. tuberculosis.
Abstract: Five different genetic elements have been found to be associated with genetic rearrangements in Mycobacterium tuberculosis complex strains. Of these elements, the insertion sequence IS6110 is presently the most frequently used genetic marker for strain differentiation of M. tuberculosis. In the present study we compared five genetic elements for their potentials to differentiate a given cluster of M. tuberculosis strains. Because of the presence of only a single copy of IS6110 or two IS6110 copies at the same chromosomal locus, a large number of strains could not be differentiated by IS6110 fingerprinting. Most strains, including the low-copy-number IS6110 strains, could be differentiated by fingerprinting with the 36-bp direct repeat or the polymorphic GC-rich repetitive DNA element. Less discriminative power was obtained with the major polymorphic tandem repeat and the insertion element IS1081. One strain which did not contain IS6110 DNA was encountered. Until now, this element has invariantly been found to be present in all M. tuberculosis complex strains. On the basis of classical taxonomic criteria and sequencing of the 16S rRNA gene, this strain was shown to be a genuine M. tuberculosis strain. Therefore, the use of this element as a target for polymerase chain reaction-facilitated detection of M. tuberculosis should be reconsidered.
TL;DR: Recent progress in the development of molecular technology for plant breeding is discussed, with a focus on genetic diagnostics in plant breeding.
TL;DR: An RFLP-based genetic map of Secale Cereale has provided evidence for multiple evolutionary translocations in the rye genome relative to that of hexaploid wheat, which has relevance for strategies designed to transfer useful genes from rye, and probably other related species, to wheat.
Abstract: An RFLP-based genetic map of Secale Cereale has provided evidence for multiple evolutionary translocations in the rye genome relative to that of hexaploid wheat. DNA clones which have previously been mapped in wheat indicated that chromosome arms 2RS, 3RL, 4RL, 5RL, 6RS, 6RL, 7RS and 7RL have all been involved in at least one translocation. A possible evolutionary pathway, which accounts for the present day R genome relative to the A, B and D genomes of wheat, is presented. The relevance of these results for strategies designed to transfer useful genes from rye, and probably other related species, to wheat is discussed.
TL;DR: A large block of simple sequence repeat (SSR) polymorphisms for theDog genome has been isolated and characterized, and a comprehensive system of nomenclature for the dog genome is suggested.
TL;DR: The view that microsatellite markers may have wide application in genetic studies in salmonid species and fishes in general is supported.
Abstract: Thirteen (GT)n and four (CT)n microsatellite loci (n = 10 or more and n = 20 or more, respectively) have been isolated from a partial genomic library of brown trout and sequenced. On average, a (GT)n repeat sequence occurs approximately every 23 kb and a (CT)n repeat sequence every 76 kb in brown trout genome. Primers for DNA amplifications using the polymerase chain reaction (PCR) were synthesized for three single locus microsatellites. Mendelian inheritance of the observed polymorphisms was confirmed in full-sib families. Four brown trout populations (10 unrelated individuals per population) were screened for polymorphism with these three microsatellite loci. The total number of alleles detected in the four populations is five at one locus, six at the other two microsatellite loci and is three, on average, per population. Heterozygosities range from 0.18 to 0.74. The largest differences in allelic frequencies occurred between the Mediterranean and the Atlantic populations: this result is congruent with previous allozymic data. The gene-centromere distances of the three microsatellite markers were determined on gynogenetic lines: post-reduction rates range from 0.17 to 0.60. For all the three microsatellite loci, the primers designed from brown trout sequences can be used in another closely related species of salmonid, the rainbow trout (Oncorhynchus mykiss). This last aspect supports the view that microsatellite markers may have wide application in genetic studies in salmonid species and fishes in general.
TL;DR: To facilitate genetic analysis of the protozoan parasite Toxoplasma gondii, sequences derived from the parasite's fused dihydrofolate reductase-thymidylate synthase (DHFR-TS) gene have been used to produce vectors suitable for stable molecular transformation.
Abstract: To facilitate genetic analysis of the protozoan parasite Toxoplasma gondii, sequences derived from the parasite's fused dihydrofolate reductase-thymidylate synthase (DHFR-TS) gene have been used to produce vectors suitable for stable molecular transformation. Mutations introduced into the DHFR coding region by analogy with pyrimethamine-resistant malaria confer drug resistance to Toxoplasma, providing useful information on the structure of fused DHFR-TS enzymes and a powerful selectable marker for molecular genetic studies. Depending on the particular drug-resistance allele employed and the conditions of selection, stable resistance can be generated either by single copy nonhomologous insertion into chromosomal DNA or by massively amplified transgenes. Frequencies of integration are independent of selection, and transgenes are stable without continued selection. Cointegration of a reporter gene adjacent to the selectable marker (under the control of an independent promoter) shows no loss of the cointegrated sequences over many parasite generations. By bringing the full power of molecular genetic analysis to bear on Toxoplasma, these studies should greatly facilitate the development of a model genetic system for Apicomplexan parasites.
TL;DR: In this paper, the authors used random amplified polymorphic DNA (RAPD) to determine the suitability of RAPD markers for investigating genetic and evolutionary problems, particularly in organisms, such as the parasitic protozoa, unsuitable for traditional methods of genetic analysis.
Abstract: We have assayed genetic polymorphisms in several species of parasitic protozoa by means of random amplified polymorphic DNA (RAPD). One goal was to ascertain the suitability of RAPD markers for investigating genetic and evolutionary problems, particularly in organisms, such as the parasitic protozoa, unsuitable for traditional methods of genetic analysis. Another goal was to test certain hypotheses concerning Trypanosoma cruzi, and other protozoa, that have been established by multilocus enzyme electrophoresis. The RAPD results corroborate the hypothesis that the population structure of T. cruzi is clonal and yield a phylogeny of the clonal lineages in agreement with the one obtained by enzyme electrophoresis. This parity between the two sets of results confirms that RAPD markers are reliable genetic markers. The RAPD markers are also suitable for reconstructing species phylogenies and as diagnostic characters of species and subspecific lineages. The number of DNA polymorphisms that can be detected by the RAPD method seems virtually unlimited, since the number of primers can be increased effectively at will. The RAPD method is well suited for investigating genetic and evolutionary questions in certain organisms, because it is cost effective and demands no previous genetic knowledge about the organism.
TL;DR: Genetic maps for grasses show that the various grasses can best be viewed as different manifestations of one tractable genome, and that research priorities should be set to reflect this rich biological potential.
TL;DR: Cluster analysis showed that groups of inbred lines based on r were similar to those based on d with some notable exceptions, and RAPD markers can be used to gain information about genetic similarities or differences that are not evident from pedigree information.
Abstract: We investigated random amplified polymorphic DNA (RAPD) in 27 inbred barley lines with varying amounts of common ancestry and in 20 doubled-haploid (DH) lines from a biparental cross. Of 33 arbitrary 10 base primers that were tested, 19 distinguished a total of 31 polymorphisms. All polymorphisms were scored as dominant genetic markers except for 1, where Southern analysis indicated the presence of two codominant amplification products. The inheritance of 19 RAPD polymorphisms and one morphological trait was studied in the DH lines. There was no evidence for segregation distortion, but a group of four tightly linked loci was detected. The frequencies of RAPD polymorphism in pairs of inbred lines were used to compute values of genetic distance (d), which were compared to kinship coefficients (r) between the same pairs of lines. A linear relationship between r and d was evident, but low values of r gave poor predictions of d. Cluster analysis showed that groups of inbred lines based on r were similar to those based on d with some notable exceptions. RAPD markers can be used to gain information about genetic similarities or differences that are not evident from pedigree information.
01 Jan 1993
TL;DR: The use of polymorphic single genes to facilitate the process of plant breeding was proposed early in this Century and selection for characters with easily detectable phenotypes can simplify the recovery of genes of interest linked to them and more difficult to score.
Abstract: The use of polymorphic single genes to facilitate the process of plant breeding was proposed early in this Century (Sax, 1923). The basic principle is that selection for characters with easily detectable phenotypes can simplify the recovery of genes of interest linked to them and more difficult to score. The first marker loci available were those that have an obvious impact on the morphology of the plant. Genes that affect form, coloration, male sterility or disease resistance among others have been genetically analysed in many plant species. In some well characterized crops like maize, tomato, pea, barley or wheat, tens or even hundreds of such genes have been assigned to different chromosomes (O’Brien, 1990).
TL;DR: This method demonstrates that trinucleotide microsatellite loci are abundant and highly polymorphic in the social wasp Polistes annularis, whereas allozyme electrophoresis reveals very little polymorphism.
Abstract: Microsatellite loci are regions of DNA containing tandem repeats of a short sequence motif; they occur abundantly in all eukaryotic genomes and have been shown to be a rich source of highly polymorphic genetic markers in humans and other mammals. These loci are particularly suitable for population studies because they can be relatively easily scored using a combination of polymerase chain reaction (PCR) amplification of each locus followed by electrophoresis to separate alleles. This paper details a method for finding these loci in any species. This method demonstrates that trinucleotide microsatellite loci are abundant and highly polymorphic in the social wasp Polistes annularis, whereas allozyme electrophoresis reveals very little polymorphism. The first six loci examined were all polymorphic with a mean observed heterozygosity of 0.62; in comparison average heterozygosity of 33 allozymes was 0.035. We suggest that this method can be used to detect variation where other methods have failed, making it an ideal tool for population and conservation geneticists who must deal with populations lacking other types of genetic variability.
TL;DR: This chapter presents experimental protocols for random amplified polymorphic DNA (RAPD) assays and applications, emphasizing their use for genetic analysis in plants and compares restriction fragment length polymorphism (RFLP) and RAPD assays.
Abstract: Publisher Summary This chapter presents experimental protocols for random amplified polymorphic DNA (RAPD) assays and applications, emphasizing their use for genetic analysis in plants. It describes a novel type of genetic marker that is based on DNA amplification but requires no knowledge of target DNA sequence. These markers, called “RAPD markers” are generated by the amplification of random DNA segments with the single primers of arbitrary nucleotide sequence. RAPD markers can be used for genetic mapping applications as well as for genetic diagnostics. The assay is nonradioactive, requires only nanogram quantities of DNA, and is applicable to a broad range of species. The chapter compares restriction fragment length polymorphism (RFLP) and RAPD assays. RAPD markers provide the geneticist with a new tool to explore the genetics of sexually reproducing organisms, with applications in gene mapping, population genetics, molecular systematics, and marker-assisted selection in plant and animal breeding. In most cases, data can be generated faster and with less labor than by previous methods. The process can be set up in a small laboratory and there is no need to use radioactive isotopes, making it accessible to a broad range of biologists.
TL;DR: Marker-assisted methods yielded higher overall allelic richness in the simulated collections, and they were particularly effective in conserving geographically localized alleles, the class of alleles that is most subject to loss.
Abstract: Wild crop relatives are an important source of genetic variation for improving domesticated species. Given limited resources, methods for maximizing the genetic diversity of collections of wild relatives are needed to help spread protection over a larger number of populations and species. Simulations were conducted to investigate the optimal strategy of sampling materials from populations of wild relatives, with the objective of maximizing the number of alleles (allelic richness) in collections of fixed size. Two methods, based on assessing populations for variation at marker loci (e.g., allozymes, restriction fragment length polymorphisms), were developed and compared with several methods that are not dependent on markers. Marker-assisted methods yielded higher overall allelic richness in the simulated collections, and they were particularly effective in conserving geographically localized alleles, the class of alleles that is most subject to loss.
TL;DR: A survey of the entire genome, using random amplified polymorphic DNA (RAPD) analysis, again showed that Chinese and Philippine S. japonicum are remarkably similar at the DNA sequence level.
TL;DR: RAPDs appear promising for both germplasm fingerprinting and as a predictor of genetic diversity for plant breeding applications.
Abstract: Random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) markers were used to assess the variability in tomato germplasm (Lycopersicon esculentum Mill.), which in...
Journal Article•
TL;DR: LOH was observed not only in tumours of high grade or stage but also in > 50% of grade 1 and 2 superficial (pTa) tumours, the first change to be identified at significant frequency in such tumours.
Abstract: Although many genetic lesions including suppressor gene inactivation have been identified in sporadic tumours, the identity of the common initiating or early genetic events in most cases remains obscure. We have analysed tumour and leucocyte DNA from a series of 252 primary human bladder tumours of all grades and stages for deletions of chromosome 9. Probes from four polymorphic loci were used to detect loss of heterozygosity (LOH) in tumour specimens. Fifty-nine per cent of tumours from patients informative at one or more of these loci showed LOH. A comparison of LOH for markers on 9p and 9q indicated that proximal 9p or 9q is the likely site for a candidate bladder tumour-suppressor gene. Most strikingly, LOH was observed not only in tumours of high grade or stage but also in > 50% of grade 1 and 2 superficial (pTa) tumours. This is the first change to be identified at significant frequency in such tumours. Inactivation of a tumour-suppressor gene on chromosome 9 may therefore be an early genetic event in the development of bladder cancer.
TL;DR: RAPD analysis was applied to onion (Allium cepa) and other Allium species in order to assess the degree of polymorphism within the genus and to investigate if this approach was suitable for genetic studies of onion.
Abstract: RAPD analysis was applied to onion (Allium cepa) and otherAllium species in order to assess the degree of polymorphism within the genus and to investigate if this approach was suitable for genetic studies of onion. Seven cultivars ofA. cepa, including shallot, and single cultivars of Japanese bunching onion (A. fistulosum), chive (A. schoenoprasum), leek (A. ampeloprasum), and a wild relative of onion (A. roylei), were evaluated for variability using a set of 20 random 10-mer primers. Seven out of the twenty primers revealed scorable polymorphisms between cultivars ofA. cepa and these will be further evaluated for use in genetic mapping. Wide variations in banding profiles between species were observed with nearly every primer tested. These were assessed for use in systematic studies within the genus. Ninety-one band positions were scored (+/-) for all the cultivars studied. Genetic distances between each of the cultivars were calculated and cluster analysis was used to generate a dendrogram showing phylogenetic relationships between them. The resulting analysis was in broad agreement with previous classifications of the species studied, confirming the validity of the method. However, amongst the species studied, it placedA. roylei as the closest relative ofA. cepa, questioning the current classification of the former species in the section Rhizideum.
TL;DR: The I gene for bean common mosaic virus resistance is the first disease resistance gene to be located on the common bean genetic linkage map.
Abstract: A restriction fragment length polymorphism (RFLP)-based linkage map for common bean (Phaseolus vulgaris L.) covering 827 centiMorgans (cM) was developed based on a F2 mapping population derived from a cross between BAT93 and Jalo EEP558. The parental genotypes were chosen because they exhibited differences in evolutionary origin, allozymes, phaseolin type, and for several agronomic traits. The segregation of 152 markers was analyzed, including 115 RFLP loci, 7 isozyme loci, 8 random amplified polymorphic DNA (RAPD) marker loci, and 19 loci corresponding to 15 clones of known genes, 1 virus resistance gene, 1 flower color gene, and 1 seed color pattern gene. Using MAPMAKER and LINKAGE-1, we were able to assign 143 markers to 15 linkage groups, whereas 9 markers remained unassigned. The average interval between markers was 6.5 cM; only one interval was larger than 30 cM. A small fraction (9%) of the markers deviated significantly from the expected Mendelian ratios (1∶2∶1 or 3∶1) and mapped into four clusters. Probes of known genes belonged to three categories: seed proteins, pathogen response genes, and Rhizobium response genes. Within each category, sequences homologous to the various probes were unlinked. The I gene for bean common mosaic virus resistance is the first disease resistance gene to be located on the common bean genetic linkage map.
TL;DR: The usefulness of random amplified polymorphic DNA (RAPD) in assessing the genetic stability of somatic embryogenesis-derived populations of black spruce was evaluated and the utilization of RAPD markers both for the assessment of Genetic stability of clonal materials and to certify genetic stability throughout the process of somatics embryogenesis is discussed.
Abstract: The usefulness of random amplified polymorphic DNA (RAPD) in assessing the genetic stability of somatic embryogenesis-derived populations of black spruce [Picea mariana (Mill.) B.S.P.] was evaluated. Three arbitrary 11-mer primers were successfully used to amplify DNA from both in-vivo and in-vitro material. Twenty-five embryogenic cell lines, additional zygotic embryos and megagametophytes from three controlled crosses involving four selected genotypes of black spruce were used for the segregation analysis of RAPD variants. Ten markers were genetically characterized and used to evaluate the genetic stability of somatic embryos derived from three embryogenic cell lines (one cell line per cross, 30 somatic embryos per cell line). No variation was detected within clones. The utilization of RAPD markers both for the assessment of genetic stability of clonal materials and to certify genetic stability throughout the process of somatic embryogenesis is discussed.