scispace - formally typeset
Search or ask a question

Showing papers on "RAPD published in 1993"


Journal ArticleDOI
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



Journal ArticleDOI
TL;DR: These patterns of genetic variation were very different from those reported for inbred species and provide important baseline data for cultivar identification and continuing studies of the evolution of polyploid races in this species.
Abstract: RAPD markers provide a powerful tool for the investigation of genetic variation in natural and domesticated populations. Recent studies of strain/cultivar identification have shown extensive RAPD divergence among, but little variation within, inbred species or cultivars. In contrast, little is known about the pattern and extent of RAPD variation in heterogeneous, outcrossing species. We describe the population genetic variation of RAPD markers in natural, diploid sources of dioecious buffalograss [Buchloe dactyloides (Nutt.) Engelm.]. Buffalograss is native to the semi-arid regions of the Great Plains of North America, where it is important for rangeland forage, soil conservation, and as turfgrass. Most sources of buffalograss germplasm are polyploid; diploid populations are previously known only from semi-arid Central Mexico. This is the first report of diploids from humid Gulf Coastal Texas. These two diploid sources represent divergent adaptive ecotypes. Seven 10-mer primers produced 98 polymorphic banding sites. Based on the presence/ absence of bands, a genetic distance matrix was calculated. The new Analysis of Molecular Variance (AMOVA) technique was used to apportion the variation among individuals within populations, among populations within adaptive regions, and among regions. There was considerable variation within each of the four populations, and every individual was genetically distinct. Even so, genetic divergence was found among local populations. Within-population variation was larger and among-population variation smaller in Mexico than in Texas. The largest observed genetic differences were those between the two regional ecotypes. These patterns of genetic variation were very different from those reported for inbred species and provide important baseline data for cultivar identification and continuing studies of the evolution of polyploid races in this species.

814 citations


Journal ArticleDOI
TL;DR: A map of the barley genome consisting of 295 loci was constructed, which includes 152 cDNA restriction fragment length polymorphism (RFLP), 114 genomic DNA RFLP, 14 random amplified polymorphic DNA (RAPD), five isozyme, two morphological, one disease resistance and seven specific amplicon polymorphism
Abstract: A map of the barley genome consisting of 295 loci was constructed. These loci include 152 cDNA restriction fragment length polymorphism (RFLP), 114 genomic DNA RFLP, 14 random amplified polymorphic DNA (RAPD), five isozyme, two morphological, one disease resistance and seven specific amplicon polymorphism (SAP) markers. The RFLP-identified loci include 63 that were detected using cloned known function genes as probes. The map covers 1,250 centiMorgans (cM) with a 4.2 cM average distance between markers. The genetic lengths of the chromosomes range from 124 to 223 cM and are in approximate agreement with their physical lengths. The centromeres were localized to within a few markers on all of the barley chromosomes except chromosome 5. Telomeric regions were mapped for the short (plus) arms of chromosomes 1, 2 and 3 and the long (minus) arm of chromosomes 7.

649 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


Journal ArticleDOI
TL;DR: Random amplified polymorphic DNA (RAPD) analysis appears to offer a cost- and time-effective alternative to restriction fragment-length polymorphism (RFLP) analysis, but concerns about the ability to compare RAPD results from one laboratory to another have not been addressed effectively.
Abstract: Random amplified polymorphic DNA (RAPD) analysis appears to offer a cost- and time-effective alternative to restriction fragment-length polymorphism (RFLP) analysis. However, concerns about the ability to compare RAPD results from one laboratory to another have not been addressed effectively. DNA fragments that were amplified by five primers and shown to be reproducibly polymorphic between two oat cultivars (within the Ottawa laboratory) were tested in six other laboratories in North America. Four of the six participants amplified very few or no fragments using the Ottawa protocol. These same participants were able to generate a considerable number of amplified fragments by using their own protocols. The reproducibility of results among laboratories was affected by two factors. First, different laboratories amplified different size ranges of DNA fragments, and, consequently, small and large polymorphic fragments were not always reproduced. Second, although reproducible results were obtained with four of the primers, reproducible results were not obtained with the fifth primer, using the same reaction conditions. It is suggested that if the overall temperature profiles (especially the annealing temperature) inside the tubes are identical among the laboratories, then RAPD fragments are likely to be reproducible.

435 citations


Journal Article
TL;DR: It is shown that competitive PCR MIMICS can be used to accurately measure small changes in mRNA levels and is described as a rapid and reliable method for preparing competitive DNA fragments for quantitative PCR.
Abstract: A rapid and reliable method is described for preparing competitive DNA fragments for quantitative PCR. Synthetic DNAs complementary to previously established PCR primers are ligated together with the primers to both ends of a generic DNA fragment whose length differs from the natural target gene PCR product. After a short ligation step, the properly constructed ligation products (i.e., those that have the correct primer templates on opposite sides of the generic DNA fragment) are preferentially amplified by PCR. The generation of competitive PCR fragments, MIMICS, can be completed in a single day. To perform quantitative PCR, known quantities of PCR MIMICS are spiked into PCR amplification reactions containing the experimental cDNA samples. A visual or radioactive comparison of the PCR products can then be used to determine the initial quantity of target gene. We show that competitive PCR MIMICS can be used to accurately measure small changes in mRNA levels.

378 citations


Journal ArticleDOI
TL;DR: Within the DNA-oligonucleotide-DNA-polymerase-thermal cycler, reproducibility was excellent when the thermal cycler equipped with the best temperature regulation was used, but was not as good with another brand of thermalcycler.

370 citations


Journal ArticleDOI
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.

339 citations


Journal ArticleDOI
TL;DR: The degree of similarity of the banding patterns can be used to estimate nucleotide diversity and nucleotide divergence and the restrictions and criteria that must be met when RAPD data are used for estimating population genetic parameters are summarized.
Abstract: The technique of random amplification of polymorphic DNA (RAPD), which is simply polymerase chain reaction (PCR) amplification of genomic DNA by a single short oligonucleotide primer, produces complex patterns of anonymous polymorphic DNA fragments. The information provided by these banding patterns has proved to be of great utility for mapping and for verification of identity of bacterial strains. Here we consider whether the degree of similarity of the banding patterns can be used to estimate nucleotide diversity and nucleotide divergence. With haploid data, fragments generated by RAPD-PCR can be treated in a fashion very similar to that for restriction-fragment data. Amplification of diploid samples, on the other hand, requires consideration of the fact that presence of a band is dominant to absence of the band. After describing a method for estimating nucleotide divergence on the basis of diploid samples, we summarize the restrictions and criteria that must be met when RAPD data are used for estimating population genetic parameters.

310 citations


Journal ArticleDOI
TL;DR: Segregating allozyme and DNA polymorphisms were used to construct a preliminary linkage map for faba bean, suggesting that it may share some homology with chromosome 4 of garden pea on which three similar markers are syntenic.
Abstract: Segregating allozyme and DNA polymorphisms were used to construct a preliminary linkage map for faba bean. Two F2 populations were analyzed, the most informative of which was segregating for 66 markers. Eleven independently assorting linkage groups were identified in this population. One of the groups contained the 45s ribosomal array and could be assigned to the large metacentric chromosome I on which the nucleolar organizer region is located. This linkage group also contained two isozyme loci, Est and Tpi-p, suggesting that it may share some homology with chromosome 4 of garden pea on which three similar markers are syntenic. Additional aspects of the map and the extent of coverage of the total nuclear genome are discussed.

Journal ArticleDOI
TL;DR: RAPD technology provides a new alternative for cultivar identification and classification in celery and is basically consistent with the known lineage of the cultivars and the previous study using stem protein and isozyme markers.
Abstract: Twenty-one celery (Apium graveolens L. var. dulce) cultivars, one celeriac (var. rapaceum) and one annual smallage (var. secalinum) cultivar were screened for polymorphic RAPD (Random Amplified Polymorphic DNA) markers with 28 arbitrary 10-mer primers. Among a total of 309 bands observed, 29 (9.3%) were polymorphic in the 23 cultivars screened, but only 19 (6.1%) markers were polymorphic within the 21 type dulce cultivars. These markers were sufficient to distinguish each of the cultivars used. The average marker difference was 6.4 between two celery cultivars, 16.7 between celery and annual smallage, 14.7 between celery and celeriac, and 12.0 between annual smallage and celeriac. The celery cultivars surveyed were classified into three groups based on the marker differences. The relationship among the dulce-type cultivars concluded from this research is basically consistent with the known lineage of the cultivars and the previous study using stem protein and isozyme markers. RAPD technology provides a new alternative for cultivar identification and classification in celery.

Journal ArticleDOI
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.

Journal ArticleDOI
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.

Journal ArticleDOI
TL;DR: The patterns of genetic and environmental associations detected in this population suggest that assortative mating and environmental and viability selection are important in the structuring and maintenance of this hybrid zone.
Abstract: Chloroplast DNA (cpDNA) markers and 12 nuclear (random amplified polymorphic DNA, or RAPD) markers were used to examine the distribution of genetic variation among individuals and the genetic and ecological associations in a hybrid iris population. Plants in the population occurred at various distances from the edge of a bayou in a relatively undisturbed mixed hardwood forest and in an adjacent pasture dominated by herbaceous perennials with interspersed oak and cypress trees. The majority of plants sampled possessed combinations of markers from the different Iris species. Genetic markers diagnostic for Iris fulva and I. brevicaulis occurred at high frequencies, whereas markers diagnostic for I. hexagona were infrequent. For the majority of the nuclear markers, significant levels of cytonuclear disequilibria existed because of intraspecific associations among the markers in both the pasture and the forest. The distribution of nuclear markers among individuals was bimodal; intermediate genotypes were absent and the majority of RAPD markers were associated with their intraspecific cpDNA haplotypes. Strong intraspecific associations existed among RAPD markers in the forest, but associations tended to be weaker in the pasture area. Ecological correlations were detected for all but one of the I. fulva and I. brevicaulis RAPD markers. The ecological associations of hybrids similar to I. brevicaulis resembled associations of I. brevicaulis parental genotypes, suggesting that these hybrid genotypes may be relatively fit in the same habitats. The hybrids similar to I. fulva, however, were distributed in habitats that were unique relative to the parental species. The patterns of genetic and environmental associations along with other available data suggest that (1) only advanced generation hybrids were present in the population; (2) formation of F1 hybrids among Louisiana irises is rare, leading to sporadic formation of hybrid populations; and (3) selection and assortative mating have contributed to the formation of hybrid genotypes that tend to be similar to parental genotypes. The patterns of ecological and genetic associations detected in this population suggest that assortative mating and environmental and viability selection are important in the structuring and maintenance of this hybrid zone.

Journal ArticleDOI
TL;DR: A key is proposed by which one can differentiate apple cultivars using commercially available prime by using randomly amplified polymorphic DNA markers obtained by the polymerase chain reaction (PCR).
Abstract: Eleven apple cultivars were differentiated using randomly amplified polymorphic DNA (RAPD) markers obtained by the polymerase chain reaction (PCR). The variability of the technique and of the origin of the DNA extract was analyzed. A set of bands consistent in their presence or absence was chosen to create a differentiating band pattern. A key is proposed by which one can differentiate apple cultivars using commercially available prime.

Journal ArticleDOI
TL;DR: RAPD typing is far more sensitive than MLEE typing for discriminating among related strains of a species, and should be used for studies of bacterial population genetic structure and evolution, as well as for epidemiology.
Abstract: The RAPD (random amplified polymorphic DNA) fingerprinting method, which utilizes low stringency PCR amplification with single primers of arbitrary sequence to generate strain-specific arrays of anonymous DNA fragments, was calibrated relative to the widely used, protein-based multilocus enzyme electrophoretic (MLEE) typing method. RAPD fingerprinting was carried out on five isolates from each of 15 major groups of Escherichia coli strains that cause diarrheal disease worldwide (75 isolates in all). Each group consisted of isolates that were not distinguishable from one another by MLEE typing using 20 diagnostic enzyme markers. In our RAPD tests, three or more distinct subgroups in each MLEE group were distinguished with each of five primers, and 74 of the 75 isolates were distinguished when data obtained with five primers were combined. Thus, RAPD typing is far more sensitive than MLEE typing for discriminating among related strains of a species. Despite their different sensitivities, the same general relationships among strains were inferred from MLEE and RAPD data. Thus, our results recommend use of the RAPD method for studies of bacterial population genetic structure and evolution, as well as for epidemiology.

Journal ArticleDOI
TL;DR: The results indicate that trembling aspen is more genetically variable than bigtooth aspen at both the allozyme and DNA levels, one can generate more polymorphic and species-specific loci with DNA markers than with allozymes in aspen, and RAPDs provide a very powerful tool for “fingerprinting” aspen individuals.
Abstract: We examined genetic variation in allozyme loci, nuclear DNA restriction fragment length polymorphisms (RFLPs), and random amplified polymorphic DNAs (RAPDs) in 130 trembling aspen (Populus tremuloides) and 105 bigtooth aspen (P grandidentata) trees In trembling aspen 10 out of 13 allozyme loci assayed (77%) were polymorphic (P), with 28 alleles per locus (A) and an expected heterozygosity (He) of 025 In contrast, bigtooth aspen had a much lower allozyme genetic variability (P=29%; A=14; He=008) The two species could be distinguished by mutually exclusive alleles at Idh-1, and bigtooth aspen has what appears to be a duplicate 6PG locus not present in trembling aspen We used 138 random aspen genomic probes to reveal RFLPs in HindIII digests of aspen DNA The majority of the probes were from sequences of low copy number RFLP results were consistent with those of the allozyme analyses, with trembling aspen displaying higher genetic variation than bigtooth aspen (P=71%, A=27, and He=025 for trembling aspen; P=65%, A=18, and He=013 for bigtooth aspen) The two species could be distinguished by RFLPs revealed by 21 probes (15% of total probes assayed) RAPD patterns in both species were studied using four arbitrary decamer primers that revealed a total of 61 different amplified DNA fragments in trembling aspen and 56 in bigtooth aspen Assuming a Hardy-Weinberg equilibrium, estimates of P=100%, A=2, and He=030 in trembling aspen and P=88%, A=19, and He=031 in bigtooth aspen were obtained from the RAPD data Five amplified DNA fragments were species diagnostic All individuals within both species, except for 2 that likely belong to the same clone, could be distinguished by comparing their RAPD patterns These results indicate that (1) RFLPs and allozymes reveal comparable patterns of genetic variation in the two species, (2) trembling aspen is more genetically variable than bigtooth aspen at both the allozyme and DNA levels, (3) one can generate more polymorphic and species-specific loci with DNA markers than with allozymes in aspen, and (4) RAPDs provide a very powerful tool for "fingerprinting" aspen individuals


Journal ArticleDOI
01 Jun 1993-Genome
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 ArticleDOI
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.

Journal ArticleDOI
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.

Journal ArticleDOI
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.

Journal ArticleDOI
TL;DR: Randomly amplified polymorphic DNA markers were used to analyse genetic diversity within and between Hordeum spontaneum populations sampled from Israel, suggesting adaptive variation at certain RAPD loci.
Abstract: Randomly amplified polymorphic DNA (RAPD) markers were used to analyse genetic diversity within and between Hordeum spontaneum populations sampled from Israel. Nei's index of genetic differentiation was used to partition diversity into within and between population components. Fifty-seven per cent of the variation detected was partitioned within 10 H. spontaneum populations. Using principal component and multiple regression analysis, part of the variation detected between populations was seen to be associated with certain ecogeographical factors. Fifty-eight per cent of the distribution of the phenotypic frequencies of three RAPD phenotypes detected using a single primer in 20 H. spontaneum populations could be accounted for by four ecogeographical variables, suggesting adaptive variation at certain RAPD loci.


Journal ArticleDOI
TL;DR: This reference population produced by backcrossing a partially inbred Red Jungle Fowl line to a highly inbred White Leghorn line is polymorphic and gives simple segregation for two types of molecular probes, providing a good resource for collaborative mapping of the chicken genome.

Journal ArticleDOI
TL;DR: Analysis of a collection of resistant and susceptible cultivars and experimental lines revealed that observations of variable recombination among Mesoamerican bean races suggested suppression of recombination between introgressed segments and divergent recurrent backgrounds.
Abstract: Rust in bean (Phaseolus vulgaris L.), caused byUromyces appendiculatus (Pers.) Unger var.appendiculatus [ =U. phaseoli (Reben) Wint.], is a major disease problem and production constraint in many parts of the world. The predominant form of genetic control of the pathogen is a series of major genes which necessitate the development of efficient selection strategies. Our objective was focused on the identification of RAPD (random amplified polymorphic DNA) markers linked to a major bean rust resistance gene block enabling marker-based selection and facilitating resistance gene pyramiding into susceptible bean germplasm. Using pooled DNA samples of genotyped individuals from two segregating populations, we identified two RAPD markers linked to the gene block of interest. One such RAPD, OF10970 (generated by a 5′-GGAAGCTTGG-3′ decamer), was found to be closely linked (2.15±1.50 centi Morgans) in coupling with the resistance gene block. The other identified RAPD, OI19460 (generated by a 5′-AATGCGGGAG-3′ decamer), was shown to be more tightly linked (also in coupling) than OF10970 as no recombinants were detected among 97 BC6F2 segregating individuals in the mapping population. Analysis of a collection of resistant and susceptible cultivars and experimental lines, of both Mesoamerican and Andean origin, revealed that: (1) recombination between OF10970 and the gene block has occurred as evidenced by the presence of the DNA fragment in several susceptible genotypes, (2) recombination between OI19460 and the gene block has also occurred indicating that the marker is not located within the gene block itself, and (3) marker-facilitated selection using these RAPD markers, and another previously identified, will enable gene pyramiding in Andean germplasm and certain Mesoamerican bean races in which the resistance gene block does not traditionally exist. Observations of variable recombination among Mesoamerican bean races suggested suppression of recombination between introgressed segments and divergent recurrent backgrounds.

Journal ArticleDOI
TL;DR: The recently developed technique of random amplification of polymorphic DNA (RAPD) to the analysis of the relationships among ten cultivars of papaya showed that RAPD technology is a rapid, precise and sensitive technique for genomic analysis.
Abstract: We have applied the recently developed technique of random amplification of polymorphic DNA (RAPD) to the analysis of the relationships among ten cultivars of papaya (Carica papaya L.). Eleven ten-base synthetic oligonucleotides were chosen that gave multiple PCR amplification products using papaya DNA as template. These 11 primers amplified a total of 102 distinct fragments. Cultivars were scored for presence or absence of RAPD fragments and grouped by cluster analysis using simple matching coefficients of similarity. A dendrogram of the ten cultivars was constructed. Of the ten cultivars seven were of the Hawaiian type, and all of these grouped to one branch of the tree. Divisions within the Hawaiian, branch were mostly consistent with the known genetic background of these cultivars. Three non-Hawaiian, cultivars were also analyzed. The minimum similarity detected was 0.7 suggesting that the domesticated papaya germ plasm is quite narrow. Our results show that RAPD technology is a rapid, precise and sensitive technique for genomic analysis.

Journal ArticleDOI
TL;DR: The results suggest that specific types of errors can be detected in RAPDAnalysis, that uniparental inheritance is not common, and that RAPD analysis might be more prudently used for some applications than for others.
Abstract: Random amplified polymorphic DNA (RAPD) markers were analyzed in materials from a partial diallel, including 16 corn F1 hybrids (with five reciprocals) and their five parental inbreds. Using 21 primers, we scored a total of 140 different fragments for their presence/absence and intensity variation, where appropriate. When all 21 genotypes were taken into consideration, 20.7% of these fragments were nonpolymorphic, 37.1% were unambiguously polymorphic, and 42.1% were quantitatively polymorphic. Unambiguous polymorphisms were distinguished by the simple presence or absence of a specific fragment in the inbred genotypes, whereas quantitative polymorphisms exhibited a variation in the intensity of a fragment. Of the F1 patterns, 95.2% of the unambiguously polymorphic situations could be interpreted genetically by assuming complete dominance of the presence of the parental fragment, while 3.2% of the F1 patterns exhibited a fragment intensity that was intermediate between the two parental patterns (partial dominance). For quantitative polymorphisms, values of 88.1% for complete dominance and 5.0% for partial dominance were obtained. The results suggest that specific types of errors can be detected in RAPD analysis, that uniparental inheritance is not common, and that RAPD analysis might be more prudently used for some applications than for others.

Journal ArticleDOI
01 Jun 1993-Heredity
TL;DR: Allozyme variation was absent within most populations, particularly within those countries where the species was recently introduced, and cluster analyses indicated strong similarities between U.S.A. populations and collections from South Africa, Mexico, France and Turkey.
Abstract: Genetic analyses were conducted on Diuraphis noxia (Mordvilko) populations collected from wheat, barley and other grasses from various countries throughout the world. These collections had been found to contain clones that differed in virulence from various cultivars, cuticular hydrocarbon profiles and life cycle characters. Discrete genetic markers analysed in this study included allozymes and arbitrary regions of the genome amplified by the polymerase chain reaction (RAPD-PCR). In all, 23 enzymes were evaluated; 17 of these enzymes representing 20 isozyme loci, were judged suitable for allozyme analysis. Polymorphisms were detected at three (15 per cent) loci: beta-esterase (beta-EST), phosphoglucose isomerase (PGI), and 6-phosphogluconate dehydrogenase (6-PGDH). The average expected heterozygosity amongst these loci was 4.9 per cent in the worldwide collection. Allozyme variation was absent within most populations, particularly within those countries where the species was recently introduced. Much greater genetic variation was detected when populations were analysed with RAPD-PCR. Populations were analysed with 69 polymorphic bands amplified by seven primers. All populations could be distinguished with this method. Cluster analyses indicated strong similarities between U.S.A. populations and collections from South Africa, Mexico, France and Turkey. The most variation was detected among populations from the Middle East and southern Russia.