Showing papers on "RAPD published in 2001"
Journal Article•
TL;DR: Low expense, efficiency in developing a large number of DNA markers in a short time and requirement for less sophisticated equipment has made the RAPD technique valuable although reproducibility of the RAPD profile is still the centre of debate.
Abstract: Due to advances in molecular biology techniques, large numbers of highly informative DNA markers have been developed for the identification of genetic polymorphism. In the last decade, the random amplified polymorphic DNA (RAPD) technique based on the polymerase chain reaction (PCR) has been one of the most commonly used molecular techniques to develop DNA markers. RAPD markers are amplification products of anonymous DNA sequences using single, short and arbitrary oligonucleotide primers, and thus do not require prior knowledge of a DNA sequence. Low expense, efficiency in developinga large number of DNA markers in a short time and requirement for less sophisticated equipment has made the RAPD technique valuable although reproducibility of the RAPD profile is still the centre of debate.
417 citations
TL;DR: The low bootstrap values and the star-like topology of the whole Trichomonadidae tree confirm that the RAPD method is not suitable for phylogenetic analysis of protozoa at the level of higher taxa and it is proposed that the repeated bootstrap analysis should be an obligatory part of any RAPD study.
Abstract: The Win95/98/NT program FreeTree for computation of distance matrices and construction of phylogenetic or phenetic trees on the basis of random amplified polymorphic DNA (RAPD), RFLP and allozyme data is presented. In contrast to other similar software, the program FreeTree (available at http://www.natur.cuni.cz/~flegr/programs/freetree or http://ijs.sgmjournals.org/content/vol51/issue3/) can also assess the robustness of the tree topology by bootstrap, jackknife or operational taxonomic unit-jackknife analysis. Moreover, the program can be also used for the analysis of data obtained in several independent experiments performed with non-identical subsets of taxa. The function of the program was demonstrated by an analysis of RAPD data from 42 strains of 10 species of trichomonads. On the phylogenetic tree constructed using FreeTree, the high bootstrap values and short terminal branches for the Tritrichomonas foetus/suis 14-strain branch suggested relatively recent and probably clonal radiation of this species. At the same time, the relatively lower bootstrap values and long terminal branches for the Trichomonas vaginalis 20-strain branch suggested more ancient radiation of this species and the possible existence of genetic recombination (sexual reproduction) in this human pathogen. The low bootstrap values and the star-like topology of the whole Trichomonadidae tree confirm that the RAPD method is not suitable for phylogenetic analysis of protozoa at the level of higher taxa. It is proposed that the repeated bootstrap analysis should be an obligatory part of any RAPD study. It makes it possible to assess the reliability of the tree obtained and to adjust the amount of collected data (the number of random primers) to the amount of phylogenetic signals in the RAPD data of the taxon analysed. The FreeTree program makes such analysis possible.
337 citations
TL;DR: This is the first report of the partitioning of genetic variability within and among populations of O. granulata at the DNA level, which is in general agreement with a recent study on the same species in China using allozyme analysis.
Abstract: Genetic variation within and between five populations of Oryza granulata from two regions of China was investigated using RAPD (random amplified polymorphic DNA) and ISSR (inter-simple sequence repeat amplification) markers. Twenty RAPD primers used in this study amplified 199 reproducible bands with 61 (30.65%) polymorphic; and 12 ISSR primers amplified 113 bands with 52 (46.02%) polymorphic. Both RAPD and ISSR analyses revealed a low level of genetic diversity in wild populations of O. granulata. Furthermore, analysis of molecular variance (AMOVA) was used to apportion the variation within and between populations both within and between regions. As the RAPD markers revealed, 73.85% of the total genetic diversity resided between the two regions, whereas only 19.45% and 6.70% were present between populations within regions and within a population respectively. Similarly, it was shown by ISSR markers that a great amount of variation (49.26%) occurred between the two regions, with only 38.07% and 12.66% between populations within regions and within a population respectively. Both the results of a UPGMA cluster, based on Jaccard coefficients, and pairwise distance analysis agree with that of the AMOVA partition. This is the first report of the partitioning of genetic variability within and among populations of O. granulata at the DNA level, which is in general agreement with a recent study on the same species in China using allozyme analysis. Our results also indicated that the percentage of polymorphic bands (PPB) detected by ISSR is higher than that detected by RAPD. It seems that ISSR is superior to RAPD in terms of the polymorphism detected and the amplification reproducibility.
333 citations
TL;DR: The present results strongly support the view that Arachis monticola and hypogaea are very closely related, and indicate that A. villosa and A. ipaensis are the diploid wild progenitors of these tetraploid species.
Abstract: Twenty-one random and 29 SSR primers were used to assess genetic variation and interrelationships among subspecies and botanical varieties of cultivated peanut, Arachis hypogaea (2n = 4x = 40), and...
278 citations
TL;DR: In plant I, the same RAPD type (RAPD type 12) was found over a 4-year period, indicating that an established in-house flora persisted and was not eliminated by routine hygienic procedures, and indicates that persistent strains may be avoided by rigorous cleaning and sanitation.
Abstract: The contamination routes of Listeria monocytogenes in cold-smoked salmon processing plants were investigated by analyzing 3,585 samples from products (produced in 1995, 1996, 1998, and 1999) and processing environments (samples obtained in 1998 and 1999) of two Danish smokehouses. The level of product contamination in plant I varied from 31 to 85%, and no L. monocytogenes was found on raw fish (30 fish were sampled). In plant II, the levels of both raw fish and product contamination varied from 0 to 25% (16 of 185 raw fish samples and 59 of 1,000 product samples were positive for L. monocytogenes). A total of 429 strains of L. monocytogenes were subsequently compared by random amplified polymorphic DNA (RAPD) profiling, and 55 different RAPD types were found. The RAPD types detected on the products were identical to types found on the processing equipment and in the processing environment, suggesting that contamination of the final product (cold-smoked salmon) in both plants (but primarily in plant I) was due to contamination during processing rather than to contamination from raw fish. However, the possibility that raw fish was an important source of contamination of the processing equipment and environment could not be excluded. Contamination of the product occurred in specific areas (the brining and slicing areas). In plant I, the same RAPD type (RAPD type 12) was found over a 4-year period, indicating that an established in-house flora persisted and was not eliminated by routine hygienic procedures. In plant II, where the prevalence of L. monocytogenes was much lower, no RAPD type persisted over long periods of time, and several different L. monocytogenes RAPD types were isolated. This indicates that persistent strains may be avoided by rigorous cleaning and sanitation; however, due to the ubiquitous nature of the organism, sporadic contamination occurred. A subset of strains was also typed by using pulsed-field gel electrophoresis and amplified fragment length polymorphism profiling, and these methods confirmed the type division obtained by RAPD profiling.
269 citations
TL;DR: It is postulate that certain rhizobacterial genotypes have evolved a preference for colonization of specific crops by exploiting diversity of antagonistic rhizOBacteria that share a common trait, biological control can be improved significantly.
Abstract: The genotypic diversity that occurs in natural populations of antagonistic microorganisms provides an enormous resource for improving biological control of plant diseases. In this study, we determined the diversity of indigenous 2,4-diacetylphloroglucinol (DAPG)-producing Pseudomonas spp. occurring on roots of wheat grown in a soil naturally suppressive to take-all disease of wheat. Among 101 isolates, 16 different groups were identified by random amplified polymorphic DNA (RAPD) analysis. One RAPD group made up 50% of the total population of DAPG-producing Pseudomonas spp. Both short- and long-term studies indicated that this dominant genotype, exemplified by P. fluorescens Q8r1-96, is highly adapted to the wheat rhizosphere. Q8r1-96 requires a much lower dose (only 10 to 100 CFU seed(-1) or soil(-1)) to establish high rhizosphere population densities (10(7) CFU g of root(-1)) than Q2-87 and 1M1-96, two genotypically different, DAPG-producing P. fluorescens strains. Q8r1-96 maintained a rhizosphere population density of approximately 10(5) CFU g of root(-1) after eight successive growth cycles of wheat in three different, raw virgin soils, whereas populations of Q2-87 and 1M1-96 dropped relatively quickly after five cycles and were not detectable after seven cycles. In short-term studies, strains Q8r1-96, Q2-87, and 1M1-96 did not differ in their ability to suppress take-all. After eight successive growth cycles, however, Q8r1-96 still provided control of take-all to the same level as obtained in the take-all suppressive soil, whereas Q2-87 and 1M1-96 gave no control anymore. Biochemical analyses indicated that the superior rhizosphere competence of Q8r1-96 is not related to in situ DAPG production levels. We postulate that certain rhizobacterial genotypes have evolved a preference for colonization of specific crops. By exploiting diversity of antagonistic rhizobacteria that share a common trait, biological control can be improved significantly.
253 citations
TL;DR: Host specialization in Macrophomina phaseolina was isolated from soybean, corn, sorghum, and cotton root tissue and soil from fields cropped continuously to these species for 15 years, suggesting that M. phaseolina constitutes a single species.
Abstract: To investigate host specialization in Macrophomina phaseolina, the fungus was isolated from soybean, corn, sorghum, and cotton root tissue and soil from fields cropped continuously to these species for 15 years in St. Joseph, LA. Chlorate phenotype of each isolate was determined after growing on a minimal medium containing 120 mM potassium chlorate. Consistent differences in chlorate sensitivity were detected among isolates from different hosts and from soil versus root. To further explore genetic differentiation among fungal isolates from each host, these isolates were examined by restriction fragment length polymorphism and random amplified polymorphic DNA (RAPD) analysis. No variations were observed among isolates in restriction patterns of DNA fragments amplified by polymerase chain reaction covering the internal transcribed spacer region, 5.8S rRNA and part of 25S rRNA, suggesting that M. phaseolina constitutes a single species. Ten random primers were used to amplify the total DNA of 45 isolates, and banding patterns resulting from RAPD analysis were compared with the neighbor-joining method. Isolates from a given host were genetically similar to each other but distinctly different from those from other hosts. Chlorate-sensitive isolates were distinct from chlorate-resistant isolates within a given host. In greenhouse tests, soybean, sorghum, corn, and cotton were grown separately in soil infested with individual isolates of M. phaseolina that were chosen based on their host of origin and chlorate phenotype. Root colonization and plant weight were measured after harvesting. More colonization of corn roots occurred when corn was grown in soil containing corn isolates compared with isolates from other hosts. However, there was no host specialization in isolates from soybean, sorghum, or cotton. More root colonization in soybean occurred with chlorate-sensitive than with chlorate-resistant isolates.
198 citations
TL;DR: Factorial discriminant analyses showed that RAPD profiles were correlated with the use of the fruits and the country or region of origin of the cultivars, suggesting that cultivar selection has occurred in different genetic pools and in different areas.
Abstract: One hundred and two olive RAPD profiles were sampled from all around the Mediterranean Basin. Twenty four clusters of RAPD profiles were shown in the dendrogram based on the Ward’s minimum variance algorithm using chi-square distances. Factorial discriminant analyses showed that RAPD profiles were correlated with the use of the fruits and the country or region of origin of the cultivars. This suggests that cultivar selection has occurred in different genetic pools and in different areas. Mitochondrial DNA RFLP analyses were also performed. These mitotypes supported the conclusion also that multilocal olive selection has occurred. This prediction for the use of cultivars will help olive growers to choose new foreign cultivars for testing them before an eventual introduction if they are well adapted to local conditions.
190 citations
TL;DR: A phenotypically polymorphic barley mapping population was developed using morphological marker stocks as parents and several molecular markers were found to be closely linked to morphological loci, aiding in map-based cloning of genes controlling morphological traits.
Abstract: A phenotypically polymorphic barley (Hordeum vulgare L.) mapping population was developed using morphological marker stocks as parents. Ninety-four doubled-haploid lines were derived for genetic mapping from an F1 using the Hordeum bulbosum system. A linkage map was constructed using 12 morphological markers, 87 restriction fragment length polymorphism (RFLP), five random amplified polymorphic DNA (RAPD), one sequence-tagged site (STS), one intron fragment length polymorphism (IFLP), 33 simple sequence repeat (SSR), and 586 amplified fragment length polymorphism (AFLP) markers. The genetic map spanned 1,387 cM with an average density of one marker every 1.9 cM. AFLP markers tended to cluster on centromeric regions and were more abundant on chromosome 1 (7H). RAPD markers showed a high level of segregation distortion, 54% compared with the 26% observed for AFLP markers, 27% for SSR markers, and 18% for RFLP markers. Three major regions of segregation distortion, based on RFLP and morphological markers, were located on chromosomes 2 (2H), 3 (3H), and 7 (5H). Segregation distortion may indicate that preferential gametic selection occurred during the development of the doubled-haploid lines. This may be due to the extreme phenotypes determined by alleles at morphological trait loci of the dominant and recessive parental stocks. Several molecular markers were found to be closely linked to morphological loci. The linkage map reported herein will be useful in integrating data on quantitative traits with morphological variants and should aid in map-based cloning of genes controlling morphological traits.
182 citations
TL;DR: Assessment of genetic diversity among accessions that have been reported to havedisease resistance indicated that resistance to either anthracnose, downy mildew, powdery mildews, or watermelon mosaic virus is found among all major groups of Citrullus PIs.
Abstract: Genetic diversity was estimated among 42 U.S. PlantIntroduction (PI) accessions of the genusCitrullus (of these, 34 PIs are reported tohave disease resistance), and 5 watermelon cultivars, using 30RAPD primers. These primers produced 662 RAPD markers that could berated with high confidence. Based on these markers, geneticsimilarity coefficients were calculated and a dendrogram wasconstructed using the unweighted pair-group method witharithmetic average (UPGMA). The analysis delineated threemajor clusters. The first cluster consisted of a group of fivewatermelon cultivars, a group of C.lanatus var. lanatusaccessions, and a group of C.lanatus var. lanatusaccessions that contained some C.lanatus var. citroidesgenes. The second cluster consisted of the C.lanatus var. citroidesaccessions, while the third cluster consisted of theC. colocynthis accessions.The two C. lanatus clustersdifferentiated from each other and from the C.colocynthis cluster at the level of 58.8%and 38.9% genetic similarity, respectively. Assessment ofgenetic diversity among accessions that have been reported to havedisease resistance indicated that resistance to either anthracnose,downy mildew, powdery mildew, or watermelon mosaic virus is foundamong all major groups of Citrullus PIs.Additionally, resistance to gummy stem blight or Fusarium wilt mayexist among C. lanatus var.citroides PIs. This study demonstrates thatmolecular markers can be useful in assessing genetic diversity, andin sorting Citrullus PIs into phylogeneticgroups prior to their evaluation for disease or pestresistance.
177 citations
TL;DR: The results supported the hypothesis that southwestern Ethiopian coffee trees could have been introduced recently in the south and southeast, and appeared little differentiated from wild coffee growing in the southwest.
Abstract: Genetic diversity was studied using RAPD markers among119 coffee (Coffea arabica L.) individuals representing 88 accessions derived from spontaneous and subspontaneous trees in Ethiopia, the primary centre of species diversity, six cultivars grown locally in Ethiopia, and two accessions derived from the genetic populations Typica and Bourbon, spread in the 18th century, which gave rise to the most currently grown cultivars. Twenty-nine polymorphic fragments were used to calculate a similarity index and construct dendrograms. The Ethiopian material was separated from the Typica- and Bourbon-derived accessions and classified in four groups: one with most of the collected material from southwestern Ethiopia and three from southern and southeastern Ethiopia. Almost all detected diversity was found in the southwestern group while the southern and southeastern groups presented only 59% of identified markers. The genetic distances were low between the southwestern group and the southern and southeastern groups, and between the southwestern group and the Typica- and Bourbon-derived accessions. The cultivated coffee derived from the genetic populations Typica and Bourbon appeared little differentiated from wild coffee growing in the southwest. The results supported the hypothesis that southwestern Ethiopian coffee trees could have been introduced recently in the south and southeast. A separate analysis of the 80accessions classified in the southwestern group allowed identifying particular spontaneous- and subspontaneous-derived accessions and redundancies in the collected material from southwestern Ethiopia. RAPD markers did not detect any within-collection polymorphism except for two trees that were identified as off-types in the CATIE field genebank.
TL;DR: Three major groups of cultivars could be distinguished by RAPD analysis: 1) cultivars from east and northeast Spain, 2) Turkish, Syrian, and Tunisian cultivars, and 3) the majority of common olive cultivars in Spain.
Abstract: Random amplified polymorphic DNA (RAPD) analysis was performed on the main Mediterranean cultivars of olive (Olea europaea L.) from the Germplasm Bank of the Centro de Investigacion y Formacion Agraria "Alameda del Obispo" in Cordoba, Spain. One hundred and ninety reproducible amplification fragments were identified using 46 random primers followed by agarose gel electrophoresis. Some 63.2% of the amplification products were polymorphic, with an average of 2.6 RAPD markers obtained for each primer. The combination of polymorphic markers resulted in 244 banding patterns. The high degree of polymorphism detected made identification of all the cultivars (51) possible by combining the RAPD banding patterns of just only four primers: OPA-01, OPK-08, OPX-01, and OPX-03. Cultivar- specific RAPD markers and banding patterns were also found. A dendrogram based on unweighted pair-group method cluster analysis was constructed using a similarity matrix derived from the RAPD amplification products generated by the 46 primers. Three major groups of cultivars could be distinguished by RAPD analysis: 1) cultivars from east and northeast Spain, 2) Turkish, Syrian, and Tunisian cultivars, and 3) the majority of common olive cultivars in Spain. The dendrogram thus showed a good correlation between the banding patterns of olive cultivars and their geographic origin. A higher level of polymorphism was observed when polyacrylamide gel electrophoresis was used to separate the amplification products. Thus, adequate use of RAPD technology offers a valuable tool to distinguish between olive cultivars.
TL;DR: The SSR and ISSR markers were found to be useful for cultivar identification and assessment of phenetic relationships, revealing advantages, due to higher reproducibility, over other commonly employed PCR-based methods, namely RAPD and AFLP.
Abstract: In this study, two microsatellite-based methodologies (SSR and ISSR) were evaluated for potential use in fingerprinting and determination of the similarity degree between 41 commercial cultivars of apple previously characterised using RAPD and AFLP markers. A total of 13 SSR primer sets was used and 84 polymorphic alleles were amplified. Seven ISSR primers yielded a total of 252 bands, of which 176 (89.1%) were polymorphic. Except for cultivars obtained from somatic mutations, all cultivars were easily distinguishable employing both methods. The similarity coefficient between cultivars ranged from 0.20 to 0.87 for SSR analysis and from 0.71 to 0.92 using the ISSR methodology. Dendrograms constructed using UPGMA cluster analysis revealed a phenetic classification that emphasises the existence of a narrow genetic base among the cultivars used, with the Portuguese cultivars revealing higher diversity. This study indicates that the results obtained based on the RAPD, AFLP, SSR and ISSR techniques are significantly correlated. The marker index, based on the effective multiplex ratio and expected heterozygosity, was calculated for both analyses (MI = 1.7 for SSR and MI = 8.4 for ISSR assays) and the results obtained were directly compared with previous RAPD and AFLP data from the same material. The SSR and ISSR markers were found to be useful for cultivar identification and assessment of phenetic relationships, revealing advantages, due to higher reproducibility, over other commonly employed PCR-based methods, namely RAPD and AFLP.
TL;DR: A model is presented that incorporates all of the above genomic characteristics for the determination of isolate relatedness in taxonomic, typing and evolutionary studies.
Abstract: The current literature on bacterial taxonomy, typing and evolution will be critically examined from the perspective of whole-genome structure, function and organization. The following three categories of DNA band pattern studies will be reviewed: (i) random whole-genome analysis; (ii) specific gene variation and (iii) mobile genetic elements. (i) The use of RAPD, PFGE and AFLP to analyse the whole genome will provide a skeleton of polymorphic sites with exact genomic positions as whole-genome sequence data become available. (ii) Different genes provide different levels of evolutionary information for determining isolate relatedness depending on whether they are highly variable (prone to recombination events and horizontal transfer), housekeeping genes with only a small number of single nucleotide differences between isolates or part of the rrn multigene family that is prone to intragenomic recombination and concerted evolution. Comparative analyses of these different gene classes can provide enhanced information about isolate relatedness. (iii) Mobile genetic elements such as insertion sequences, transposons, plasmids and bacteriophages integrate into the bacterial genome at specific (e.g. tRNA genes) or non-specific sites to alter band patterns produced by PFGE, RAPD or AFLP. From the literature it is not clear what level of genetic element duplication constitutes non-relatedness of isolates. A model is presented that incorporates all of the above genomic characteristics for the determination of isolate relatedness in taxonomic, typing and evolutionary studies.
TL;DR: In this paper, concordance of AFLP and RAPD markers for estimating genetic distances of 47 pepper inbred lines belonging to five varietal types was evaluated and the precision of the estimation of the genetic distance was given.
Abstract: We evaluated concordance of AFLP and RAPD markers for estimating genetic distances of 47 pepper inbred lines belonging to five varietal types. It enabled us to see the efficiency of these markers for identification, estimation of distances between varieties and variety discrimination. Genetic distance and multidimensional scaling results showed a general agreement between AFLP and RAPD markers. Based on pattern scores, dendrograms were produced by the UPGMA method. Phenetic trees based on molecular data were consistent with the classification of variety group. The precision of the estimation of the genetic distance was given. The molecular genetic distances were correlated with distances based on a set of discriminating agronomic traits measured for identification and distinctiveness tests. The relationship between molecular and morphological distances appeared to be triangular. These results and their implications in the cultivar protection purposes of pepper hybrids are discussed.
TL;DR: The DNA of this type of mobile elements is evolving faster than the DNA of other markers in this clonal lineage, and two geographical distant groups have evolved in agreement with polymorphisms based on IRAP markers anchored to at least, two different Copia-like retrotransposon sequences.
TL;DR: A molecular investigation of the plant partners' phylogeny of the Macaranga-Crematogaster system suggests multiple rather than a single evolutionary origin of myrmecophytism, at least one reversal from obligate myrmicine genus Crem atogaster to nonmyrmecoptera, and one loss of mutualistic specifity.
TL;DR: The genetic and genotypic diversity within and between four Swedish populations of the clonal shrub lingonberry, Vaccinium vitis‐idaea L, suggests that sexual reproduction has played a significant role in these populations despite low levels of seedling recruitment in present‐day populations.
Abstract: Numerous plant species reproduce mainly by clonal growth, implying that levels of genetic variation may be comparatively low. In this study we describe the genetic and genotypic diversity within and between four Swedish populations of the clonal shrub lingonberry, Vaccinium vitis-idaea L. Two approaches were used to assess the amount and partitioning of variation: automated image analysis of leaf shape and random amplified polymorphic DNA (RAPD) analysis. Morphometric analyses, using moment invariants and elliptic Fourier coefficients, revealed that most of the variation could be attributed to within-population variation. With the use of 43 polymorphic RAPD markers, we were able to identify 29 different genotypes (i.e. putative clones) among 129 plants from two populations. The genotypic diversity (D: mean 0.84) and evenness (E: mean 0.81) were higher than the average for clonal plant species. Within-population gene diversity was similar to values reported in nonclonal plants, suggesting that sexual reproduction has played a significant role in these populations despite low levels of seedling recruitment in present-day populations. An analysis of molecular variance revealed that most of the variation (89.2%) resided within populations. Comparisons between the different suites of characters indicated a congruent pattern of partitions of diversity, particularly when comparing moment invariants and RAPDs. When comparing the ability of the two descriptor suites to assign the plants to the RAPD-defined clones, elliptic Fourier coefficients yielded the best result; a classification test correctly reassigned 96.9% and 98.1% of the plant material in the two respective populations.
TL;DR: The analyses indicated that L. obtectus exhibits high levels of genetic diversity despite small population sizes and the lack of clear population differentiation suggest that this species comprises a single, genetically diverse group.
Abstract: Leucopogon obtectus Benth. is a declared rare species found in the kwongan vegetation in Western Australia. Plants on a mineral sand mine and the rehabilitation area are subject to disturbance. Genetic diversity was examined within and among all known populations using random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphisms (AFLPs) for conservation. Both molecular markers revealed a high percentage (> 89%) of polymorphic markers and a high mean genetic distance among individuals (D = 0.3). Analysis of molecular variance showed that 86.7% (RAPD) and 89.7% (AFLP) of variability was partitioned among individuals within populations. Exact tests showed no significant population differentiation. The analyses indicated that L. obtectus exhibits high levels of genetic diversity despite small population sizes. The high levels of variability among individuals and the lack of clear population differentiation suggest that this species comprises a single, genetically diverse group. Conservation and management of L. obtectus should concentrate on maintaining the high levels of genetic variability through mixing genotypes and promoting outcrossing.
TL;DR: The results indicate that current accessions from Japan and S. Korea are genetically very distinct from those from China and more similar to each other, consistent with previous research using enzymes and morphological data to classify soybean germplasm from Asia.
Abstract: Soybean [Glycine max (L.) Merr.] was domesticated in China but has a long history of cultivation on the Korean peninsula and in Japan. All three areas are considered important sources of soybean germplasm. The objectives of this study were to evaluate the genetic variation in soybean within and among China, S. Korea, and Japan by means of 120 accessions from eight Chinese and three S. Korean provinces, and three Japanese districts; and to relate genetic diversity patterns to geographical regions. Genetic relationships were estimated by 115 random amplified polymorphic DNA (RAPD) markers with simple matching coefficients expressed as Euclidean distances. Hierarchical and nonhierarchical cluster analyses as well as principal component analysis were used to define relationships among the genotypes. The results indicate that the mean genetic distance within China is much larger than that within Japan or S. Korea, but smaller than that between China and Japan or S. Korea. Cluster and principal component analyses almost completely separated the accessions from China from those of Japan and S. Korea, but could not distinguish between the accessions from Japan and S. Korea. These results are consistent with previous research using enzymes and morphological data to classify soybean germplasm from Asia. The groups formed by cluster analysis were mainly based on the frequencies of RAPD fragments among accessions and generally reflected the geographical regions of origin. No clear relationship was found between latitude and genetic diversity among accessions from these countries. Although the soybean accessions from Japan and S. Korea originally came from China, these data indicate that current accessions from Japan and S. Korea are genetically very distinct from those from China and more similar to each other.
TL;DR: The low genetic diversity among watermelon cultivars in this study empha- sizes the need to expand the genetic base of cultivated watermelon.
Abstract: Genetic diversity and relatedness were assessed among 46 American cultivars of watermelon (Citrullus lanatus var. lanatus), and 12 U.S. Plant Introduction accessions (PIs) of Citrullus sp. using 25 randomly amplified polymorphic DNA (RAPD) primers. These primers produced 288 distinct reproducible bands that could be scored with high confidence among cultivars and PIs. Based on the RAPD data, genetic similarity coeffi- cients were calculated and a dendrogram was constructed using the unweighted pair- group method with arithmetic average (UPGMA). The cultivars and C. lanatus var. lanatus PIs differentiated at the level of 92% to 99.6% and 88% to 95% genetic similarity, respectively. In contrast, the C. lanatus var. citroides, and C. colocynthis PIs were more divergent and differentiated at the level of 65% to 82.5% and 70.5% genetic similarity, respectively. The low genetic diversity among watermelon cultivars in this study empha- sizes the need to expand the genetic base of cultivated watermelon.
TL;DR: Data indicate that most of the invasive Campylobacterstrains could be differentiated from noninvasive isolates by RAPD analysis and PCR using specific primers that amplify a fragment of theiam locus.
Abstract: Campylobacter jejuni is one of the most common causes of bacterial diarrhea worldwide and is the primary bacterial cause of food-borne illness. Adherence to and invasion of epithelial cells are the most important pathogenic mechanisms of Campylobacter diarrhea. Molecular characterization of invasive and noninvasive Campylobacter isolates from children with diarrhea and symptom-free children was performed by random amplified polymorphic DNA techniques (RAPD). A distinct RAPD profile with a DNA band of 1.6 kb was observed significantly more frequently among invasive (63%) than among noninvasive (16%) Campylobacter isolates (P = 0.000005). The 1.6-kb band was named the invasion-associated marker (IAM). Using specifically designed primers, a fragment of 518 bp of the iam locus was amplified in 85% of invasive and 20% of noninvasive strains (P = 0.0000000). Molecular typing with a PCR-restriction fragment length polymorphism assay which amplified the entire iam locus showed a HindIII restriction fragment polymorphism pattern associated mainly with invasive strains. Although cluster analysis of the RAPD fingerprinting showed genetic diversity among strains, two main clusters were identified. Cluster I comprised significantly more pathogenic and invasive isolates, while cluster II grouped the majority of nonpathogenic, noninvasive isolates. These data indicate that most of the invasive Campylobacter strains could be differentiated from noninvasive isolates by RAPD analysis and PCR using specific primers that amplify a fragment of the iam locus.
TL;DR: Environmental isolates of Vibrio cholerae of eight randomly amplified polymorphic DNA (RAPD) fingerprint types from Calcutta, India, that were unusual in containing toxin-coregulated pilus or cholera toxin genes but not O1 or O139 antigens of epidemic strains were studied by PCR and sequencing to gain insights into V. Cholerae evolution.
Abstract: Environmental isolates of Vibrio cholerae of eight randomly amplified polymorphic DNA (RAPD) fingerprint types from Calcutta, India, that were unusual in containing toxin-coregulated pilus or cholera toxin genes but not O1 or O139 antigens of epidemic strains were studied by PCR and sequencing to gain insights into V. cholerae evolution. We found that each isolate contained a variant form of the VPI pathogenicity island. Distinguishing features included (i) four new alleles of tcpF (which encodes secreted virulence protein; its exact function is unknown), 20 to 70% divergent (at the protein level) from each other and canonical tcpF; (ii) a new allele of toxT (virulence regulatory gene), 36% divergent (at the protein level) in its 5' half and nearly identical in its 3' half to canonical toxT; (iii) a new tcpA (pilin) gene; and (iv) four variant forms of a regulatory sequence upstream of toxT. Also found were transpositions of an IS903-related element and function-unknown genes to sites in VPI. Cholera toxin (ctx) genes were found in isolates of two RAPD types, in each case embedded in CTXphi-like prophages. Fragments that are inferred to contain only putative repressor, replication, and integration genes were present in two other RAPD types. New possible prophage repressor and replication genes were also identified. Our results show marked genetic diversity in the virulence-associated gene clusters found in some nonepidemic V. cholerae strains, suggest that some of these genes contribute to fitness in nature, and emphasize the potential importance of interstrain gene exchange in the evolution of this species.
TL;DR: Inter-simple sequence repeat analysis was evaluated for its usefulness in generating markers to extend the genetic linkage map of Citrus using a backcross population previously mapped with restriction fragment length polymorphism, random amplified polymorphic DNA and isozyme markers.
Abstract: Inter-simple sequence repeat (ISSR) analysis was evaluated for its usefulness in generating markers to extend the genetic linkage map of Citrus using a backcross population previously mapped with restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD) and isozyme markers. ISSR markers were obtained through the simple technique of PCR followed by analysis on agarose gels, using simple sequence repeat (SSR) primers. Optimization of reaction conditions was achieved for 50% of the SSR primers screened, and the primers amplified reproducible polymorphic bands in the parents and progeny of the backcross population. Mendelian segregation of the polymorphic bands was demonstrated, with an insignificant number of skewed loci. Most of the SSR primers produced dominant loci; however co-dominance was observed with loci derived from three primers. A new genetic map was produced by combining the segregation data for the ISSR markers and data for the RFLP, RAPD and isozyme markers from the previous map and creating genetic linkages among all the markers using JoinMap 2.0 mapping software. The new map has an improved distribution of markers along the linkage groups with fewer gaps, and marker order showed partial or complete conservation in the linkage groups. The incorporation of ISSR markers into the genetic linkage map demonstrates that ISSR markers are suitable for genetic mapping in Citrus.
TL;DR: It is concluded that Foc races 0, 1B/C, 5, and 6 can be characterized by the RAPD markers.
Abstract: Ninety-nine isolates of Fusarium oxysporum f. sp. ciceris (Foc), representative of the two pathotypes (yellowing and wilt) and the eight races described (races 0, 1A, 1B/C, 2, 3, 4, 5, and 6), were used in this study. Sixty isolates were analyzed by the RAPD technique using DNA bulks for each race and 40 primers. Bands presumably specific for a DNA bulk were identified and this specificity was confirmed by further RAPD analysis of individual isolates in each DNA bulk. Primers OPI-09, OPI-18, OPF-06, OPF-10, and OPF-12 generated RAPD marker bands for races 0, 1B/C, 2, 3, 4, 5, and 6. The reliability and utility of this procedure was validated in ‘blind trials’ using 39 new Foc isolates. Ten of the 39 isolates had already been typed to race by pathogenicity tests and 29 were typed both by pathogenicity and RAPD testing in this study. In these ‘blind trials’, we assigned the 39 new isolates to a race solely on the basis of their RAPD haplotype. Thus, we concluded that Foc races 0, 1B/C, 5, and 6 can be characterized by the RAPD markers. Cluster analysis of the RAPD data set resulted in three clusters of isolates within Foc. The yellowing isolates were grouped in two distinct clusters which correspond to races 0 and 1B/C. The wilt isolates constitute a third cluster that included races 1A, 2, 3, 4, 5, and 6. These results provide a means of studying the distribution of Foc races, to assist in the early detection of introduced race(s) and to facilitate the efficient deployment of available host resistance.
TL;DR: The cluster analysis of ten hop (Humulus lupulus L.) varieties and the comparison of amplified DNA polymorphism were assessed using RAPD, STS, ISSR and AFLP molecular methods and the similarities between varieties were revealed by cluster analyses.
Abstract: The cluster analysis of ten hop (Humulus lupulus L) varieties and the comparison of amplified DNA polymorphism were assessed using RAPD, STS, ISSR and AFLP molecular methods Thirty-five RAPD primers generated an average of 134 products with 57 polymorphic products (423% of polymorphism) Ten STS primer combinations generated an average of 93 products with 66 polymorphic products (71% of polymorphism) Seven ISSR microsatellite polymorphic primers and seven primer combinations generated an average of 129 products with 42 polymorphic products (326% of polymorphism) in agarose gels and 862 products with 243 polymorphic products (283% of polymorphism) in polyacrylamide gels A total of 56 AFLP primer combinations generated an average of 91 products with 525 polymorphic products (576% of polymorphism) All molecular methods accurately distinguished all tested varieties, except for Osvald’s clones (31, 72 and 114), which were only distinguished by AFLP The similarities between varieties were revealed by cluster analyses These analyses were very similar for all molecular methods Pairwise values of JCS (Jaccard’s similarity coefficient) ranged from 002 to 10 and the mean JCS values ranged from 0395 (AFLP) to 0462 (ISSR) The highest correlation coefficient was between ISSR and RAPD (0966) and the lowest was between AFLP and STS (0867) STS had the highest correlation of chemical data with molecular methods (0592) and ISSR had the lowest (0435)
TL;DR: One hundred and forty-eight Listeria monocytogenes isolates originating from vacuum packed cold-smoked salmon produced in 10 different Danish smokehouses were compared by Random Amplified Polymorphic DNA (RAPD) profiling.
TL;DR: The lack of molecular variation in the Australian and New Zealand collection is consistent with the stepwise mutation theory of pathotype evolution from a single introduction.
Abstract: Since its initial detection in Australia in 1979, wheat yellow (stripe) rust (Puccinia striiformis f.sp. tritici) has evolved in Australia and New Zealand into more than 20 pathotypes with assorted virulence characteristics. This evolution is believed to have occurred in a stepwise fashion from an original single pathotype, with no subsequent new introductions. A combination of random amplified polymorphic DNA (RAPDs) and amplified fragment length polymorphisms (AFLPs) was used to examine the level of molecular variation in Australian and New Zealand isolates, and to compare this with variation amongst other isolates of P. striiformis. Using 60 RAPD primers on seven Australian isolates representing seven different pathotypes collected between 1979 and 1991, more than 300 potentially polymorphic loci were analysed and no polymorphisms were detected. Using the same primers on two UK isolates, 3% of loci showed a polymorphism. A similar level of polymorphism was found between UK isolates using AFLP primers, and between 5 and 15% of fragments were polymorphic between an isolate from the UK, an isolate from Denmark, and one from Colombia. However, no AFLP polymorphisms were found amongst 14 Australian and New Zealand isolates tested, at over 100 potentially polymorphic loci. The lack of molecular variation in the Australian and New Zealand collection is consistent with the stepwise mutation theory of pathotype evolution from a single introduction.
TL;DR: These maps will be a starting point for studies on the structure, evolution and function of the chestnut genome, and Identification of QTLs for adaptive traits in chestnut will be the primary target.
Abstract: A genetic linkage map of European chestnut (Castanea sativa Mill.) based on RAPD, ISSR and isozyme markers was constructed using the two-way pseudo-testcross strategy. A total of 96 individuals from a F1 full-sib family was genotyped with 381 molecular markers (311 RAPDs, 65 ISSRs, 5 isozymes). Markers in testcross configuration, segregating 1:1, were used to establish two separate maternal and paternal maps including 187 and 148 markers, respectively. The markers identified 12 linkage groups based on the haploid number of chestnut. The female and male framework maps reached a total length of 720 and 721 cM (Kosambi), respectively, representing a 76% and 68% coverage of the overall genome. A total of 46 markers, found in intercross configuration, segregating 3:1 and 1:2:1, were used to identify homologous linkage groups between parental maps; out of 12 linkage groups 11 could be joined. RAPD and ISSR markers showed a good and comparable reliability, allowing for the first time the establishment of a saturated linkage map for European chestnut. These maps will be a starting point for studies on the structure, evolution and function of the chestnut genome. Identification of QTLs for adaptive traits in chestnut will be the primary target.
TL;DR: A linkage map of eggplant using an F2 population derived from a cross between a breeding line, EPL-1 and an introduced line, WCGR112-8, from India, which shows contrasting responses to several pathogens and differences in several morphological traits is constructed.
Abstract: We have constructed a linkage map of eggplant (Solanum melongena L.) using an F2 population derived from a cross between a breeding line, EPL-1 and an introduced line, WCGR112-8, from India. The two parental lines showed contrasting responses to several pathogens and differences in several morphological traits. Parental lines were screened with 1, 232 random primers for RAPD and 64 primer combinations for AFLP. The link-age map consisted of 181 loci, comprising 88 RAPD and 93 AFLP markers. These markers identified 21 linkage groups spanning 779.2cM with an average distance of 4.9cM. The linkage groups ranged from 1.9 to 95.6cM in length and included 2 to 32 markers, respectively. The fruit shape and color development trait were scored and the linkage to the markers was investigated. The fruit shape showed a significant association with markers on linkage group 2. Color development in fruit, stem and calyx showed a significant association with markers on linkage group 7. These markers may provide valuable information for eggplant breeding.