Showing papers on "Dendrogram published in 2002"

Genetic relationships of sesame germplasm collection as revealed by inter‐simple sequence repeats

Abstract: Inter-simple sequence repeats (ISSR) polymorphism was used to determine genetic relationships among 75 Sesamum indicum L. accessions of Korean and exotic sesame. Fourteen reliable ISSR primers were selected for the assessment of genetic diversity, yielding 79 amplification products. Of these polymerase chain reaction products, 33% revealed polymorphism among the 75 accessions. Genetic distances ranged from 0 to 0.255, with a mean genetic distance of 0.0687. The 75 accessions were divided into seven groups on the basis of unweighted pair-group method with arithmetic averages (UPGMA) cluster analysis. The largest group consisted of 25 Korean cultivars, eight Korean breeding lines and 17 world-wide accessions. The other groups included 25 accessions, several of which contained useful traits. The dendrogram did not indicate any clear division among sesame accessions based on their geographical origin. However, all Korean sesame cultivars except ‘Namsankkae’ were clustered in the same group, indicating a narrow gene pool. Some of the Korean breeding lines were spread along the dendrogram, showing enlargement of genetic diversity. The genetic diversity data uncovered in this study can be used in future breeding programmes.

Assessment of genetic diversity among wheat ( Triticum aestivum L.) cultivars from a range of localities across Pakistan using random amplified polymorphic DNA (RAPD) analysis

Abstract: Genetic diversity among 20 wheat genotypes/cultivars from diverse locations of Pakistan was studied using random amplified polymorphic DNA (RAPD) analysis. A total of 445 DNA fragments were amplified with50 random decamer primers 64.38% of which were polymorphic. Genetic similarity matrix based on Nei & Li's (1979) index detected coefficients ranging from 75.60% to 92.74%. These coefficients were used to construct a dendrogram using unweighted pair group of arithmetic means (UPGMA). The wheat genotypes were clustered into one major group (A) and two small groups (B and C). The most distant genotype in the dendrogram was PARC-1 that was 75.60% to 84.94% genetically similar with the other genotypes and clustered with PARC-3 which formed a group distantly related with the other clusters. Moreover, most of the wheat genotypes developed from the same breeding centre clustered in one group. It has been clearly shown that most of the cultivars except PARC-1possessed narrow genetic background. The information would be helpful for future genome mapping programs as well as for the application of intellectual breeder rights in the country. The study will also work as indicator for wheat breeders to evolve varieties with diverse genetic background to achieve sustainability in wheat production in the country.

Combining Hierarchical Clustering and Self-Organizing Maps for Exploratory Analysis of Gene Expression Patterns

Abstract: Self-organizing maps (SOM) constitute an alternative to classical clustering methods because of its linear run times and superior performance to deal with noisy data. Nevertheless, the clustering obtained with SOM is dependent on the relative sizes of the clusters. Here, we show how the combination of SOM with hierarchical clustering methods constitutes an excellent tool for exploratory analysis of massive data like DNA microarray expression patterns. Keywords: DNA array, gene expression patterns, hierarchical clustering, SOM, SOTA

DNA fingerprinting of jute germplasm by RAPD.

Abstract: The genotype characteristic of cultivars was investigated, along with varieties of both of the jute species, Corchorus olitorius and Corchorus capsularis, in the germplasm collection at the Bangladesh Jute Research Institute (BJRI) DNA fingerprinting was generated for 9 different varieties and 12 accessions of jute cultivars by using random amplified polymorphic DNA (RAPD) A total of 29 arbitrary oligonucleotide primers were screened Seven primers gave polymorphism within the varieties, and 6 primers detected polymorphism within the accessions that were tested A dendrogram was engendered from these data, and this gave a distinct clustering of the cultivated species of jute Therefore, we generated RAPD markers, which are species-specific These primers can distinguish between C olitorius and C capsularis From the dendrogram that we generated between the various members of these two species, we found the existing genetic classification that agrees with our molecular marking data A different dendrogram showed that jute accessions could be clustered into three groups These data will be invaluable in the conservation and utilization of the genetic pool in the germplasm collection

Evaluation of ribosomal RNA gene restriction patterns for the classification of Bacillus species and related genera

Abstract: Aims: To identify Bacillus species and related genera by fingerprinting based on ribosomal RNA gene restriction patterns; to compare ribosomal RNA gene restriction patterns-based phylogenetic trees with trees based on 16S rRNA gene sequences; to evaluate the usefulness of ribosomal RNA gene restriction patterns as a taxonomic tool for the classification of Bacillus species and related genera. Methods and Results: Seventy-eight bacterial species which include 42 Bacillus species, 31 species from five newly created Bacillus-related genera, and five species from five phenotypically related genera were tested. A total of 77 distinct 16S rRNA gene hybridization banding patterns were obtained. The dendrogram resulting from UPGMA analysis showed three distinct main genetic clusters at the 75% banding pattern similarity. A total of 77 distinct 23S and 5S rRNA genes hybridization banding patterns were obtained, and the dendrogram showed four distinct genetic clusters at the 75% banding pattern similarity. A third dendrogram was constructed using a combination of the data from the 16S rRNA gene fingerprinting and the 23S and 5S rRNA genes fingerprinting. It revealed three distinct main phylogenetic clusters at the 75% banding pattern similarity. Conclusions: The Bacillus species along with the species from related genera were identified successfully and differentiated by ribosomal RNA gene restriction patterns, and most were distributed with no apparent order in various clusters on each of the three dendrograms. Significance and Impact of the Study: Our data indicate that ribosomal RNA gene restriction patterns can be used to reconstruct the phylogeny of the Bacillus species and derived-genera that approximates, but does not duplicate, phylogenies based on 16S rRNA gene sequences.

Hierarchical model-based clustering of large datasets through fractionation and refractionation

Abstract: The goal of clustering is to identify distinct groups in a dataset. Compared to non-parametric clustering methods like complete linkage, hierarchical model-based clustering has the advantage of offering a way to estimate the number of groups present in the data. However, its computational cost is quadratic in the number of items to be clustered, and it is therefore not applicable to large problems. We review an idea called Fractionation, originally conceived by Cutting, Karger, Pedersen and Tukey for non-parametric hierarchical clustering of large datasets, and describe an adaptation of Fractionation to model-based clustering. A further extension, called Refractionation, leads to a procedure that can be successful even in the difficult situation where there are large numbers of small groups.

Genetic diversity amongst landraces of rye (Secale cereale l.) from northern Europe

Abstract: Genetic variation and diversity were estimated for three improved varieties and 18 landraces of Secale cereale, originating from the northern Europe. This material was compared with eight improved varieties and 16 landraces from Sweden, which were analysed before. The analysis used starch gel electrophoresis with the enzymes ACO, GPI, MDH, PGD and PGM and resulted in one fixed locus and seven polymorphic loci. Most of the genetic diversity was found within the accessions and it was very small between accessions. The results show that the landraces from Germany and Norway have a low genetic variation compared to the other landraces in this study. This can possibly be explained with a small original sample size of some accessions. However, in the dendrogram these accessions are well separated. The landraces from Sweden and Finland showed a high genetic variation, which is almost the same for all these accessions. In the dendrogram all of the Finnish landraces and 11 of the Swedish ones were grouped together with a very small diversity index; they can almost be considered as part of the same accession. This is probably due to the fact that a high number of Finnish immigrants arrived in Sweden during the 17th century bringing their own rye material. The early Finnish rye landraces may have the same original source. The data also show that landraces as well as improved varieties have a high heterozygosity but they are separated in the dendrogram into different clusters. The currently used varieties show a large genetic distance variation, different from that in the landraces.

Genetic Relationship among Exotic Soybean Introductions in Thailand: Consequence for Varietal Registration

Abstract: This research was designed to identify forty-eight exotic germplasm lines that were genetically and geographically distinct from the existing Thai soybean lines. Using 11 morphological descriptors, all genotypes were classified according to 37 morphological markers which allowed fully discrimination of the cultivars. Similarity indices between cultivars were calculated from 37 binary character states using Dice coefficient, which varied from 0.0 to 0.92 with an average of 0.449. The UPGMA cluster analysis revealed two groups, one formed by 32 cultivars and the other by the remaining 16 cultivars. DNA samples from forty-eight exotic soybean cultivars was examined to determine the efficiency of randomly amplified polymorphic DNA (RAPD) markers in identifying cultivars and determining level of genetic similarity. Out of 80 random primers, 37 generated highly reproducible polymorphic RAPD fragments. With these primers, 274 clear-cut RAPD markers were produced and only 85 (31%) were polymorphic, which indicated that high level of genetic similarities existed in these exotic cultivars. One to six alleles per primer were detected with a polymorphic information content varying from 0.04 to 0.50. The use of only 14 RAPD markers amplified from five primers was sufficient to identify uniquely all the cultivars, indicating that RAPD markers are efficient for use in genetic fingerprinting in soybean. Genetic similarities of 85 RAPD profiles were estimated via the DICE coefficient and then the data were processed using UPGMA clustering method. Each genotype was clearly identified and separated from the others. RAPD based dendrogram revealed that the 48 cultivars could be classified into four groups at 0.57 similarity scale, between which the similarity coefficient was as low as 0.51, even though the cultivars are morphologically or geographically very close. The Principal Component Analysis (PCA) yielded rather similar results to the UPGMA dendrogram. RAPD genetic similarity coefficients were correlated with morphological similarity coefficients (r = 0.241). Comparing agronomic performance and RAPD analysis via dendrogram, a total of 11 cultivars were ear-marked for crossing program. These genotypes can be useful to soybean breeders in Thailand who want to utilize genetically diverse introductions in soybean improvement.

Assessment of coconut tree genetic divergence by compound sample RAPD marker analysis

Abstract: The coconut tree (Cocos nucifera L.) is a tropical species widely cultivated throughout the world, which is found in all intertropical regions. The species shows wide phenotypic variability, which, however, is little understood at the genetic level. This study of the variability among the various coconut tree populations is important to increase the efficiency of the development of superior cultivars adapted to different ecological conditions. It also helps the selection of divergent progenies that can maximize heterosis in hybridizations. Genetic divergence among 19 coconut tree populations available in the BAG - Coco at EMBRAPA/CPATC was estimated by RAPD. Leaf samples from 21 plants of each cultivar were squashed together (compound samples) in liquid nitrogen and the DNA extracted using the modified Doyle and Doyle (1990) protocol. Samples of these DNA were amplified with 24 primers of the OPERON Technologies series. One hundred and twenty-seven polymorphic and 61 monomorphic loci were obtained. Six different clusters, possibly heterotic groups, were formed by the Tocher optimized clustering analysis which used the matrix of the complement of the Jaccard index. Group 1 included the dwarf group cultivars. Giant accessions, abbreviated to GBR (Brazilian Giant), formed group 2, except GBRPF, which together with West African Giant (GOA) formed group 4. The most distant accession was the Tonga Giant cultivar (GTG) that did not group with the others and presents potential for hybridization with the six cultivars in the dwarf group cultivars and with the five in the GBR group. Group 3 consisted of GRL, GPY and GRT and Group 5 of GML and GVT. The dendrogram obtained by the nearest neighbor method was in line with the clustering obtained by the Tocher optimization method. The markers used permitted identification of each one of the populations showing that they were genetically different (absence of duplicity). The use of compound samples was effective to investigate the interpopulational genetic diversity. However, to understand the intrapopulation genetic variability, individual sampling should be used.

Genetic variation analysis in the genus Lathyrus using RAPD markers

Abstract: RAPD analysis was applied to five species belonging to the genusLathyrus (Fabaceae): L.sativus, L.cicera, L.ochrus, L.sylvestris and L.latifolius. All the species under study belong to thesection Lathyrus except L.ochrus which is in section Clymenum.Nine populations representing these species were used and ten random10-mer primers were sampled. A total of 129 amplification products,ranging in size from 0.3 to 3 Kb, were generated. Partitioning ofvariation was studied using the AMOVA technique. The genetic variation proved tobe nearly equally distributed among species and among populations withinspecies. A similar approach was carried out to distinguish populations, whichproved to be efficient. The between population dissimilarities were calculatedand a dendrogram of genetic relationships was drawn. The RAPDs obtained weresufficient to distinguish between the two accessions of a species and toseparate these accessions by clustering them according to species. A highgenetic similarity between the populations of L.sylvestris and L.latifolius was established. A similar result is also shownfor the populations of L. sativus andL. cicera.

Regression Tree Cartography

Abstract: We illustrate several types of cartographic displays that can enhance understanding from hierarchical analysis techniques such as regression trees. When the observations have spatial locations, maps of the predicted values, maps of the residuals, and maps of the predicting relationships of the tree may help to reveal associations between predictors and response. We propose an objective method for constructing maps that may help to show the geographical similarities and differences between observations based on their positions in the prediction tree. This mapping method divides the color spectrum to assign colors to the leaves, using the same hierarchical pattern as the prediction tree does to divide the data. We illustrate regression tree cartography with two examples and suggest how the prediction tree mapping method could be used for classification trees and for dendrograms produced by hierarchical clustering methods.

Seed proteins as genetic markers in the study of phylogenetic relations in pepper

Abstract: On the basis SDS - PAGE electrophoresis of eight genotypes, which belong to different varieties of pepper (Capsicum annuum L.), was found that the seed protein profile could be useful in the study of phylogenetic relationships. The analysis of soluble seed proteins showed that all studied genotypes had a specific protein pattern. Based on obtained electrophorograms the indices of similarity were calculated. The dendrogram was constructed using an unweighted pair - group method with arithmetical averages (UPGMA) and computer program NTSYS - pe. The distinctness of genotypes, within different varieties and also within the same variety, has been confirmed. The clustering of investigated genotypes on dendrogram is not complete according to the classifications within Capsicum annuum L., which were done on the basis morphological traits. The highest values of the index of similarity was calculated for the genotypes KP068 (C. annum var. chipca) and KP075 (C. annuum var. chipca), while the lowest values were obtained for the genotypes KP005 (C. annuum var. grossum) and KP049 (C. annuum var. longum). Considering the importance of proper systematisation for successful work on pepper breeding, the results of this investigation could be useful as an attempt to clarify taxonomy, origin and phylogenetic affinities within Capsicum annuum L.

Dendrogram display method

Abstract: PROBLEM TO BE SOLVED: To provide a method for comparing dendrograms based on different standards/technique. SOLUTION: Separate dendrograms 201, 202 are displayed on one picture by overlapping them at a state that they are distinguished. In this case, overlap of parts to display trees are displayed by shifting them in up, down, left and right and different display colors are used for the respective dendrograms. In addition, difference of integration of the respective elements between the overlapped dendrograms is made possible to be easily determined by highlighting a specified branch and the elements to be hung down from it, etc.

COMPARATIVE ANALYSIS OF NUMERICAL TAXONOMY AND 16S rDNA PCR-RFLP OF FAST-GROWING RHIZOBIA ISOLATED FROM WESTERN CHINA

Abstract: strains of fast-growing rhizobia isolated from Chinas western (mainly from Qinghai province),and 4 representative strains were compared by performing numerical taxonomy. 132 phenotypic characteristics were analyzed. The results of numerical taxonomy constructed a dendrogram. It shows that all the strains examined clustered into five phena at a similarity level of 79%. 16S rDNA PCR-RFLP were applied to 57 rhizobial strains (among the 61 strains) and 10 reference strains. The 16S rDNA-RFLP analysis described 20 different genotypic characteristics and form one dendrogram. For some large groups, the results of 16S rDNA-RFLP were agreement with that of numerical analysis of phenotypic characteristics.

Trees, dendrograms and sensitivity

Abstract: Dendrograms and minimum-weight spanning trees (MWST) are discrete structures which arise in clustering theory, networks, and where strategic choices are made between discrete options. The discrete structure of the solution tree varies discontinuously with respect to changes in the dissimilarity or cost matrix. Tarjan [1982] has obtained bounds on the changes to the elements of the cost matrix, where the structure is not altered. These results are extended to describe the sensitivity of the tree structure with respect to changes in the cost matrix. The sensitivity of the structure to the addition of a node and arcs is solved using potential loops in the tree. This phase of the solution process builds onto the solution to the original MWST. The full sensitivity analysis of a dendrogram to changes in the attribute matrix is very complex, due partly to the corresponding cost matrix being a function of the full attribute matrix. Statistical methods are used to compare changes in the tree structure with changes in the attribute matrix. Analytical results are obviously difficult to obtain. The Kruskal clustering algorithm is used on the similarity or cost matrix to construct both the MWST and the dendrogram. Thus the sensitivity of the dendrogram to the similarity or cost matrix corresponds to the sensitivity of the MWST for this method of clustering.

The genetic diversity of barley cultivars from the Baltic States and Belarus, as determined by RAMPs.

Abstract: A Random Amplified Microsatellite Polymorphism (RAMP) analysis was carried out on 30 barley cultivars from the Baltic states and Belarus. Seven primer combinations produced 60 polymorphic DNA fragments ranging in size from 54 b to 400 b. A Genetic Distance coefficient (GDxy) matrix was generated and a dendrogram constructed using cluster analysis of the unweighted pair-group method of arithmetic averages (UPGMA). The genetic distance between cultivars ranged from 0.067 to 0.714. The results were compared with available pedigree information. The dendrogram did not indicate any clear pattern of division among the barley cultivars based on geographic origin.

Development of Clustering and Leaf Ordering Tool for Gene Expression Profiles

Abstract: The hierarchical clustering algorithm is widely used for analysis of gene expression profiles. The output of the hierarchical clustering algorithms is a dendrogram, whose topology is a binary tree with the leaves corresponding to genes. A leaf ordering is a post-processing of the hierarchical clustering, which rearranges the leaves of a binary tree, while preserving its topology, so that genes with similar expression profiles get close in a new arrangement while those with dissimilar profiles part far. Most leaf ordering algorithms are designed for all leaf nodes at once [1, 2, 3]. In this paper, we first propose an approach that applies several leaf-ordering algorithms to each cluster and, then present a new tool that is an implementation of hierarchical clustering and leaf ordering algorithm including our proposed approach.