scholarly journals Genetic Relatedness among Dendrobium (Orchidaceae) Species and Hybrids Using Morphological and AFLP Markers

HortScience ◽  
2014 ◽  
Vol 49 (5) ◽  
pp. 524-530
Author(s):  
Lydia E. Wahba ◽  
Nor Hazlina ◽  
A. Fadelah ◽  
Wickneswari Ratnam
Keyword(s):  
Genetic Relatedness ◽  
Morphological Characters ◽  
Similarity Coefficient ◽  
Aflp Analysis ◽  
Jaccard Similarity ◽  
Aflp Data ◽  
Data Set ◽  
Combined Analysis ◽  
Jaccard Similarity Coefficient ◽  
Combined Data

Dendrobium is one of the largest genera in the Orchidaceae family. Information on the genetic diversity and relationships among species and hybrids is important for breeding purposes and species conservation. The objectives of this study were to assess genetic relatedness and to determine whether morphological, molecular, or combined analysis can discriminate among Dendrobium species, commercial hybrids, and interspecific hybrids. A total of 81 Dendrobium accessions were characterized with 12 amplified fragment length polymorphism (AFLP) primer pairs and 21 morphological characters. Mean genetic relatedness for morphological characters, AFLP analysis, and combined analysis were 0.61, 0.37, and 0.43, respectively. Dendrograms were generated using an unweighted pair group method with arithmetic averages (UPGMA); the analysis was performed on a Jaccard similarity coefficient matrix. The data from morphological characters revealed that the Jaccard similarity coefficient ranged from 0.20 to 1.0, where the tested 81 Dendrobium accessions could be grouped into four clusters. For the AFLP analysis, the number of polymorphic fragments for each primer varied from 80 to 284 with 78% average percentage of polymorphic loci and the similarity coefficient ranging from 0.125 to 1.0 with Dendrobium accessions grouped into three clusters. The similarity coefficients estimated through a combined analysis of morphological and AFLP data ranged from 0.21 to 1.0 and the Dendrobium accessions appeared clustered into two groups. The results revealed some similarities among the three data sets. The combined data set was the most useful in discriminating Dendrobium accessions based on species sections and relationship among species and their hybrids. The correlation between the AFLP data and the combined data was highly significant (r = 0.98, P > 0.001), indicating the usefulness of AFLP data for species discrimination and hybrid identity in the absence of floral morphological characters.

A new genus and a major temperate bamboo lineage of the Arundinarieae (Poaceae: Bambusoideae) from Sri Lanka based on a multi-locus plastid phylogeny 

Phytotaxa ◽  
2014 ◽  
Vol 174 (4) ◽  
pp. 187 ◽  
Author(s):  
Lakshmi Attigala ◽  
Jimmy K. Triplett ◽  
Hashendra-Suvini Kathriarachchi ◽  
Lynn G Clark
Keyword(s):  
Sri Lanka ◽  
Sequence Data ◽  
Alternative Hypothesis ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Sri Lankan ◽  
Data Set ◽  
Woody Bamboos ◽  
Cpdna Markers ◽  
Combined Data

Kuruna, a new temperate woody bamboo (Poaceae, Bambusoideae, Arundinarieae) genus from Sri Lanka, is recognized based on chloroplast sequence data from five markers (coding: ndhF 3’ end; non-coding: rps16-trnQ, trnC-rpoB, trnD-trnT, trnT-trnL). This genus represents the twelfth major lineage of temperate woody bamboos and is characterized by pachymorph culm bases with short necks, unicaespitose clumps, culm leaf girdles ca. 1 mm wide, usually abaxially hispid culm leaves with non-irritating hairs, persistent foliage leaf sheaths, complete branch sheathing and acute to biapiculate palea apices. Maximum Parsimony, Bayesian Inference and Maximum Likelihood analyses of a combined data set consistently strongly supported the monophyly of this Sri Lankan temperate woody bamboo clade. Although the Kishino-Hasegawa test is unable to reject the alternative hypothesis of monophyly of the Sri Lankan clade plus Bergbambos tessellata from South Africa, Kuruna and Bergbambos are distinguishable by a combination of morphological characters. A few additional cpDNA markers not previously used in phylogenetic analyses of Arundinarieae were tested to evaluate their utility in this taxonomically difficult tribe.

scholarly journals AFLP MARKER IN GENETIC DIVERSITYASSESSMENT OF FIG (Ficus carica L.) POPULATIONS IN KURDISTAN REGION – IRAQ.

2021 ◽  
Vol 52 (4) ◽  
pp. 859-867
Author(s):  
Hussein & Jubrael
Keyword(s):  
Genetic Similarity ◽  
Genetic Relatedness ◽  
Aflp Marker ◽  
Genetic Distances ◽  
Similarity Coefficient ◽  
Kurdistan Region ◽  
Aflp Data ◽  
Different Populations ◽  
Cultivar Improvement ◽  
Similarity Matrices

In this study, the genetic relatedness of 12 cultivars of fig from different populations in Kurdistan region- Iraq were analyzed using eleven AFLP primers pairs combinations by using the technology of molecular analysis the DNA. Genetic similarity matrices were produced for the AFLP data to calculate genetic distances among their cultivars. Genetic similarity coefficient ranged from 0.1261 to 0.3905. The lowest genetic similarity was observed between Kola and Gala Zard (0.1261). The Hejeera Rash and Shela cultivars were most similar ones with a coefficient of 0.3905. Clustering based on AFLP data for the 12 fig cultivars was identified at the 0.32 similarity level. In the developed dendogram two main groups were found, the first one combined Ketek and Shela together, while the second group contained two sub group Shingaly and Benatty combined together, while in the other sub group cluster three other sub-group were identified. The results of this study may help in the formulation of appropriate strategies for conservation and cultivar improvement in figs, for which limited knowledge of the genetic diversity is available.

scholarly journals ANALYSIS WINNOWING ALGORITHM FOR TEXT PLAGIARISM DETECTION USING THREE METHOD SIMILARITY

2021 ◽  
Vol 2 (2) ◽  
pp. 42
Author(s):  
Luke Michael Febriansyah ◽  
Shinta Estri Wahyuningrum
Keyword(s):  
Detection Algorithm ◽  
Similarity Coefficient ◽  
Dice Similarity Coefficient ◽  
Plagiarism Detection ◽  
Jaccard Similarity ◽  
Jaccard Similarity Coefficient ◽  
Percentage Similarity ◽  
Check Algorithm

Cases of plagiarism in recent years has been an issues. Based on that issues, this research will create a system to detect similarity in a text. There is an aspect as reference of the research that is analyze the plagiarism algorithm. This research will analyze the accuracy one of plagiarism check algorithm, winnowing algorithm. Winnowing algorithm is a plagiarism detection algorithm based on document fingerprinting. To calculate percentage similarity of document fingerprinting in text, there are 3 methods to measure similarity that will be used in this research, which is jaccard similarity coefficient, sorensen dice similarity coefficient, and berg similarity coefficient.

scholarly journals Diversity in Cucumber Genotypes Based on Morphological Traits and SSR Molecular Markers

2017 ◽  
Vol 14 (2) ◽  
pp. 775-782 ◽  
Author(s):  
Sobhan Normohamadi ◽  
Mahmood Solouki ◽  
Forouzan Heidari
Keyword(s):  
Cluster Analysis ◽  
Ssr Markers ◽  
Genetic Similarity ◽  
Morphological Traits ◽  
Polymorphic Information Content ◽  
Germplasm Collection ◽  
Similarity Coefficient ◽  
Jaccard Similarity ◽  
Jaccard Similarity Coefficient ◽  
High Diversity

ABSTRACT: Biodiversity is one of the most important factors in the survival and improvement of any species. Therefore, germplasm collection is the first step for plant improvement. To investigate their genetic and morphological relationships, 10 morphological traits of 20 genotypes of local cucumbers were evaluated using 9 SSR primers. A high genetic variability was observed for the number of flowers per plant. The values of the Jaccard similarity coefficient ranged between 0.51 and 0.92, indicating a high diversity of the genotypes. To evaluate the genetic similarity among genotypes, a cluster analysis using the UPGMA method was performed based on the Jaccard similarity coefficient. The average genetic distance between genotypes (using the Jaccard similarity coefficient) was 0.74 and the mean polymorphic information content (PIC) was 0.69. The primer SSR13251 had the highest PIC (0.8). The clustering pattern of the SSR markers did not coincide with the groupings based on quantitative traits. A dendrogram of the cluster analysis of molecular data showed a high diversity among the studied genotypes. The highest genetic similarity was between genotypes 2 and 3 (0.94), and the lowest genetic similarity was between genotypes 6 and 12 (0.51). The results suggest that SSR markers are a suitable tool to study the genetic diversity and relationships among different genotypes in cucumber.

scholarly journals AFLP Analysis of Genetic Relationships among Container-grown Anthurium Cultivars

HortScience ◽  
2004 ◽  
Vol 39 (4) ◽  
pp. 861C-861 ◽  
Author(s):  
Pachanoor S. Devanand ◽  
C. Thomas Chao* ◽  
Jianjn Chen ◽  
Richard J. Henny
Keyword(s):  
Near Infrared ◽  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Group Method ◽  
Aflp Analysis ◽  
Limited Information ◽  
Cut Flowers ◽  
Similarity Coefficients ◽  
Jaccard Similarity ◽  
Pair Group

Anthurium is the largest genus in the family Araceae, consisting of about 1000 species. Anthuriums are valued for their colorful spathes and traditionally used as cut flowers. With the introduction of compact cultivars through breeding, a series of container-grown cultivars have been released and widely produced as flowering foliage plants. However, limited information is available about genetic relatedness among these container-grown cultivars. This study analyzed genetic relationships of 58 cultivars using amplified fragment length polymorphism (AFLP) markers with near infrared fluorescence labeled primers. Forty-eight EcoR I + 2/Mse I + 3 primer set combinations were screened from which six primer sets were selected and used in this investigation. Each selected primer set generated 94 to 115 scorable fragments. A total of 647 AFLP fragments were detected of which 401 were polymorphic (67%). All cultivars were clearly differentiated by their AFLP finger-prints. A dendrogram was constructed using the unweighted pair-group method of arithmetic averages (UPGMA) technique and a principal coordinated analysis (PCA) was used to analyze the relationships. The 58 cultivars were divided into three clusters; clusters I, II, and III had 40, 10, and 8 cultivars, respectively. Most commonly grown cultivars were positioned in cluster I, where had Jaccard similarity coefficients among them ranged from 0.7 to 0.98. Eighteen of the 40 shared Jaccard similarity coefficient of 0.8 or higher, indicating that genetic diversity for cultivated container-grown Anthurium is needed.

scholarly journals Analysis of genetic diversity of sugar beet genotypes using random amplified polymorphic DNA marker

Genetika ◽  
2014 ◽  
Vol 46 (3) ◽  
pp. 975-984 ◽  
Author(s):  
Ali Ghasemi ◽  
Ahmad Golparvar ◽  
Mehdi Isfahani
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Sugar Beet ◽  
Plant Breeding ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Coefficient ◽  
Jaccard Similarity ◽  
Jaccard Similarity Coefficient ◽  
Plant Breeding Program ◽  
Efficiency Of Selection

Plant breeding programs are formulated based on the diversity and selection of superior quantitative and qualitative traits. Hence, assessment of genetic diversity is the first step of every plant breeding program. In this regard, use of new methods for studying genetic diversity seems necessary. In the present study, the genetic diversity of thirty sugar beet genotypes was determined using Random Amplified Polymorphic DNA (RAPD) marker. Following the DNA extraction and optimization of experiment conditions, of the 40 primers under study, 10 primers that induced polymorphism and produced good and clear bands in the genotypes of sugar beet were randomly selected. Statistical calculations were carried out based on the Jaccard similarity coefficient and UPGMA-based grouping in the NTSYS software (version 2.02). The amplitude of the multiplied bands varied between 100 and 3000 of alkaline pair. The polymorphism of all primers was 82.33% within the similarity limit. The Cophenetic coefficient for the similarity matrix and the resulting curve was obtained to be r=0.75. Genotypes 4 and 18 with a similarity coefficient of 0.91% demonstrated the highest similarity while genotypes 21 and 15 with a similarity coefficient of 0.63% showed the lowest similarity. Of the primers in use, the OPB-18 primer produced 12 bands (the highest number of bands) and the OPA-09 primer produced 5 bands (the lowest number of bands). Cluster analysis also confirmed the results obtained from the profiles produced in the genetic differentiation of cultivars under study as well as the correlations resulting from the Jaccard similarity coefficient. Finally, genotypes were categorized into 13 groups based on the results and resulting dendrogram. Results of the cluster analysis performed using the Jaccard similarity coefficient revealed the genetic diversity among genotypes that emphasize on efficiency of selection in sugar beet genotypes.

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