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 Characterization of Ugandan Sweetpotato Germplasm Using Fluorescent Labeled Simple Sequence Repeat Markers

HortScience ◽  
2010 ◽  
Vol 45 (2) ◽  
pp. 225-230 ◽  
Author(s):  
Benard Yada ◽  
Phinehas Tukamuhabwa ◽  
Bramwell Wanjala ◽  
Dong-Jin Kim ◽  
Robert A. Skilton ◽  
...  
Keyword(s):  
Cluster Analysis ◽  
Genetic Distance ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Ipomoea Batatas ◽  
Polymorphic Information Content ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Sequence Repeat ◽  
Simple Sequence

The genetic relationships among 192 superior, high–yielding, and disease-resistant sweetpotato [Ipomoea batatas (L.) Lam] accessions from the Ugandan germplasm collection were analyzed using 10 fluorescent labeled simple sequence repeat (SSR) markers. Relatedness among the genotypes was estimated using the Nei and Li genetic distance coefficient, cluster analysis and principle component analysis methods of NTSYS-pc software. The polymorphic information content of the SSR markers used in this study ranged from 0.23 to 0.76 for loci IB-S07 and IB-R12, respectively, with a mean value of 0.62. The number of polymorphic alleles detected per locus ranged from two to six with a mean of four, a confirmation of the effectiveness of microsatellite detection on an automated ABI 3730 sequencer. The mean pairwise genetic distance among the 192 genotypes was 0.57, an indication of moderately high genetic diversity. Cluster analysis divided the accessions into four major groups with no relationship to the district of origin. Two sets of duplicates were identified through SSR genotyping in this study. Up to 190 distinct accessions for use as potential parental genotypes in hybridization schemes for cultivar development in the region were identified.

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.

scholarly journals EVALUATION OF GENETIC DIVERSITY IN CACAO COLLECTED FROM KOLAKA, SOUTHEAST SULAWESI, USING SSR MARKERS

2016 ◽  
Vol 16 (2) ◽  
pp. 71
Author(s):  
Rubiyo Rubiyo ◽  
Nur Kholilatul Izzah ◽  
Indah Sulistiyorini ◽  
Cici Tresniawati
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gel Electrophoresis ◽  
Genetic Similarity ◽  
Similarity Coefficient ◽  
Breeding Program ◽  
New Variety ◽  
Average Value ◽  
The Third ◽  
Ctab Method

Kolaka, which is located in Southeast Sulawesi, has long been known as one of cacao production centers in Indonesia. Therefore, many different cacao germplasms can be found in this region. The study aimed to evaluate genetic diversity and relationships of 12 cacao genotypes collected from Kolaka. Genomic DNA was extracted by using a modified CTAB method. Meanwhile, genetic diversity was analyzed based on 16 SSR markers, which then separated by 6% non-denaturing polyacryl-amide gel electrophoresis. The result showed that all of those markers, 14 markers exhibited polymorphism and subsequently used for data analysis using NTSYS and PowerMarker program. About 70 different alleles were generated from 12 cacao genotypes analyzed with an average of 5 alleles per locus. Average value of polymorphism information content (PIC) resulted in this study was 0.59. The cluster analysis using UPGMA method based on the genetic similarity coefficient revealed that all cacao genotypes were separated into three major groups. The first group consisted of five cacao genotypes, the second one held four cacao genotypes, whereas the third group contained three genotypes. This result indicates that three genotypes that clustered separately from the others could be used as a good clonal candidate for cacao breeding program. The information resulted from this present study would be useful for future cacao breeding program, especially in efforts to release a new variety.

scholarly journals Genetic Diversity of Vitis davidii Accessions Revealed Using Microsatellite and Sequence-related Amplified Polymorphism Markers

HortScience ◽  
2018 ◽  
Vol 53 (3) ◽  
pp. 283-287
Author(s):  
Xiu Cai Fan ◽  
Hai Sheng Sun ◽  
Ying Zhang ◽  
Jian Fu Jiang ◽  
Min Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Similarity ◽  
Similarity Coefficient ◽  
Srap Markers ◽  
Average Percentage ◽  
Allele Number ◽  
Ssr Primers ◽  
Vitis Davidii ◽  
Simple Sequence

In this study, simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) markers were used to analyze the genetic diversity of 48 wild Vitis davidii accessions. A total of 78 distinct alleles were amplified by 11 SSR primers, and the average allele number was 8.8. The average observed heterozygosity (Ho) and expected heterozygosity (He) values were 0.785 and 0.814, respectively. The effective allele numbers ranged from 3.92 to 9.61. The average polymorphism information content (PIC) was 0.798. Twelve of 169 SRAP primer combinations were selected for SRAP analysis. A total of 188 bands were produced, and the average was 15.7 bands per primer combination; the average percentage of polymorphic bands was 84.0%. The average PIC was 0.76. The results of the clustering analysis based on SSR markers showed that the 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient level of 0.68. The dendrogram obtained from the SRAP data showed that 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient of 0.72. SSR and SRAP markers differentiated all accessions studied including those with a similar pedigree. We speculated on the origin of Ciputao 0941♀, Ciputao 0940♂, and Fu’an-ci-01 using SSR markers and used both SSR and SRAP markers to resolve homonymy. The result will be valuable for further management and protection of V. davidii germplasm resources.

scholarly journals Application of the ISSR method to estimate the genetic similarity of Dasypyrum villosum (L.) P. Candargy Greek populations to Triticum and Secale species

2011 ◽  
Vol 21 (1) ◽  
pp. 7-12
Author(s):  
Agnieszka Grądzielewska
Keyword(s):  
Information Content ◽  
Genetic Similarity ◽  
Polymorphic Information Content ◽  
Similarity Index ◽  
Issr Markers ◽  
Mean Value ◽  
Dasypyrum Villosum ◽  
Reproducible Method ◽  
The Mean ◽  
High Diversity

Application of the ISSR method to estimate the genetic similarity of Dasypyrum villosum (L.) P. Candargy Greek populations to Triticum and Secale species In the study, the genetic similarity between Dasypyrum villosum L. (P.) Candargy and Triticum L. and Secale L. species was studied on the basis of ISSR markers. As a very polymorphic, effective and reproducible method, ISSR can be successfully employed to evaluate polymorphism between and inside different species. The polymorphic information content values (PIC) of ISSR method ranged from 0.57 to 0.87, with the mean value of 0.7. The genetic similarity of the forms analyzed ranged from 0.27 to 0.97, with the mean value of 0.47, indicating their high diversity. A higher similarity of Dasypyrum villosum to Triticum species, in comparison with Secale was found - the mean Dice genetic similarity index between genera was calculated at 0.40 for Dasypyrum and Triticum, and at 0.31 for Dasypyrum and Secale.

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 Genetic Diversity Among Old Local Grape Cultivars in South of Syria

2019 ◽  
Vol 8 (2) ◽  
pp. 43-54
Author(s):  
Bayan M. Muzher ◽  
Ola T. Al-Halabi
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Morphological Traits ◽  
Principal Component ◽  
Hierarchical Cluster ◽  
The Other ◽  
Jaccard Coefficient ◽  
Eigen Values ◽  
Grape Cultivars ◽  
High Diversity

 This investigation was carried out in Sweida governorate of Syria from 2014 to 2015. The purpose of this investigation was to estimate the genetic diversity among 17 old local grape cultivars using morphological traits and SSR molecular markers. Principal Component Analysis (PCA) of morphological traits revealed that four main components were accountable for 50.34 % of variance, with Eigen values of 16.77%, 13.31%, 10.59% and 9.67%, respectively. While distribution of cultivars was found significantly dependent of first and second components, which separated Aswad Sharar and Derbly cultivars rather than other studied cultivars. Hierarchical cluster of morphological traits showed high diversity among studied cultivars. On the other hand, molecular characterization was conducted using eight informative SSR primer pairs, polymorphism was detected by seven SSR's primers. As a result, 18 polymorphic alleles were revealed with a polymorphism percentage of 100%, which reflected the genetic variation among studied cultivars. Genetic similarity was achieved, where 0.875 was the highest between Zeiny and Khedry cultivars, while the other two cultivars Ebeidy and AhmarMokamaa showed the lowest genetic similarity as 0.077. Cluster analysis of SSR markers grouped the studied cultivars into three clusters as per Jaccard coefficient. The first cluster grouped Ebeidy, Aswad Helwany and Derbly cultivars together, the second cluster contained two cultivars Beiady and Alb Atair, while the third cluster contained the remaining cultivars. Consequently, the results showed high diversity among studied cultivars, and some morphological traits were useful for cultivar discrimination.

scholarly journals Implementation of a limited set of SSR markers for screening of genetic variability in Latvian and Swedish sour cherry (Prunus cerasus L.) genetic resources collections

2011 ◽  
Vol 65 (1-2) ◽  
pp. 21-28
Author(s):  
Gunārs Lācis ◽  
Isaak Rashal ◽  
Viktor Trajkovski
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Genetic Resources ◽  
Ssr Markers ◽  
Genetic Similarity ◽  
Polymorphic Information Content ◽  
Sour Cherry ◽  
Prunus Cerasus ◽  
Discrimination Power ◽  
Ssr Loci

Implementation of a limited set of SSR markers for screening of genetic variability in Latvian and Swedish sour cherry (Prunus cerasusL.) genetic resources collectionsForty-one sour cherry (Prunus cerasusL.) accessions were evaluated using three SSR markers to characterise genetic diversity in the sour cherry genetic resource collections at the Latvia State Institute of Fruit-Growing (LIFG), Dobele, Latvia and the Division of Horticultural Genetics and Plant Breeding at Balsgård, Department of Crop Sciences, Swedish University of Agricultural Sciences (SLU-Balsgård), Sweden, and to test the usability and reliability of a small set of SSR markers for preliminary characterisation of sour cherry germplasm collections. The SSR loci were highly polymorphic with 7-14 alleles per locus. Heterozygosity and Polymorphic Information Content values ranged from 0.750 to 1.000 and 0.748-0.899, respectively, while discrimination power per locus varied from 0.716 to 0.965. Five to thirty genotypes were found in the sour cherry collections for the three tested SSR loci. The combined discrimination power of all loci was effectively 0.994 and 0.999 for the LIFG and SLU-Balsgård collections, respectively. The SSRs used were able to uniquely identify all accessions in the analysed genetic resources collections. The genotype data allowed estimation of genetic diversity and genetic characterisation of accessions in the collections. Genetic similarity analysis showed higher genetic similarity among the Baltic and Scandinavian sour cherry varieties, than between Baltic and Eastern European varieties.

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