scholarly journals Genetic diversity analysis using molecular marker in Terminalia chebula

2015 ◽  
Vol 7 (2) ◽  
pp. 997-1000
Author(s):  
T. N. Ranjini ◽  
K. Bhanuprakash ◽  
M. A. Suryanarayana ◽  
B. G. Yamuna
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Rapd Markers ◽  
Molecular Diversity ◽  
Crop Improvement ◽  
Group Method ◽  
Terminalia Chebula ◽  
Pair Group ◽  
Improvement Programme ◽  
Important Medicinal Plant

Terminalia chebula is an important medicinal plant, extensively used in Ayurveda, Unani and Homoeopathic medicines. The present study was aimed to reveal its genetic diversity based on molecular markers from twelve T. chebula accessions. Molecular diversity was studied using RAPD markers. A total of 8 polymorphic primers produced 314 polymorphic bands and 195 monomorphic bands. Unweighted Pair Group Method with Arithmetic Mean (UPMGA) dendrogram divided the accessions into 2 major clusters. Accession IIHRTc2 and IIHRTc10 showed maximum genetic diversity with 55% similarity. This characterization based on molecular markers will help in identification of economically useful accessions for further crop improvement programme.

scholarly journals Evaluation of Genetic Diversity among Persian Fig Cultivars by Morphological Traits and RAPD Markers

HortScience ◽  
2018 ◽  
Vol 53 (5) ◽  
pp. 613-619 ◽  
Author(s):  
Ghazal Baziar ◽  
Moslem Jafari ◽  
Mansoureh Sadat Sharifi Noori ◽  
Samira Samarfard
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Hierarchical Cluster ◽  
Fruit Trees ◽  
Group Method ◽  
Fars Province ◽  
Pair Group

Ficus carica L. is one of the most ancient fruit trees cultivated in Persia (Iran). The conservation and characterization of fig genetic resources is essential for sustainable fig production and food security. Given these considerations, this study characterizes the genetic variability of 21 edible F. carica cultivars in the Fars Province using random amplified polymorphic DNA (RAPD) markers. The collected cultivars were also characterized for their morphological features. A total of 16 RAPD primers produced 229 reproducible bands, of which, 170 loci (74.43%) were polymorphic with an average polymorphic information content (PIC) value of 0.899. Genetic analysis using an unweighted pair-group method with arithmetic averaging (UPGMA) revealed genetic structure and relationships among the local germplasms. The dendrogram resulting from UPGMA hierarchical cluster analysis separated the fig cultivars into five groups. These results demonstrate that analysis of molecular variance allows for the partitioning of genetic variation between fig groups and illustrates greater variation within fig groups and subgroups. RAPD-based classification often corresponded with the morphological similarities and differences of the collected fig cultivars. This study suggests that RAPD markers are suitable for analysis of diversity and cultivars’ fingerprinting. Accordingly, understanding of the genetic diversity and population structure of F. carica in Iran may provide insight into the conservation and management of this species.

scholarly journals Analysis of genetic diversity in Prunus sibirica L. in inner Mongolia using SCoT molecular markers

2022 ◽  
Author(s):  
Ha Buer ◽  
Sa Rula ◽  
Zi Yuan Wang ◽  
Shu Fang ◽  
Yu´e Bai
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Differentiation ◽  
Inner Mongolia ◽  
Start Codon ◽  
Group Method ◽  
Pair Group ◽  
Protection And Utilization ◽  
Minimum Number ◽  
Polymorphic Bands

AbstractPopulation genetic diversity contributes to the protection and utilization of germplasm resources, especially via genetic breeding. In the present study, start codon targeted polymorphism (SCoT) molecular markers were used to study the genetic diversity of 278 individuals from 10 Prunus sibirica L. populations in Inner Mongolia. A total of 289 polymorphic bands were amplified with 23 SCoT primers, showing a polymorphism percentage of 98.87% and an average of 12.6 polymorphic bands per primer. The SCoT21, SCoT32, and SCoT53 primers amplified up to 17 bands, and the polymorphism percentage was 100%. The minimum number of bands amplified by SCoT25 was 9, and the polymorphism percentage was 90%. Therefore, SCoT molecular markers were shown to be highly polymorphic and suitable for genetic diversity studies of P. sibirica in Inner Mongolia. The analysis of molecular variance showed that 39% of the observed genetic differentiation occurred among populations and 61% occurred within populations, indicating that the genetic differentiation within populations was greater than that among populations. The results of the unweighted pair-group method with an arithmetic cluster analysis, principal coordinate analysis and STRUCTURE analysis were basically the same and divided the 278 individuals from the 10 populations into 2 groups. The results indicated that the efficient SCoT molecular marker-based genetic diversity analysis of P. sibirica in Inner Mongolia can provide a reference for P. sibirica variety breeding and resource development.

scholarly journals Genetic diversity analysis in Brassica varieties through RAPD markers

1970 ◽  
Vol 34 (3) ◽  
pp. 493-503 ◽  
Author(s):  
KK Ghosh ◽  
ME Haque ◽  
S Parvin ◽  
F Akhter ◽  
MM Rahim
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Arithmetic Mean ◽  
Polymorphic Band ◽  
Group Method ◽  
Polymorphic Loci ◽  
Pair Group

This investigation was aimed at exploring the genetic diversity and relationship among nine Brassica varieties, namely BARI Sharisha-12, Agrani, Sampad, BINA Sharisha-4, BINA Sharisha-5, BARI Sharisha-13, Daulot, Rai-5, Alboglabra using Random Amplified Polymorphic DNA (RAPD) markers. In total, 59 reproducible DNA bands were generated by four arbitrary selected primers of which 58 (98.03%) bands were proved to be polymorphic. These bands ranged from 212 to 30686 bp in size. The highest proportion of polymorphic loci and gene diversity values were 37.29% and 0.1373, respectively, for BARI Sharisha-12 and the lowest proportion of polymorphic loci and gene diversity values were 8.47% and 0.0318, 8.47% and 0.0382 for BINA Sharisha-4 and Rai-5, respectively. A dendrogram was constructed using unweighted pair group method of arithmetic mean (UPGMA). The result of cluster analysis indicated that the 9 accessions were capable of being classified into 2 major groups. One group consists of BARI Sharisha-12, Agrani, Sampad, Daulot, Rai-5, Alboglabra. where Daulot and Rai-5 showed the lowest genetic distance of 0.049. And another group contains BINA Sharisha-4, BINA Sharisha-5, and BARI Sharisha-1 3, where BINA Sharisha-5 and BARI sharisha-13 showed genetic distance of 0.071. Key Words: RAPD, Brassica, genetic distance, polymorphic band. DOI: 10.3329/bjar.v34i3.3976 Bangladesh J. Agril. Res. 34(3) : 493-5032, September 2009

scholarly journals Description and analysis of genetic diversity among squash accessions

2009 ◽  
Vol 52 (2) ◽  
pp. 271-283 ◽  
Author(s):  
Athanasios L. Tsivelikas ◽  
Olga Koutita ◽  
Anastasia Anastasiadou ◽  
George N. Skaracis ◽  
Ekaterini Traka-Mavrona ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Clustering Algorithm ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Molecular Data ◽  
Optimal Number ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group

In this work, the part of the squash core collection, maintained in the Greek Gene Bank, was assessed using the morphological and molecular data. Sixteen incompletely classified accessions of the squash were characterized along with an evaluation of their resistance against two isolates of Fusarium oxysporum. A molecular analysis using Random Amplified Polymorphic DNA (RAPD) markers was also performed, revealing high level of polymorphism. To study the genetic diversity among the squash accessions, a clustering procedure using Unweighed Pair Group Method and Arithmetic Average (UPGMA) algorithm was also adopted. Two independent dendrograms, one for the morphophysiological and one for molecular data were obtained, classifying the accessions into two and three main clusters, respectively. Despite the different number of the clusters there were many similarities between these two dendrograms, and a third dendrogram resulting from their combination was also produced, based on Gower's distance and UPGMA clustering algorithm. In order to determine the optimal number of clusters, the upper tail approach was applied. The more reliable clustering of the accessions was accomplished using RAPD markers as well as the combination of the two different data sets, classifying the accessions into three significantly different groups. These groups corresponded to the three different cultivated species of C. maxima Duch., C. moschata Duch., and C. pepo L. The same results were also obtained using Principal Component Analysis.

scholarly journals Performance of salinity tolerance of F3 rice lines of BRRI dhan 29 × PBRC (STL-20) using RAPD markers

2019 ◽  
Vol 6 (2) ◽  
pp. 215-225
Author(s):  
Nazmul Islam Mazumder ◽  
Tania Sultana ◽  
Prtitish Chandra Paul ◽  
Dinesh Chandra Roy ◽  
Deboprio Roy Sushmoy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Salinity Tolerance ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Susceptible Variety ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
Tolerant Line

Twenty six rice lines of PBRC (salt tolerant line-20) × BRRI dhan-29 were used to evaluate salinity tolerance at the seedling stage and tested for salt tolerance using RAPD markers. Salinity screening was done using hydrophonic system at the greenhouse following IRRI standard protocol. Among the studied line, ten were moderately salinity tolerant, nine susceptible and rest of the lines highly susceptible. For assessing genetic diversity and relationship of F3 rice lines including two parents were tested against PCR-based Random Amplified Polymorphic DNA (RAPD) technique using three arbitrary decamer primers; OPA02, OPC01, and OPC12. Selected three primers generated a total of 14 bands. Out of 14 bands, 12 bands (86.67%) were polymorphic and 2 bands (13.33%) were monomorphic. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei’s (1972) genetic distance produced 2 main clusters of the 28 rice genotypes. Most of the moderately tolerant lines and PBRC (STL-20) (tolerant variety) were grouped in same cluster due to lower genetic distance, while maximum susceptible along with BRRI dhan29 (susceptible variety) showed higher genetic distance with PBRC (STL-20) and moderately tolerant lines. This result indicates that the lines which formed grouped together, they are less diversed. On the other hand the lines remain in different clusters or different groups, are much diversed. Thus RAPD perform a potentially simple, rapid and reliable method to evaluate genetic diversity and molecular characterization as well. Res. Agric., Livest. Fish.6(2): 215-225, August 2019

scholarly journals Genetic Variability of 21 Tea Genotypes [Camellia sinensis (L.) O. Kuntze] Based on RAPD Markers

2018 ◽  
Vol 5 (2) ◽  
pp. 77
Author(s):  
Budi Martono ◽  
Syafaruddin Syafaruddin
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Similarity ◽  
Binary Data ◽  
Rapd Markers ◽  
Group Method ◽  
Breeding Programs ◽  
Pair Group ◽  
Monomorphic Band ◽  
And Cluster Analysis

<em>Knowing the genetic diversity in the tea germplasms collection is one of important conditions for assembling new superior varieties. Information of genetic diversity can be obtained through analysis using RAPD molecular markers. The study aimed to determine the genetic diversity of 21 tea genotypes based on RAPD markers. The research was conducted in Integrated Laboratory, Seameo Biotrop, Bogor, from July to September 2013. Genomic DNA was isolated from 21 tea genotypes leaf samples, then amplified with primer OPA 03, OPA 05, OPB 04, OPB 06, OPC 06, and OPD 08. Electrophoresis result was converted into binary data. The genetic similarity and cluster analysis calculation was done using NTSYS-pc version 2.10. In this research, 50 polymorphic bands (94,34%) and 3 monomorphic band (5,66%) were obtained. Cluster analysis based on Nei's genetic distance using the unweighted pair-group method with arithmatic (UPGMA) divided 21 tea genotypes into two groups at a genetic similarity value of 0,48. Group 1 consisted of 20 tea genotypes, while the second group comprised only a one genotype (Sin 27). The range of genetic similarity matrix was between 28%–92%, the lowest genetic similarity (28%) was found between GMB 4 and Sin 27 genotypes, while the highest (92%) was found between AS 2 and AS 1 genotypes. The information obtained can be utilized in breeding programs with the support of agronomic characters as well as in the conservation of tea germplasm.</em>

Genetic Diversity of Iranian Clones of Common Reed (Phragmites australis) Based on Morphological Traits and RAPD Markers

Weed Science ◽  
2011 ◽  
Vol 59 (3) ◽  
pp. 366-375 ◽  
Author(s):  
Marjan Diyanat ◽  
Ali A. S. Booshehri ◽  
Hassan M. Alizadeh ◽  
Mohammad R. Naghavi ◽  
Hamid R. Mashhadi
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Common Reed ◽  
Group Method ◽  
Successful Management ◽  
Morphological Comparison ◽  
Pair Group ◽  
High Level ◽  
Methods Of Control

The genetic diversity of 39 clones of common reed originating from different geographical areas of Iran were evaluated using morphological and RAPD analyses. High level of morphological variation was observed among clones. The 16 primers used in this study amplified 149 scorable RAPD loci among which 123 were polymorphic (83.1%). A dendrogram was prepared on the basis of a similarity matrix of RAPD data using the unweighted pair-group method with arithmetic averages (UPGMA) algorithm and separated the 39 clones into four groups, which mainly were in accordance with geographical origins. The results of the morphological comparison mostly corresponded with the results of RAPD analysis. It is possible that these variations among clones will affect successful management of common reed using chemical or the other methods of control.

scholarly journals Characterization of potato genotypes using molecular markers

2004 ◽  
Vol 39 (9) ◽  
pp. 871-878 ◽  
Author(s):  
Eliana Antonia Silveira Collares ◽  
Eva Choer ◽  
Arione da Silva Pereira
Keyword(s):  
Molecular Markers ◽  
Gel Electrophoresis ◽  
Rapd Markers ◽  
Polyacrylamide Gel Electrophoresis ◽  
Group Method ◽  
Jaccard Coefficient ◽  
Leaf Extracts ◽  
Arithmetic Average ◽  
Pair Group

The objective of this work was to characterize 27 potato genotypes, using molecular markers. Polyacrylamide gel electrophoresis, RAPD techniques and isozymes of esterase, phosphoglucomutase and soluble proteins were analyzed in tubers, and isocitrate dehydrogenase, aspartate transaminase, phosphoglucomutase and peroxidase, in leaves. Eighteen primers were tested and four were chosen, kits OPX (01, 04 and 09) and OPY (07), to analyze RAPD markers in leaf extracts. Similarity and cluster analysis were conducted using Jaccard coefficient and the unweighted pair-group method using arithmetic average. Despite the differences detected in the analysis of proteins and isozymes in the tubers, as well as of isozymes in the leaves, the characterization of all genotypes through gel electrophoresis was not possible, while RAPD markers were efficient to characterize all the 27 genotypes.

scholarly journals Discrimination and Genetic Diversity among Cultivated Olives of Greece Using RAPD Markers

2003 ◽  
Vol 128 (5) ◽  
pp. 741-746 ◽  
Author(s):  
N. Nikoloudakis ◽  
G. Banilas ◽  
F. Gazis ◽  
P. Hatzopoulos ◽  
J. Metzidakis
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Fruit Size ◽  
Similarity Index ◽  
Group Method ◽  
Poor Correlation ◽  
Pair Group ◽  
Electrophoretic Patterns

Random amplified polymorphic DNA (RAPD) markers were used to study the genetic diversity and to discriminate among 33 Greek olive (Olea europaea L.) cultivars. Three feral forms from Crete and five foreign cultivars recently introduced into Greece were also included. Nineteen primers were selected which produced 64 reproducible polymorphic bands in the 41 olive genotypes studied, with an average of 3.4 informative markers per primer. The RAPD markers resulted in 135 distinct electrophoretic patterns, with an average of 7.1 patterns per primer. Based on either unique or combined patterns, all genotypes could be identified. Genetic similarities between genotypes were estimated using the Dice similarity index and these indicated that a high degree of diversity exists within the Greek olive germplasm. Using the unweighted pair-group method (UPGMA) most cultivars were clustered into two main groups according to their fruit size or commercial use (table or olive oil). However, poor correlation was detected between clustering of cultivars and their principal area of cultivation. RAPD marker data were subjected to nonmetric multidimentional scaling (NMDS) which produced results similar to those of the UPGMA analysis. The results presented here contribute to a comprehensive understanding of cultivated Greek olive germplasm and provide information that could be important for cultural purposes and breeding programs.

scholarly journals Assessment of genetic diversity of Curcuma aromatica from eastern India using ISSR and RAPD markers

2018 ◽  
Vol 1 (1) ◽  
pp. 24
Author(s):  
Reena Parida ◽  
Sujata Mohanty ◽  
Sanghamitra Nayak
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Pair Group ◽  
Inter Simple Sequence Repeats ◽  
Different Populations ◽  
Clustering Pattern ◽  
Simple Sequence ◽  
Important Medicinal Plant

Application of Inter Simple Sequence Repeats and Random Amplified Polymorphic DNA markers in Curcuma aromatica collected from 4 different populations of Odisha. A dendrogram was constructed through sequential agglomerative hierarchial and nested (SAHN) clustering and unweighted pair group method with arithmetic mean (UPGMA) analysis using Jaccard’s similarity coefficient of combined markers using this particular species. Two major clusters were found i.e., cluster-I (Koraput-1, Koraput-2, Koraput-3, G.Udaigiri-1, G.Udaigiri-2, G.Udaigiri-3 and Phulabani-1, Phulabani-2, Phulabani-3) and cluster-II (Raikia-1, Raikia-2 and Raikia-3). The clustering pattern also revealed moreover the extent of genetic similarity between germplasms collected from those populations. This technique would be further utilized for identification and tagging of important novel gene present in different taxa or improvement work in family Zingiberaceae. This study would be of immense significance for conservation and characterization of important medicinal plant species.

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