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.

Genetic diversity among accessions of an ancient olive variety of Cyprus

Genome ◽  
2003 ◽  
Vol 46 (3) ◽  
pp. 370-376 ◽  
Author(s):  
Georgios Banilas ◽  
John Minas ◽  
Costas Gregoriou ◽  
Cathrine Demoliou ◽  
Anna Kourti ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Rapd Marker ◽  
Fruit Size ◽  
Germplasm Collection ◽  
Group Method ◽  
Dice Similarity Coefficient ◽  
Pair Group ◽  
Electrophoretic Patterns ◽  
Olive Variety

To evaluate germplasm variability and to discriminate between accessions of 'Ladolia', an ancient olive variety of Cyprus, different accessions from a germplasm collection were screened with 11 selected oligonucleotide primers in RAPD-PCRs. A total of 49 polymorphic markers were scored, the combination of which resulted in 70 distinct electrophoretic patterns. Based on either unique or combined patterns, all accessions were identified. Seven genotype-specific markers were detected. One RAPD marker could distinguish accessions according to fruit size. Genetic similarities between accessions, estimated using the Dice similarity coefficient, indicated a high degree of genetic diversity among 'Ladolia' accessions. Genetic relationships were estimated by the unweighted pair-group method with arithmetic averaging (UPGMA) and principal components analysis (PCA). Three main groups of accessions were detected. The first group was generally composed of accessions with small-sized fruits and could be further divided into two subgroups. According to PCA, most accessions with medium- or large-sized fruits were clustered together. Our results support previous observations suggesting that 'Ladolia' is actually a highly variable mixture of genetically distinct landraces.Key words: DNA polymorphism, germplasm variability, RAPD markers, Olea europaea.

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 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 Evaluation of genetic diversity in geranium (Geraniaceae) using RAPD marker

Genetika ◽  
2021 ◽  
Vol 53 (1) ◽  
pp. 363-378
Author(s):  
Juan Yin ◽  
Majid Khayatnezhad ◽  
Abdul Shakoor
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Morphological Characters ◽  
Mantel Test ◽  
Group Method ◽  
Plant Resources ◽  
High Genetic Diversity ◽  
Pair Group ◽  
Genetic Structure Of Populations

Genetic diversity studies are essential to understand the conservation and management of plant resources in any environment. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Geranium genetic diversity. Therefore, we collected and analyzed thirteen species from nine provinces. Overall, one hundred and twenty-five plant specimens were collected. Our aims were 1) to assess genetic diversity among Geranium species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. Unweighted pair group method with arithmetic mean and multidimensional scaling divided Geranium species into two groups. G. sylvaticum depicted unbiased expected heterozygosity (UHe) in the range of 0.11. Shannon information was high (0.38) in G. columbinum. G. sylvaticum showed the lowest value, 0.14. The observed number of alleles (Na) ranged from 0.25 to 0.55 in G. persicum and G. tuberosum. The effective number of alleles (Ne) was in the range of 1.020-1.430 for G. tuberosum and G. collinum. Gene flow (Nm) was relatively low (0.33) in Geranium. The Mantel test showed correlation (r = 0.27, p=0.0002) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Geranium species can adapt to changing environments since high genetic diversity is linked to species adaptability. Present results highlighted the utility of RAPD markers and morphometry methods to investigate genetic diversity in Geranium species.

scholarly journals Assessment of genetic diversity of different tomato genotypes using RAPD markers

2019 ◽  
Vol 29 (4) ◽  
pp. 276-283
Author(s):  
M Paul ◽  
SR Saha
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Breeding Programs ◽  
Pair Group ◽  
Information Indices ◽  
Tomato Breeding ◽  
Tomato Genotypes

The present investigation was carried out for assessment of genetic diversity among the 28 tomato genotypes though three random amplified polymorphic DNA (RAPD) markers. A total of 15 distinct DNA fragments ranging form 100-1000 bp were amplified by using three selected primers of which 5.00 polymorphic bands per primer and over all polymorphic loci was 100 percent. The extent of genetic diversity among these genotypes was computed through parameters of genetic diversity and Shanon’s information indices. The highest genetic distance was observed among the accession Cl-3d-0-99 (V93)  vs. F1 (G X V12), F1 (G X V17), F1 (G X V29) and  Durch fuegel  (G) vs. F1 (G X V17) and F1 (G X V93) vs. F1 (G X V12), F1 (G X V17), while the lowest genetic distance was observed among the accessions Fut. Wed Abrid (V94) vs. Sunlight pole (V67) and F1 (V67 X VG) vs. F1 (V17 X VG), F1 (V93 X VG) and F1 (V93 X V17) vs. F1 (V17 X VG), F1 (V67 X VG), F1 (V93 X VG). The Unweighted Pair Group Method of Arithmetic Mean (UPGMA) dendrogram based on Nei’s genetic distance divided the genotypes into two main clusters: A & B. Cluster ‘A’ consists of 19 accessions and cluster ‘B’ consists of 9 accessions. The information generated from this study could be useful in gene mapping and marker assisted breeding for future tomato breeding programs. Progressive Agriculture 29 (4): 276-283, 2018

scholarly journals GENETIC DIVERSITY AMONG AND WITHIN BRAVE BEAN (Capparis flexuosa L.) POPULATIONS ASSESSED USING RAPD MARKERS

2019 ◽  
Vol 32 (1) ◽  
pp. 81-91
Author(s):  
Jorge Xavier de Almeida Neto ◽  
Mailson Monteiro do Rêgo ◽  
Elizanilda Ramalho do Rêgo ◽  
Ana Paula Gomes da Silva
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Polymorphic Information Content ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Jaccard Similarity ◽  
Cophenetic Correlation ◽  
Pair Group ◽  
Cophenetic Correlation Coefficient ◽  
Bean Leaves

ABSTRACT Brave bean (Capparis flexuosa L.) is a Caatinga species that is used as forage, mainly during the dry season when some plant species lose their leaves. The aim of this study was to assess genetic diversity within and among brave bean populations using Random Amplified Polymorphic DNA (RAPD) markers. Brave bean leaves were collected from 30 accessions in the following municipalities of Paraíba state, Brazil: Barra de Santa Rosa (BSR), Cuité (C), São João do Cariri (SJC), Damião (D), Baraúna (B), and Picuí (P). DNA extraction followed the standard methodology of CTAB with modifications. RAPD analyses were carried out using 18 primers, and polymorphism of the amplified DNA fragments was visualized using agarose gel electrophoresis. Data were used to calculate Jaccard Similarity Coefficient values, which were then used to group samples with the Unweighted Pair Group Method with Arithmetic Mean. Cophenetic Correlation Coefficient, Stress, and Distortion Coefficient values were also calculated from these analyses. Band polymorphism was generated with 14 primers, but the sampled populations showed low numbers of polymorphic loci (27 in BSR, 18 in C, 7 in SJC, 9 in D, and 0 in B and P). The highest polymorphic information content was found in samples from the BSR (9 groups), C (22 groups), SJC (7 groups), and D (6 groups) municipalities. In the interpopulation analysis, 34 groups were formed, the matrices of which showed high cophenetic correlations (0.95 to 0.98), but low stress (12.9 to 17.45%) and distortion (3.05%). Therefore, results showed that there was genetic variability both among and within brave bean populations.

scholarly journals Molecular Characterization of Olive Cultivars Using RAPD Markers

2001 ◽  
Vol 126 (1) ◽  
pp. 7-12 ◽  
Author(s):  
F. Sanz-Cortés ◽  
M.L. Badenes ◽  
S. Paz ◽  
A. Íñiguez ◽  
G. Llácer
Keyword(s):  
Morphological Traits ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Fruit Size ◽  
Geographic Origin ◽  
Group Method ◽  
Polymorphic Markers ◽  
Pair Group ◽  
Olive Cultivars

Forty olive (Olea europaea L.) cultivars from Valencia, Spain, were screened using random amplified-polymorphic DNA (RAPD) markers. Eighteen selected decamer primers produced 34 reproducible amplification fragments that were then used as polymorphic markers. The resulting combinations of these RAPD markers were used to discriminate 40 cultivars. Results were analyzed for similarity among cultivars and the relatedness of polymorphisms obtained between cultivars agreed with previous results using isozymes. Unweighted pair group method cluster analysis of their similarity values revealed two main groups divided according to geographic origin within Valencia. A third group, which included two Spanish cultivars from regions outside of Valencia, was clustered separately from the Valencian cultivars. RAPD technology proved useful in discriminating closely related cultivars. There was no apparent clustering of cultivars by fruit size or other morphological traits.

scholarly journals Determination of genetic variations among different Trichoderma isolates using RAPD marker in Bangladesh

1970 ◽  
Vol 9 (1) ◽  
pp. 9-20 ◽  
Author(s):  
MSI Sagar ◽  
MB Meah ◽  
MM Rahman ◽  
AK Ghose
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Genetic Variations ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
High Level ◽  
Cluster 2

Some Trichoderma isolates were collected from different locations of Bangladesh for evaluating their bioefficiency by determining their genetic variations. PCR-based Random Amplified Polymorphic DNA (RAPD) Marker employing 3 decamer primers produced 29 scorable bands of which all (100%) were polymorphic. The co-efficient of gene differentiation (Gst) was 1.0000 reflecting the existence of high level of genetic diversity among the isolates. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei’s (1972) genetic distance produced 2 main clusters (16 isolates in cluster 1 and 19 isolates in cluster 2). The result indicating their genetic diversity has opened new possibility of using the most efficient and more isolates of Trichoderma in the preparation of effective biopesticide. Keywords: Genetic diversity; Trichoderma; RAPD DOI: http://dx.doi.org/10.3329/jbau.v9i1.8738 JBAU 2011; 9(1): 9-20

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