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 Polymorphism and Discrimination Capacity of Randomly Amplified Polymorphic Markers in an Olive Germplasm Bank

2001 ◽  
Vol 126 (1) ◽  
pp. 64-71 ◽  
Author(s):  
A. Belaj ◽  
I. Trujillo ◽  
R. de la Rosa ◽  
L. Rallo ◽  
M.J. Giménez
Keyword(s):  
Gel Electrophoresis ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Origin ◽  
Group Method ◽  
Polymorphic Markers ◽  
Germplasm Bank ◽  
Banding Patterns ◽  
Olive Cultivars

Random amplified polymorphic DNA (RAPD) analysis was performed on the main Mediterranean cultivars of olive (Olea europaea L.) from the Germplasm Bank of the Centro de Investigación y Formación Agraria “Alameda del Obispo” in Cordoba, Spain. One hundred and ninety reproducible amplification fragments were identified using 46 random primers followed by agarose gel electrophoresis. Some 63.2% of the amplification products were polymorphic, with an average of 2.6 RAPD markers obtained for each primer. The combination of polymorphic markers resulted in 244 banding patterns. The high degree of polymorphism detected made identification of all the cultivars (51) possible by combining the RAPD banding patterns of just only four primers: OPA-01, OPK-08, OPX-01, and OPX-03. Cultivar-specific RAPD markers and banding patterns were also found. A dendrogram based on unweighted pair-group method cluster analysis was constructed using a similarity matrix derived from the RAPD amplification products generated by the 46 primers. Three major groups of cultivars could be distinguished by RAPD analysis: 1) cultivars from east and northeast Spain, 2) Turkish, Syrian, and Tunisian cultivars, and 3) the majority of common olive cultivars in Spain. The dendrogram thus showed a good correlation between the banding patterns of olive cultivars and their geographic origin. A higher level of polymorphism was observed when polyacrylamide gel electrophoresis was used to separate the amplification products. Thus, adequate use of RAPD technology offers a valuable tool to distinguish between olive cultivars.

Molecular Diversity Analysis of Lentil (Lens culinaris Medik.) through RAPD Markers

2012 ◽  
Vol 22 (1) ◽  
pp. 51-58 ◽  
Author(s):  
M.E. Hoque ◽  
M.M. Hasan
Keyword(s):  
Genetic Distance ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Group Method ◽  
Diversity Analysis ◽  
Pair Group ◽  
Molecular Genetic Diversity

Random Amplified Polymorphic DNA (RAPD) markers were used to study the molecular genetic diversity analysis among six BARI released lentil varieties viz. BARI masur-1, BARI masur-2, BARI masur-3, BARI masur-4, BARI masur-5 and BARI masur-6. PCR amplified products were visualized on 1.0% agarose gel and the band for each primer were scored. Ten RAPD markers were used in this study. Out of them 7 primers showed amplification of 53 DNA fragments with 60.37% of them being polymorphic. The highest number of polymorphic loci was noticed in the variety BARI masur-3. The same variety also showed maximum Nei’s gene diversity value (0.0552). The highest Nei’s genetic distance (0.5002) was observed in BARI masur-1 vs. BARI masur-5 whereas, the lowest genetic distance (0.0692) was found in BARI masur-1 vs. BARI masur-2. The unweighted pair group method of arithmetic mean (UPGMA) dendrogram based on Nei’s genetic distance grouped the six cultivars into two main clusters. BARI masur-1, BARI masur-2 and BARI masur-3 were in cluster I and BARI masur-4, BARI masur-5 and BARI masur-6 were in cluster II. The cultivar BARI masur-4 was closest to the cultivar BARI masur-6 with the lowest genetic distance (0.0972) and the highest genetic distance (0.5002) was found between BARI masur-1 and BARI masur-5. The RAPD markers were found to be useful in molecular characterization of lentil varieties which could be utilized by the breeders for the improvement of lentil cultivars. DOI: http://dx.doi.org/10.3329/ptcb.v22i1.11260 Plant Tissue Cult. & Biotech. 22(1): 51-58, 2012 (June)

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 Characterization of Induced Sugarcane Somaclones and their Sources Varieties Using Random Amplified Polymorphic DNA

2016 ◽  
Vol 25 (2) ◽  
pp. 223-229 ◽  
Author(s):  
Kuasha Mahmud ◽  
KM Nasiruddin ◽  
MA Hossain ◽  
L Hassan
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Arithmetic Means ◽  
Sugarcane Varieties ◽  
Main Cluster ◽  
Pair Group ◽  
The Relationship ◽  
Linkage Distance

Sugarcane somaclones and their sources varieties were analyzed by RAPD molecular markers to check the variation at molecular level based on 1.4% agarose gel electrophoresis (AGE). Six RAPD primers generated 237 bands with average 39.5 varied from 15 to 63 with size ranging 145 - 1000 bp among the four sugarcane varieties and their 12 somaclones. Genetic diversity or polymorphism information content (PIC) value ranged from 0.39 to 0.50 for all loci across the 4 varieties and their 12 somaclones based on RAPD markers. Dendrogram based on linkage distance using unweighted pair group method of arithmetic means (UPGMA) based on 6 RAPD primers indicated segregation of the 4 sugarcane varieties and their somaclones into two main clusters at linkage distance 36. Variety Isd 39 was observed in main cluster C1 while its (Isd 39) somaclones and other varieties (Isd 37, Isd 38 and Isd 40) and also their somaclones were found in main cluster C2 having different sub-clusters. Theirfore, it may be concluded that RAPD markers can be used for identification of somaclonal variation and the relationship between sources varieties and their somaclones.Plant Tissue Cult. & Biotech. 25(2): 223-229, 2015 (December)

scholarly journals Molecular characterization of onion (Allium cepa) using RAPD markers

1970 ◽  
Vol 35 (2) ◽  
pp. 313-322 ◽  
Author(s):  
M Maniruzzaman ◽  
ME Haque ◽  
MM Haque ◽  
MA Sayem ◽  
M Al-Amin
Keyword(s):  
Allium Cepa ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Amplification ◽  
Group Method ◽  
Genetic Studies ◽  
Pair Group ◽  
Genetic Level ◽  
Polymerase Chain

A polymerase chain reaction (PCR) based approach, namely random amplified polymorphic DNA (RAPD) analysis was applied to l0 varieties of onion (Allium cepa) in order to assess the degree of polymorphism within the genes and to investigate if this approach was suitable for genetic studies of onion. For this study, ten cultivars of onion were evaluated for variability using a set of 15 random l0-mer primers. The polymorphisms in PCR amplification products were subjected to the unweighed pair group method for arithmetic averages (UPGMA) and plotted in a phenogram. The dendogram constructed from the similarity data showed that all the cultivars analyzed were related. Among them, 12 of the primers revealed scorable (168 bands) polymorphisms between cultivars of A. cepa and the rest did not show polymorphism in their genetic level. In this study, it was found that Bermis and India-2 were more dissimilar and on the other hand, Faridpuri and Bhati were the most similar in their genetic level. Keywords: RAPD; onion; genetic diversity; polymorphism. DOI: 10.3329/bjar.v35i2.5894Bangladesh J. Agril. Res. 35(2) : 313-322, June 2010

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.

scholarly journals Genetic Diversity of Major Greek Olive Cultivars Using Molecular (AFLPs and RAPDs) Markers and Morphological Traits

2005 ◽  
Vol 130 (2) ◽  
pp. 211-217 ◽  
Author(s):  
Marianna Hagidimitriou ◽  
Andreas Katsiotis ◽  
George Menexes ◽  
Constantinos Pontikis ◽  
Michael Loukas
Keyword(s):  
Morphological Traits ◽  
Genetic Relationships ◽  
Fruit Size ◽  
Correlation Coefficients ◽  
Group Method ◽  
Reference Database ◽  
Aflp Data ◽  
Cophenetic Correlation ◽  
Pair Group ◽  
Olive Cultivars

The aim of the present study was to develop a reliable reference database to discriminate between the major Greek olive (Olea europaea L.) cultivars and reveal their genetic relationships, since Greece is considered a secondary center of diversity. In order to establish genetic relationships among the 26 Greek and eight international cultivars, four amplified fragment length polymorphism (AFLP) primer pairs, 12 randomly amplified polymorphic DNA (RAPD) primers, along with measurements from 10 morphological traits, were used. A total of 576 AFLP and 113 RAPD markers were produced. Genetic similarities, estimated using the Jaccard algorithim, ranged from 0.45 to 0.83 for the AFLP data and 0.27 to 0.87 for the RAPD data. The cophenetic correlation coefficients between the genetic similarities and the unweighted pair group method of arithmetic averages (UPGMA) phenograms were 0.77 for the AFLPs, 0.81 for the RAPDs, and 0.69 for the morphological traits. However, limited clustering similarities among the phenograms derived from the three methods were observed. This was also reflected by the low correlation between the three genetic similarity matrices produced (AFLP and RAPD, r = 0.39; AFLP and morphological traits, r = 0.11; RAPD and morphological traits, r = 0.02). According to the molecular results, olive cultivars are clustered according to fruit size but not according to geographical origin. Three of the cultivars tested, `Vasilicada,' `Throumbolia', and `Lianolia Kerkiras', were found to branch distantly to the others, according to the AFLP results, and can be considered as ancient Greek cultivars.

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

2018 ◽  
Vol 3 (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.

Characterization of Pyrenophora tritici-repentis in Tunisia and Comparison with a Global Pathogen Population

Plant Disease ◽  
2021 ◽  
Author(s):  
Marwa Laribi ◽  
Alireza Akhavan ◽  
Sarrah M'Barek ◽  
Amor Yahyaoui ◽  
Stephen Ernest Strelkov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Geographic Origin ◽  
Tan Spot ◽  
Pcr Analysis ◽  
Group Method ◽  
Region Of Origin ◽  
Pyrenophora Tritici Repentis ◽  
Pair Group ◽  
Necrotrophic Effector

Pyrenophora tritici-repentis (Ptr) causes tan spot, an important foliar disease of wheat. A collection of Ptr isolates from Tunisia, located in one of the main secondary centers of diversification of durum wheat, was tested for phenotypic race classification based on virulence on a host differential set, and for the presence of the necrotrophic effector (NE) genes ToxA, ToxB , and toxb by PCR analysis. While races 2, 4, 5, 6, 7, and 8 were identified according to their virulence phenotypes, PCR testing indicated the presence of ‘atypical’ isolates that induced necrosis on the wheat differential ‘Glenlea’, but lacked the expected ToxA gene, suggesting the involvement of other NEs in the Ptr/wheat interaction. Genetic diversity and the Ptr population structure were explored further by examining 59 Tunisian isolates and 35 isolates from Algeria, Azerbaijan, Canada, Iran, and Syria using 24 simple sequence repeat markers. Average genetic diversity, overall gene flow and percentage polymorphic loci were estimated as 0.58, 2.09 and 87%, respectively. Analysis of molecular variance showed that 81% of the genetic variance occurred within populations and 19% between populations. Cluster analysis by the unweighted pair group method indicated that ToxB- isolates grouped together and were distantly related to ToxB+ isolates. Based on Nei’s analysis, the global collection clustered into two distinct groups according to their region of origin. The results suggest that both geographic origin and the host-specificity imposed by different NEs can lead to differentiation among Ptr populations.

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