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)

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 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 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 Molecular characterization of oil seed Brassica using RAPD markers

2020 ◽  
Vol 55 (1) ◽  
pp. 1-8
Author(s):  
M Islam ◽  
A Habib ◽  
S Khan ◽  
S Akter ◽  
B Goswami ◽  
...  
Keyword(s):  
Genetic Distance ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Arithmetic Means ◽  
Oil Seed ◽  
Pair Group ◽  
Brassica Spp ◽  
Breeding Programmes ◽  
High Level

Twelve varieties of oil seed Brassica spp. were characterized at molecular level using Random Amplified Polymorphic DNA (RAPD) primers to explore genetic diversity and to find out relationship among them. Twelve random primers used in the study generated 94 RAPD fragments and 53 (56.38%) of them were considered as polymorphic indicating high level of polymorphism within the materials. The size of amplified fragments ranged between 300-3000 bp. The values of pair-wise genetic distance ranged from 0.1613 to 0.5543. To find out phylogenetic relationships among the varieties, dendrogram based on Nei’s genetic distance was constructed using Unweighted Pair Group Method of Arithmetic Means (UPGMA) separating the 12 Brassica spp into two major clusters C1 and C2. This result will be useful for designing future breeding programmes for improvement of Brassica varieties. Bangladesh J. Sci. Ind. Res.55(1), 1-8, 2020

scholarly journals Identities and Relationships among Chinese Vegetable Brassicas as Determined by Random Amplified Polymorphic DNA Markers

1995 ◽  
Vol 120 (3) ◽  
pp. 548-555 ◽  
Author(s):  
Jianping Ren ◽  
James R. McFerson ◽  
Rugang Li ◽  
Stephen Kresovich ◽  
Warren F. Lamboy
Keyword(s):  
Chinese Cabbage ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
Diversity Assessment ◽  
Wide Range ◽  
Chinese Vegetable ◽  
Vegetable Brassicas

Fifty-two germplasm accessions of Chinese vegetable brassicas were analyzed using 112 random amplified polymorphic DNA (RAPD) markers. The array of material examined spanned a wide range of morphological, geographic, and genetic diversity, and included 30 accessions of Brassica rapa L. (Chinese cabbage, pakchoi, turnip, and broccoletto), 18 accessions of B. juncea (L.) Czern. (leaf, stem, and root mustards), and four accessions of B. oleracea L. ssp. alboglabra (Chinese kale). The RAPD markers unambiguously identified all 52 accessions. Nei-Li similarities were computed and used in unweighed pair group method using arithmetic means (UPGMA) cluster analyses. Accessions and subspecies were clustered into groups corresponding to the three species, but some accessions of some subspecies were most closely related to accessions belonging to other subspecies. Values for Nei-Li similarities suggest that Chinese cabbage is more likely to have been produced by hybridization of turnip and pakchoi than as a selection from either turnip or pakchoi alone. RAPD markers are a fast, efficient method for diversity assessment in Chinese vegetable brassicas that complements techniques currently in use in genetic resources collections.

Cultivar identification in upland cotton using RAPD markers

2002 ◽  
Vol 53 (6) ◽  
pp. 637 ◽  
Author(s):  
A. A. Linos ◽  
P. J. Bebeli ◽  
P. J. Kaltsikes
Keyword(s):  
Upland Cotton ◽  
Rapd Markers ◽  
Cultivar Identification ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Gossypium Hirsutum L ◽  
Arithmetic Means ◽  
Arbitrary Primers ◽  
Pair Group ◽  
Base Cluster

Using the random amplified polymorphic DNA (RAPD) method, the identification and the genetic description of 28 upland cotton (Gossypium hirsutum L.) cultivars currently cultivated in Greece was attempted. Based on the results of a preliminary experiment using 50 ten-base arbitrary primers, 24 were selected for the main experiment. DNA bands totaling 181 were observed, 118 (65.2%) of which were polymorphic. On the average, 7.5 DNA bands were amplified per primer, 4.9 of which were polymorphic. The unique identification of all cultivars studied was made possible using 27 specific polymorphic bands (markers) corresponding to 16 primers and a specially constructed key. The genetic similarity of the cultivars was estimated using Jaccard's similarity coefficient, which ranged from 0.614 to 0.922, indicating a relatively narrow genetic base. Cluster analysis by the Unweighted Pair Group Method of Arithmetic means (UPGMA) showed that 21 of the cultivars could be placed into 3 major groups. A similar clustering of the cultivars was obtained using principal coordinate analysis.

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 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 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.

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