scholarly journals Molecular characterization of sesame germplasms of West Bengal, India using RAPD markers

2019 ◽  
Vol 63 (1) ◽  
pp. 15-24
Author(s):  
Soumen Saha ◽  
Tarak Nath Dhar ◽  
Parthadeb Ghosh ◽  
Tulsi Dey
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
West Bengal ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Group Method ◽  
Similarity Coefficients ◽  
Principal Coordinates Analysis ◽  
High Genetic Diversity ◽  
Principal Coordinates

The aim of this research was to assess the genetic diversity of sesame (Sesamum indicum L.) and also to reveal the genetic relationships using the Random Amplified Polymorphic DNA (RAPD) markers. Fifteen sesame germplasms were collected from seven districts or four zones of West Bengal, India. A high genetic diversity was revealed by ten RAPD primers within and among the fifteen germplasms. The value of Jaccard’s similarity coefficients among and within the fifteen germplasms ranged from 0.287 to 0.725 which indicated high degree of genetic variability. Cluster analysis using Unweighted Pair Group Method with Arithmetic Mean (UPGMA) grouped all the germplasms into three main clusters. Analysis of various genetic diversity indices strongly indicated high level of genetic diversity among the populations of four different regions. UPGMA analysis of four populations resulted into two groups and the results of Principal Coordinates Analysis (PCoA) depicted a clear distinction among the germplasms.

scholarly journals Efficiency of RAPD and ISSR markers in assessing genetic diversity and relationships in black gram (Vigna mungo L. Hepper) vari

2010 ◽  
Vol 90 (4) ◽  
pp. 443-452 ◽  
Author(s):  
T. Karuppanapandian ◽  
H W Wang ◽  
T. Karuppudurai ◽  
J. Rajendhran ◽  
M. Kwon ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Vigna Mungo ◽  
Polymorphic Band ◽  
Black Gram ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Rapd And Issr

The DNA fingerprinting methodologies, random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR), were used to estimate genetic diversity and relationships among 20 black gram (Vigna mungo L. Hepper) varieties. Thirty selected RAPD primers amplified 255 bands, 168 of which were polymorphic (66.5%). On average, these primers produced 8.5 bands, 5.6 of which were polymorphic. Polymorphic band number varied from 2 (A-05) to 10 (OPA-02), with sizes ranging from 100 to 2550 bp. Twenty-four selected ISSR primers produced 238 amplified products, 184 of which were polymorphic (77.8%). On average, these primers generated 9.8 bands, with 7.7 polymorphic bands ranging in number from 4 (ISSR-13) to 11 (ISSR-03), and size from 100-2650 bp. Genetic relationships were estimated using similarity coefficient (Jaccard’s) values between different accession pairs; these varied from 30.7 to 85.0 for RAPD, and from 37.2 to 88.4 with ISSR. UPGMA analysis indicated that the varieties ranged in similarity from 0.50 to 1.00 (mean of 0.75) for RAPD, and from 0.47 to 1.00 (mean of 0.76) with ISSR. Cluster analysis of RAPD and ISSR results identified three clusters with significant bootstrap values, which revealed greater homology between the varieties. Principal coordinates analysis also supported this conclusion. Among the black gram varieties, WBU-108 and RBU-38 were highly divergent, whereas LBG-648 and LBG-623 were genetically similar. The markers generated by RAPD and ISSR assays can provide practical information for the management of genetic resources and these results will also provide useful information for the molecular classification and breeding of new black gram varieties.Key words: Black gram, cluster analysis, genetic diversity, ISSR, molecular markers, RAPD

scholarly journals Molecular techniques in the assessment of genetic relationships between populations of Consolida (Ranunculaceae)

Caryologia ◽  
2021 ◽  
Vol 74 (2) ◽  
pp. 149-161
Author(s):  
Jing Ma ◽  
Wenyan Fan ◽  
Shujun Jiang ◽  
Xiling Yang ◽  
Wenshuai Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Morphological Characters ◽  
Mantel Test ◽  
Molecular Techniques ◽  
Group Method ◽  
Plant Resources ◽  
High Genetic Diversity

Genetic diversity studies are essential to understand the conservation and management of plant resources in any environment. The genus Consolida (DC.) Gray (Ranuculaceae) belongs to tribe Delphinieae. It comprises approximately 52 species, including the members of the genus Aconitella Spach. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Consolida genetic diversity. Therefore, we collected and analyzed 19 species from 12 provinces of regions. Overall, one hundred and twenty-seven plant specimens were collected. We showed significant differences in quantitative morphological characters in plant species. Unweighted pair group method with arithmetic mean and principal component analysis (PCA) divided Consolida species into two groups. All primers produced polymorphic amplicons though the extent of polymorphism varied with each primer. The primer OPA-06 was found to be most powerful and efficient as it generated a total of 24 bands of which 24 were polymorphic. The Mantel test showed correlation (r = 0.34, p=0.0002) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Consolida 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 Consolida species. Our aims were 1) to assess genetic diversity among Consolida species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa.

Genetic relationships and variation among ecotypes of seashore paspalum (Paspalum vaginatum) determined by random amplified polymorphic DNA markers

Genome ◽  
1994 ◽  
Vol 37 (6) ◽  
pp. 1011-1017 ◽  
Author(s):  
Zhao-Wei Liu ◽  
Robert L. Jarret ◽  
Ronny R. Duncan ◽  
Stephen Kresovich
Keyword(s):  
Rapd Markers ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
The United States ◽  
Principal Coordinates Analysis ◽  
Data Set ◽  
Seashore Paspalum ◽  
Principal Coordinates ◽  
Paspalum Vaginatum ◽  
High Level

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic relationships and variation among ecotypes of the turfgrass seashore paspalum (Paspalum vaginatum Swartz). Vegetative tissues or seeds of 46 seashore paspalum ecotypes were obtained from various locations in the United States, Argentina, and South Africa. Leaf DNA extracts were screened for RAPD markers using 34 10-mer random primers. A total of 195 reproducible RAPD fragments were observed, with an average of six fragments per primer. One hundred and sixty-nine fragments (87% of the total observed) were polymorphic, among which 27 fragments (16%) were present in three or less ecotypes, indicating the occurrence of a high level of genetic variation among the examined accessions of this species. Cluster analysis (UPGMA) and principal coordinates analysis were performed on the RAPD data set. The results illustrate genetic relationships among the 46 ecotypes, and between ecotypes and their geographical origins. Ecotypes from southern Africa could be differentiated from the U.S. and most of the Argentinean ecotypes. With a few exceptions, ecotypes collected from Argentina, Hawaii, Florida, and Texas were separated into distinct clusters.Key words: RAPDs, polymerase chain reaction, genetic diversity, phenetic analysis.

Genetic diversity in four cabbage populations based on random amplified polymorphic DNA markers

2005 ◽  
Vol 143 (5) ◽  
pp. 377-384 ◽  
Author(s):  
O. KOUTITA ◽  
K. TERTIVANIDIS ◽  
T. V. KOUTSOS ◽  
M. KOUTSIKA-SOTIRIOU ◽  
G. N. SKARACIS
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Random Amplified Polymorphic Dna ◽  
Population Diversity ◽  
Group Method ◽  
Jaccard Coefficient ◽  
Gene Frequencies ◽  
Principal Coordinates Analysis ◽  
Arithmetic Average ◽  
Principal Coordinates

Genetic diversity in four local Greek cabbage open-pollinated populations was investigated using RAPD (Random Amplified Polymorphic DNA) DNA markers in 18 individual plants from each population. A total of 24 random primers detected 90 polymorphic bands in the four populations studied, with an average of 3·75 bands/primer. The mean between-population differentiation was close to 40%, leaving 60% for within-population diversity. The individual plants were grouped, based on the Jaccard coefficient, by clustering (Unweighted Pair Group Method and Arithmetic Average – UPGMA) and an ordination (Principal Coordinates Analysis – PCO) methods, resulting in 7 and 6 groups, respectively. In general, there was a notable similarity in the grouping of the individuals with these two methods. In addition, Nei's standard genetic distance between populations, as calculated on the basis of within-population gene frequencies, was employed to group the populations by the UPGMA method. Clustering results were in good agreement with previously reported results based on morphological descriptors applied to the same populations. It was concluded that RAPD markers could be exploited as alternative or supplementary tools to already established methods for the evaluation and classification of cabbage genetic resources.

scholarly journals Genetic Structure and Eco-Geographical Differentiation of Wild Sheep Fescue (Festuca ovina L.) in Xinjiang, Northwest China

2017 ◽  
Author(s):  
Chenglin Zhang ◽  
Jianbo Zhang ◽  
Yan Fan ◽  
Ming Sun ◽  
Wendan Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Abiotic Factors ◽  
Northwest China ◽  
Group Method ◽  
Principal Coordinates Analysis ◽  
High Genetic Diversity ◽  
Festuca Ovina ◽  
Principal Coordinates ◽  
Genetic Diversity And Structure

Glaciation and mountain orogeny have generated new ecologic opportunities for plants, favoring an increase in the speciation rate. Moreover, they also act as corridors or barriers for plant lineages and populations. High genetic diversity ensures that species are able to survive and adapt. Gene flow is one of the most important determinants of the genetic diversity and structure of out-crossed species, and it is easily affected by biotic and abiotic factors. The aim of this study was to characterize the genetic diversity and structure of an alpine species, Festuca ovina L., in Xingjiang, China. A total of 100 individuals from 10 populations were analyzed using six amplified fragment length polymorphism (AFLP) primer pairs. A total of 583 clear bands were generated, of which 392 were polymorphic; thus, the percentage of polymorphic bands (PPB) was 67.24%. The total and average genetic diversities were 0.2722 and 0.2006 (0.1686-0.2225), respectively. The unweighted group method with arithmetic mean (UPGMA) tree, principal coordinates analysis (PCoA) and STRUCTURE analyses revealed that these populations or individuals could be clustered into two groups. The analysis of molecular variance analysis (AMOVA) suggested that most of the genetic variance existed within a population, and the genetic differentiation (Fst) among populations was 20.71%. The Shannon differentiation coefficient (G’st) among populations was 0.2350. Limited gene flow (Nm = 0.9571) was detected across all sampling sites. The Fst and Nm presented at different levels under the genetic barriers due to fragmentation. The population genetic diversity was significant relative to environmental factors such as temperature, altitude and precipitation.

scholarly journals Clustering Analysis and Genome Inference of Pisang Raja Local Cultivars (Musa spp.) from Java Island by Random Amplified Polymorphic DNA (RAPD) Marker

2019 ◽  
Vol 4 (2) ◽  
pp. 42 ◽  
Author(s):  
Rasyadan Taufiq Probojati ◽  
Didik Wahyudi ◽  
Lia Hapsari
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Molecular Techniques ◽  
Principal Coordinates Analysis ◽  
Local Cultivars ◽  
Principal Coordinates ◽  
Polymorphic Bands ◽  
Cluster 2

Pisang Raja is an important local banana cultivar in the economy and cultural life in Indonesia, especially at Java. There are many Pisang Raja cultivars found on Java Island with various local names in each region, resulted in problems on taxonomic identification and grouping. Conventional research for grouping banana cultivars is still using morphological characters but considered inaccurate because of its subjectivity. This study aims to analyze the genetic diversity, grouping, and genome estimation of 13 local cultivars of Pisang Raja based on molecular approach using RAPD markers (OPA primers 1-20). Clustering and Principal Coordinates Analysis were performed to the amplified products using Paleontological Statistics (PAST) application version 3.15. Results showed that there were 12 primers which successfully amplified and produced DNA polymorphic bands in Pisang Raja, specifically OPA 1, OPA 2, OPA 3, OPA 4, OPA 5, OPA 8, OPA 16, OPA 17, OPA 18, OPA 19, and OPA 20. Pisang Raja cultivars considered have high genetic diversity, indicated by high polymorphic bands (95.17%) and low similarity coefficient values (0.2-0.6). Clustering and PCo analysis resulted in 3 clusters following its genomic group consist of AAA, AAB and ABB genomes, with Pisang Raja Bali as an outgroup (ABB). However, the separation of each cluster for genome inference was unclear. Cluster 1 consists of Pisang Raja Madu (AAB) and Raja Sereh (AAB). Cluster 2 consists of AAA and AAB genomes; includes Pisang Raja Jambe (AAA), Raja Kriyak (AAA), Raja Kutuk (AAB), Raja Brentel (AAB), Raja Seribu (AAB), and Raja Lini (AAB). Cluster 3 consists of AAA and AAB genomes, includes Pisang Raja Kisto (AAA), Raja Delima (AAA), Raja Bandung (AAB) and Raja Gareng (AAB). While Pisang Monyet (AAw) and Klutuk Wulung (BBw) as wild relatives were nested in Cluster 2. There were some different results of genome estimation based on RAPD markers compared to morphological characterization, and other molecular techniques. The use of RAPD markers is quite efficient and effective for studying genetic diversity and identifying genomes in bananas.

scholarly journals Extreme homogeneity among Brazilian wheat genotypes determined by RAPD markers

2000 ◽  
Vol 35 (11) ◽  
pp. 2255-2260 ◽  
Author(s):  
LORETA BRANDÃO DE FREITAS ◽  
LEANDRO JERUSALINSKY ◽  
SANDRO LUIS BONATTO ◽  
FRANCISCO MAURO SALZANO
Keyword(s):  
Rapd Markers ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Dna Amplification ◽  
Triticum Aestivum L ◽  
Genetic Distances ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Future Improvement ◽  
Improvement Programs

Random amplified polymorphic DNA markers (RAPD) were used to estimate the variability of 14 genotypes of Brazilian wheat (Triticum aestivum L.), using a set of 50 random 10mer primers. A total of 256 reproducibly scorable DNA amplification products were obtained from 48 of the primers, 83% of which were polymorphic. Genetic distances among genotypes were calculated and a dendrogram and a principal coordinates analysis showing the genetic relationships among them were obtained. Despite the low variability found (average genetic distance of 27%), two groups of genotypes could be identified, which probably reflect how they were formed. Studies such as this one may be important in the planning and development of future improvement programs for this plant species.

scholarly journals Genetic Diversity of Salvia Species Assessed by ISSR and RAPD Markers

2016 ◽  
Vol 44 (2) ◽  
pp. 431-436 ◽  
Author(s):  
Masoumeh YOUSEFIAZARKHANIAN ◽  
Ali ASGHARI ◽  
Jafar AHMADI ◽  
Behvar ASGHARI ◽  
Ali Ashraf JAFARI
Keyword(s):  
Genetic Diversity ◽  
Genetic Polymorphisms ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Genetic Variations ◽  
Molecular Techniques ◽  
Wild Populations ◽  
Similarity Coefficients ◽  
The World

The genus Salvia includes an enormous assemblage of nearly 1,000 species dispersed around the world. Due to possible threats to this genus, there is an immediate requirement to evaluate the diversity of its wild populations. ISSR and RAPD molecular techniques were used to evaluate the genetic relationships among twenty-one ecotypes of eight Salvia species. Amplification of genomic DNA using 23 primers (15 RAPD and eight ISSR) produced 280 bands, of which 91% were polymorphic. The results of marker parameters showed no clear difference between two marker systems. It was generally observed that both ISSR and RAPD markers had similar efficiency in detecting genetic polymorphisms with remarkable ability to differentiate the closely related ecotypes of Salvia. Nei’s similarity coefficients for these techniques ranged from 0.48 to 0.98. Based on the results of clustering, PCoA and AMOVA, the genetic diversity between and within species was confirmed. So, conservation and domestication of the genus Salvia must be due to levels of genetic variations.

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 Similarity of Commerson’s Anchovy across Segara Anakan Cilacap Assessed Using Randomly Amplified Polymorphic DNA (RAPD) Markers

Jurnal Biota ◽  
2021 ◽  
Vol 7 (1) ◽  
pp. 42-50
Author(s):  
Muhammad Khoerol Anam ◽  
Adi Amurwanto ◽  
Kusbiyanto Kusbiyanto ◽  
Hendro Pramono ◽  
M Husein Sastranegara ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Differences ◽  
Population Genetic Study ◽  
Randomly Amplified Polymorphic Dna ◽  
High Genetic Diversity ◽  
Impressive Result

Segara Anakan areas can be divided into three different regions according to their salinity. Salinity differences suggested that Commerson’s anchovy population in that area can be divided into three subpopulations due to genetic differences. Genetic differences among subpopulation can be assessed through a population genetic study using random amplified polymorphic DNA. This study aims to evaluate the genetic variation and differences of Commerson's anchovy (Stolephorus commersonnii) collected at three different water salinities in Segara Anakan estuary Cilacap Indonesia. Total genomic DNA was isolated using the Chelex method. Genetic diversity and differences were assessed using RAPD markers and were analyzed statistically using an analysis of molecular variance, as implemented in Arlequin software.  The results showed that high genetic diversity was observed within the subpopulations. However, no significant genetic differences were observed among subpopulations which indicate genetic similarity. A high number of offspring are likely to cause high genetic variation within subpopulations.  Adult and larvae migration is the cause of genetics similarity across Segara Anakan. Another impressive result is that water salinity did not affect the genetic characteristic of Commerson,s anchovy. Genetic similarity of Commerson’s anchovy indicates that Segara Anakan forms a single genetic conservation unit.

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