scholarly journals Molecular Characterization of Vitex agnus-castus L. (Verbenaceae) Populations Grown in Aydin, Turkey

2019 ◽  
Vol 11 (2) ◽  
pp. 218-221
Author(s):  
Emre SEVİNDİK ◽  
Serkan CANER ◽  
Mahmut COŞKUN
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Genetic Distances ◽  
Purple Flower ◽  
A Value ◽  
Pink Flower ◽  
Agnus Castus

In this study, we performed a genetic diversity analysis using RAPD markers for some Vitex agnus-castus populations grown in Aydin, Turkey. Total genomic DNA isolation from the leaves of Vitex agnus-castus was performed using a commercial kit. Seven RAPD primers (OPA-02, OPA-05, OPA-13, OPA-15, OPA-16, OPA-18, OPA-20) were used to determine genetic diversity among populations. Polymerase Chain Reaction (PCR) was performed with all genomic DNA samples and primers. PCR products were run in agarose gel electrophoresis and visualized under UV light. The amplified products were scored as bands (1) and no bands (0) for all gel images and their matrix files were generated. A total of 36 characters were obtained from the primers. Phylogenetic relationships and genetic distances between the cultivars were calculated by using the PAUP* (Phylogenetic Analysis Using Parsimony and other methods) program. According to PAUP analysis, the closest genetic distances were between Çine pink flower and Çakmar purple flower, and Çakmar pink flower and Çakmar purple flower populations with a value of 0.05556; and the greatest genetic distance was between Çakmar pink flower and Köşk purple flower populations with a value of 0.36111. In the phylogenetic analysis obtained using UPGMA algorithms, the phylogenetic tree consisted of four groups. The results suggest that RAPD markers are useful tools for determining genetic relationships among Vitex agnus-castus genotypes.

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 Genetic Diversity Based on ISSR Markers of Apple Genotypes in Ardahan/Turkey

2018 ◽  
Vol 10 (4) ◽  
pp. 554-558
Author(s):  
Emre SEVİNDİK ◽  
Hüseyin UYSAL ◽  
Zehra Tuğba MURATHAN
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Distance ◽  
Uv Light ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Genetic Distances ◽  
The Matrix ◽  
Commercial Kits ◽  
Issr Primers

Within the present study, it was conducted a genetic diversity analysis using ISSR markers for some apple genotypes grown in Ardahan region, Turkey. Total genomic DNA (gDNA) isolation from apple leaves was performed using commercial kits. Five ISSR primers were used to determine the genetic diversity among the genotypes studied. Polymerase Chain Reaction (PCR) was performed with all gDNA samples to produce bands to score. PCR products were run in agarose gel and visualized under UV light. Bands on the gels were scored as “1”, while no bands at the corresponding positions were scored as “0”, to generate the matrix file. Five ISSR primers produced a total of 35 bands, and 20 of them were polymorphic. The polymorphic bands rated approximately 57%. Phylogenetic relationships and genetic distances between the genotypes were calculated by using the PAUP [Phylogenetic Analysis Using Parsimony (and Other Methods)] program.  According to the PAUP data, the closest genetic distance was 0.03704 between ‘Kaburga’ and ‘Japon Apple’ genotypes, while the furthest genetic distance was 0.48148 between ‘Karanfil Apple’ and ‘Sisli Uruset’. The phylogenetic analysis obtained using UPGMA algorithm produced a phylogenetic tree with two clades. The results suggest that ISSR markers are useful tools for determining genetic relationships among apple genotypes.

scholarly journals Genetic Diversity of Elaeagnus angustifolia L. (Elaeagnaceae) Populations in İzmir (Turkey)

2021 ◽  
Vol 78 (1) ◽  
pp. 35
Author(s):  
Erengül SOFYALIOĞLU ◽  
Emre SEVİNDİK ◽  
Hüseyin UYSAL
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Uv Light ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Genetic Distances ◽  
Elaeagnus Angustifolia ◽  
A Value ◽  
Pcr Products ◽  
Issr Primers

This study was performed out genetic diversity of some Elaeagnus angustifolia L. populations growing in İzmir province by using ISSR markers. In the study, PCR was performed using 15 ISSR primers. PCR products were run in agarose gel and visualized under UV light. Amplified products were scored as follows. A total of 46 bands were produced from 15 ISSR primers, of which 27 were polymorphic. The proportion of polymorphic bands was evaluated as approximately 58.7%. Genetic distances between phylogenetic trees and genotypes were calculated using the PAUP program. The phylogenetic tree consists of two large clades. The longest distance between populations was between Gümüldür-Özdere and Çeşme-Alaçatı population with a value of 0.50, while the closest distance was between Çeşme-Ayayorgi and Konak-Hatay populations with a value of 0.06. The results show that ISSR markers are useful tools for determining genetic relationships between E. angustifolia populations

scholarly journals Genetic diversity in table grapes based on RAPD and microsatellite markers

2011 ◽  
Vol 46 (9) ◽  
pp. 1035-1044 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Sérgio Yoshimitsu Motoike
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Similarity Index ◽  
Genetic Distances ◽  
Table Grape ◽  
Group Method ◽  
Molecular Characteristics ◽  
Table Grapes ◽  
Pair Group

The objective of this work was to analyze the genetic diversity of 47 table grape accessions, from the grapevine germplasm bank of Embrapa Semiárido, using 20 RAPD and seven microsatellite markers. Genetic distances between pairs of accessions were obtained based on Jaccard's similarity index for RAPD data and on the arithmetic complement of the weighted index for microsatellite data. The groups were formed according to the Tocher's cluster analysis and to the unweighted pair‑group method with arithmetic mean (UPGMA). The microsatellite markers were more efficient than the RAPD ones in the identification of genetic relationships. Information on the genetic distance, based on molecular characteristics and coupled with the cultivar agronomic performance, allowed for the recommendation of parents for crossings, in order to obtain superior hybrids in segregating populations for the table grape breeding program of Embrapa Semiárido.

scholarly journals Divergência genética entre acessos de mentrasto do Estado do Tocantins através de marcadores RAPD

2013 ◽  
Vol 4 (4) ◽  
pp. 290-298
Author(s):  
Elainy Martins Oliveira ◽  
Waldesse Oliveira Junior ◽  
Jaqueline Oliveira ◽  
Henrique Guilhon De Castro
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Geographic Location ◽  
Genetic Distances ◽  
Similarity Coefficients ◽  
Ageratum Conyzoides ◽  
Genetic Studies ◽  
Low Degree ◽  
Medicinal Properties ◽  
Degree Of Association

Ageratum conyzoides (Asteraceae) is known in Brazil for its medicinal properties being mainly used as painkiller and anti-inflammatory. Due to the existence of few genetic studies for this species, this work aimed to characterize the genetic diversity among nine accessions from different sites at Tocantins state, to provide information about its genetic resources. Similarity coefficients obtained varied from 48% to 80%, result of amplification of 102 fragments, of which 72 (70.5%) were polymorphic. Groupment analysis allowed the differentiation in three groups. One of them was distinguished because it presented the highest similarity among all, being composed by ANA and NAT (80% similarity). In general, these data showed there is low degree of association between the geographic location of the accessions and the genetic distances. So, the collected accession ns in Tocantins state presented considerable genetic variability and the efficiency of RAPD markers for such characterization was here proven.

scholarly journals Assessment of genetic diversity among surian Toona sinensis Roem in progenies test using random amplified polymorphic DNA markers

2018 ◽  
Vol 22 (1) ◽  
pp. 22
Author(s):  
Jayusman Jayusman ◽  
Muhammad Na’iem ◽  
Sapto Indrioko ◽  
Eko Bhakti Hardiyanto ◽  
ILG Nurcahyaningsih
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Management Strategies ◽  
Genetic Distances ◽  
Sampled Data ◽  
Toona Sinensis ◽  
The Mean ◽  
Individual Trees

Surian Toona sinensis Roem is one of the most widely planted species in Indonesia. This study aimed to estimate the genetic diversity between a number of surian populations in a progeny test using RAPD markers, with the goal of proposing management strategies for a surian breeding program. Ninety-six individual trees from 8 populations of surian were chosen as samples for analysis. Eleven polymorphic primers (OP-B3, OP-B4, OP-B10, OP-H3, OP-Y6, OP-Y7, OP-Y8, OP-Y10, OP-Y11, OP-Y14, and OP-06) producing reproducible bands were analyzed for the 96 trees, with six trees per family sampled. Data were analyzed using GenAlEx 6.3, NTSYS 2.02. The observed percentage of polymorphic loci ranged from 18.2% to 50%. The mean level of genetic diversity among the surian populations was considered to be moderate (He 0.304). Cluster analysis grouped the genotypes into two main clusters, at similarity levels of 0.68 and 0.46. The first two axes of the PCoA explained 46.16% and 25.54% of the total variation, respectively. The grouping of samples into clusters and subclusters did not correspond with family and their distances, but the grouping was in line with the genetic distances of the samples.

scholarly journals Evaluation of the genetic variability in bamboo using RAPD markers

2011 ◽  
Vol 49 (No. 1) ◽  
pp. 24-28 ◽  
Author(s):  
S. Nayak ◽  
G.R. Rout ◽  
P. Das
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Growth Habit ◽  
Floral Morphology ◽  
Genetic Relationships ◽  
Species Cluster ◽  
Wide Range ◽  
Bambusa Vulgaris ◽  
Bambusa Ventricosa ◽  
Taxonomic Studies

Classical taxonomic studies of the bamboos are based on floral morphology and growth habit, which can cause problems in identification due to erratic flowering. Identification and genetic relationships in 12 species of bamboo were investigated using random amplified polymorphic DNAs (RAPD) technique. Analysis started by using thirty 10-mer primers that allowed us to distinguish 12 species and to select a reduced set of primers. The selected primers were used for identification and for establishing a profiling system to estimate genetic diversity. A total of one hundred thirty seven distinct polymorphic DNA fragments (bands), ranging from 0.4–3.3 kb were amplified by using 10 selected primers. The genetic similar analysis was conducted based on presence or absence of bands, which revealed a wide range of variability among the species. Cluster analysis clearly showed two major clusters belonging to 12 species of bamboo. Two major clusters were further divided into three minor clusters. The species of Bambusa vulgaris and Bambusa vulgaris var. striata were the most closely related and formed the first minor cluster along with Bambusa ventricosa. The variety of Bambusa multiplex var. Silver stripe and Bambusa multiplex were very closely related and there was no variation with Bambusa ventricosa. Another minor cluster was obtained between Bambusa arundinacea, Cephalostachyum pergracil and Bambusa balcooa. The RAPD technique has the potential for use in species identification and genetic relationships between taxa and species of bamboo for breeding program.

Microsatellite analysis of genetic variability in Waler horses from Australia

2013 ◽  
Vol 61 (5) ◽  
pp. 357 ◽  
Author(s):  
Anas M. Khanshour ◽  
Rytis Juras ◽  
E. Gus Cothran
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Bayesian Method ◽  
Genetic Relationships ◽  
Similarity Measures ◽  
Genetic Distances ◽  
Microsatellite Analysis ◽  
Population Subdivision ◽  
Factorial Correspondence Analysis ◽  
Horse Breed

The Waler horse breed is an integral part of Australian history. The purposes of this study were to analyse the genetic variability in Waler horses from Australia and to investigate genetic relationships with other horse breeds. We examined the genetic diversity of 70 Waler horses sampled from seven breeding stations in Australia. Also we analysed the relationships of these horses with 11 other horse breeds. Analysis of the genetic structure was carried out using 15 microsatellite loci, genetic distances, AMOVA, factorial correspondence analysis and a Bayesian method. We found that the genetic diversity in the Waler was greater than the domestic horse mean and exceeded that of all endangered horse breeds. Our findings also revealed moderate population subdivision rather than inbreeding. All genetic similarity measures indicated that the Thoroughbred might be a key ancestor to the Waler. This study indicates that there is no immediate concern for loss of variation in Waler horses. Also, there clearly has been a strong input from the Thoroughbred into the Waler horse breed. However, the genetic evidence suggests that this input was not just direct but also came through other types of horses with a Thoroughbred cross background.

scholarly journals Genetic variation of Indian potato (Solanum tuberosum L.) genotypes using chromosomal and RAPD markers

2010 ◽  
Vol 10 (3) ◽  
pp. 238-246 ◽  
Author(s):  
Anath Bandhu Das ◽  
Iswar Chandra Mohanty ◽  
Dawanidhi Mahapatra ◽  
Suprava Mohanty ◽  
Ashutosh Ray
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Solanum Tuberosum L ◽  
Chromosome Analysis ◽  
Genetic Distances ◽  
Chromosome Length ◽  
Similarity Coefficients ◽  
Varietal Improvement ◽  
And Cluster Analysis ◽  
4C Dna Content

Genetic diversity in thirty Indian potatoes were analyzed employing karyotype, genome size and RAPD markers. Chromosome analysis revealed 2n = 4x = 48 except cv. K. Chandramukhi (2n = 4x + 2 = 50). Total genomic chromosome length and chromosome volume varied from 21.14µm in cv. K. Pukhraj to 31.91µm in cv. MS/89-60 and 14.31µm³ in cv. MS/92-1090 to 33.16µm³ in cv. JW-160 respectively. 4C DNA content was significantly varied from 3.640 pg (~891 Mbp) in cv. MS/92-1090 to 11.12 pg (~2747 Mbp) in cv. K. Chandramukhi. RAPD revealed 131 amplified DNA fragments (300 to 2200 bp) with 79 unique bands (7 to 71% polymorphism) among the genotypes. Similarity coefficients (ranged from 0.29 to 0.93) and cluster analysis reflected the expected trends in relationships of the full and half-sib potato genotypes. Genetic distances obtained from a dendrogram could help breeders to choose the diverse parents for a breeding program aimed at varietal improvement.

scholarly journals Reindeer Population as an Indicator of Sustainable Development of the Arctic Territory

2021 ◽  
Vol 9 (4) ◽  
pp. 21-28
Author(s):  
Natalia V. Karmanovskaya
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Genetic Relationships ◽  
Animal Husbandry ◽  
Komi Republic ◽  
Genetic Distances ◽  
The Arctic ◽  
Murmansk Oblast ◽  
The Matrix ◽  
Breeding Programmes

The objectives of this study are to carry out genetic monitoring of domestic reindeer of Nenets breed raised on the territory of Taimyr; establishment of the genetic bank of domestic reindeer of Nenets breed; as well as a comparative analysis with populations of the Nenets breed from other breeding regions (Nenets and Yamalo-Nenets Autonomous Okrug, Murmansk Oblast and the Komi Republic) using DNA markers. The microsatellites were used in the studies as DNA markers of genetic diversity. Genotyping was carried out by the methods of the Laboratory of molecular selection basis of L.K. Ernst Federal Research Center for Animal Husbandry. Statistical data processing was performed using the GenAlEx 6.5, SplitsTree 4.14.5 software, as well as the software packages “diveRsity”, “pophelper”, and “adegenet” for the R computing environment. As a result of the study, it was found that the population of reindeer of Taimyr breed in the village of Tukhard is characterised by the minimum level of polymorphism and genetic diversity, as indicated by the minimum values of all population genetic indicators. The authors assume that the patterns that have been identified are primarily the result of breeding programmes on the samples presented in this study (such studies have not been conducted before). The results of the PCA analysis and the phylogenetic dendrogram of genetic relationships, built on the basis of the matrix of Jost's D pairwise genetic distances using the NeighborNet, revealed a similar genetic structure of Taimyr populations, which, most likely, could be due to the close geographical localisation of the studied individuals. The authors come to the conclusion that a low level of both allelic and genetic diversity in the future may negatively affect the adaptation of animals to environmental conditions.

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