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 of Turkish lathyrus L. landraces using ISSR markers

Genetika ◽  
2018 ◽  
Vol 50 (2) ◽  
pp. 395-402
Author(s):  
Hüseyin Uysal ◽  
Zeki Acar ◽  
İlknur Ayan ◽  
Orhan Kurt
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Genetic Relationships ◽  
Issr Markers ◽  
The Other ◽  
High Similarity ◽  
Pairwise Genetic Distance ◽  
Dna Fragment ◽  
Lathyrus Sativus L ◽  
Issr Primers

Fifty-one Lathyrus sativus L. landraces and one L. clymenum L. landrace collected from Turkey and one L. sativus cultivar, G?rb?z, were evaluated with ISSR markers in this study to molecular characterization. Three ISSR primers were used and 45 DNA fragment were evaluated, of which 44 bands were polymorphic. The frequencies of scored bands ranged from 0.009 to 0.888 and averaged 0.363. The genotypes MLT04 and NEV02 had high similarity with 0.825 according to pairwise grouping. The furthest pairwise group was G?rb?z and MLT02 with 0.244. The nearest genotype to G?rb?z was CNR03 with 0.577. The pairwise genetic distance between L. clymenum and L. sativus ranged from 0.353 (accession NEV01) to 0.637 (accession DEN04) and pairwise genetic distance to the cultivar G?rb?z was 0.375. Assessment of genetic relationships among Lathyrus genotypes made two main groups. One of them covered only G?rb?z variety and the other covered 52 Lathyrus landrace. L. sativus and L. clymenum separated prominently in the second group.

scholarly journals Intersimple Sequence Repeat Markers for Fingerprinting and Determining Genetic Relationships of Walnut (Juglans regia) Cultivars

2002 ◽  
Vol 127 (1) ◽  
pp. 75-81 ◽  
Author(s):  
Daniel Potter ◽  
Fangyou Gao ◽  
Giovanna Aiello ◽  
Charles Leslie ◽  
Gale McGranahan
Keyword(s):  
Genetic Relationships ◽  
Juglans Regia ◽  
Issr Markers ◽  
Genetic Distances ◽  
Sequence Repeat ◽  
Geographic Origins ◽  
Pcr Products ◽  
Extensive Exchange ◽  
The One ◽  
Issr Primers

The utility of intersimple sequence repeat (ISSR) markers for identification of English or Persian walnut (Juglans regia L.) cultivars was explored. Four cultivars were screened with 47 ISSR primers; eight of these primers, which generated reproducible and informative data, were selected for further study. Two individuals from each of 48 cultivars, including many currently important in the California walnut industry as well as accessions from Europe and Asia, were then examined with the eight ISSR primers. Polymerase chain reaction (PCR) products were separated on agarose gels and stained with ethidium bromide. Fifty-four bands were scored as present or absent in each cultivar; of these, 31 (57%) were polymorphic among the 48 cultivars. Combined data from the eight ISSR primers provided a unique fingerprint for each of the cultivars tested. Fifteen of the cultivars could be distinguished from all others with just one primer, 31 with a minimum of two primers, and two required three primers. Pairwise genetic distances between the cultivars were calculated and a dendrogram was generated using the neighbor-joining algorithm. Some of the groupings in the dendrogram corresponded to groups which, based on known pedigrees, are genealogically closely related. Others included accessions from diverse genetic and/or geographic origins. These results can be attributed to a combination of the limitations of the ISSR method for inferring genetic relationships, on the one hand, and the complex history of walnut cultivar development involving extensive exchange and breeding of germplasm from different geographic regions, on the other.

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.

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 Efficiency of different PCR-based marker systems for assessment of Iris pumila genetic diversity

Biologia ◽  
2013 ◽  
Vol 68 (4) ◽  
Author(s):  
Olena Bublyk ◽  
Igor Andreev ◽  
Ruslan Kalendar ◽  
Kateryna Spiridonova ◽  
Viktor Kunakh
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Issr Markers ◽  
Genetic Distances ◽  
Resolving Power ◽  
Abiotic Stress Response ◽  
Genetic Population ◽  
Iris Pumila ◽  
Polymorphic Bands

AbstractWe investigated informativeness and effectiveness of different marker types (ISSR, IRAP, REMAP, RGAP and LP-PCR that employ primers based on the conservative sequences of abiotic stress response genes) to study genetic diversity of Iris pumila L. By the number of amplicons per primer, number of polymorphic amplicons per primer and resolving power index (Rp), ISSR-markers were the most efficient followed by LP-PCR-markers. In order of decreasing value of indicators of genetic diversity “the percentage of polymorphic bands”, and “the average Jaccardś genetic distance between plants”, marker systems may be arranged as follows: ISSR > RAPD > LP-PC > RGAP ≈ IRAP. For ISSR-markers, the percentage of polymorphic bands was 1.3–1.7 times higher than for the others, and the average genetic distance was 1.2–1.3 times higher. Different marker systems were ranked by the value of Neiś gene diversity and the Shannonś index as follows: ISSR > RAPD ≈ LP-PCR > RGAP ≈ IRAP, with the highest and the lowest values differing 1.4 times. Genetic population structure was investigated with program Structure 2.3. The data of all marker systems suggest that all genomes under study belonged to one population. The PCoA and cluster analyses based on genetic distances showed distinctions in clustering generated from different markers data and summarized data, as well as the lack of strong clusters. Mantel test revealed significant positive correlation between the matrices of genetic distances generated by the data of almost all marker systems. The strongest correlation was found between RGAP- and IRAP-markers (r = 0.452, p = 0.01) and between RGAP and ISSR (r = 0.430, p = 0.01). ISSR, RAPD and LP-PCR proved to be more effective for the study of I. pumila genetic diversity, nevertheless, joint use of different marker systems will provide a more comprehensive assessment of variation in different genomic regions.

Genetic relationships of Chinese prickly ash as revealed by ISSR markers

Biologia ◽  
2015 ◽  
Vol 70 (1) ◽  
Author(s):  
Shijing Feng ◽  
Tuxi Yang ◽  
Xiao Li ◽  
Lv Chen ◽  
Zhenshan Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationship ◽  
Genetic Divergence ◽  
Genetic Similarity ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Similarity Coefficient ◽  
Chinese Prickly Ash ◽  
New Cultivars ◽  
Issr Primers

AbstractChinese prickly ash, belonging to the genus Zanthoxylum L., has been one of the most important commerciallyexploited plants for its alimentary, industrial and medicinal applications. However, the breeding and promotion of Chinese prickly ash have been severely restricted due to its confusing classification. Therefore, we assessed genetic diversity and phylogenetic relationship among 45 Chinese prickly ash samples collected from 6 main cultivated regions using 11 ISSR primers. These eleven selected primers generated a total of 102 scorable bands ranging from 150 to 2000 bp, corresponding to an average of approximately 9.3 bands per primer. The percentage of polymorphic loci for all samples ranged from 75% to 100%, with an average of 84.3%. The genetic similarity coefficient across all samples varied from 0.460 to 0.919. Remarkably, UPGMA analysis showed that 45 samples were divided into six clusters with a genetic similarity of 0.7. The closest genetic relationship was observed between Dahongpao collected from Qin’an and Tianshui, and the greatest genetic divergence was found between Dahongpao collected from Hengshui and Jiuyeqing collected from Jiangjin. It could serve as a basis for identifying Chinese prickly ash cultivars, breeding new cultivars and protecting the Chinese prickly ash resources in main regions.

scholarly journals Determination of Camellia oleifera Abel. Germplasm Resources of Genetic Diversity in China using ISSR Markers

2018 ◽  
Vol 46 (2) ◽  
pp. 501-508
Author(s):  
Junyong CHENG ◽  
Dezhi JIANG ◽  
Hua CHENG ◽  
Xihua ZHOU ◽  
Yingyou FANG ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Germplasm Management ◽  
Camellia Oleifera ◽  
High Genetic Diversity ◽  
Upgma Cluster Analysis ◽  
Close Genetic Relationship ◽  
Issr Primers

Camellia oleifera is one of the four woody oil plants in the world, which is widely cultivated in South China. To examine the genetic diversity of C. oleifera in China, the diversity and genetic relationships among and within major populations of 109 varieties of C. oleifera were analyzed using ISSR markers. Twenty-three ISSR primers out of 49 primers yielded approximately 487 legible bands. A total of 335 of these bands were polymorphic markers, and the ratio of polymorphism was 68.86%. From the results, Zhejiang province showed the highest populations genetic diversity (H value 0.18), while Guangxi population showed the lowest genetic diversity (H 0.0851). Base on the bands, the genetic similarity coefficient ranged from 0.61 to 0.93 using NTSYS2.10e software. When coefficient was 0.75, 109 cultivars were divided into 11 categories and categories I contain 79 varieties by UPGMA cluster analysis. The test varieties divided into 7 sub-groups when categories were 0.75, which show a close genetic relationship. Results advised that Hunan is the main producing area of C. oleifera, with enriched C. oleifera variety and complex topography, and therefore has a high genetic diversity. Meanwhile, the main varieties of C. oleifera in Hubei are imported from Hunan, which results in fewer varieties and reduces the genetic diversity of C. oleifera. The ISSR profiles can improve C. oleifera germplasm management and provide potential determine correlations between different varieties and its distribution in different province.

scholarly journals Study of genetic diversity in Tunisian local cattle populations using ISSR markers

2019 ◽  
Vol 42.3 ◽  
pp. 7296-7302
Author(s):  
Haifa EL HENTATI ◽  
Najia THAMRI ◽  
Wissal DEROUICH ◽  
Mouna HADHLI ◽  
Taoufik BOUKHORSA
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Issr Markers ◽  
Genetic Distances ◽  
Sequence Repeat ◽  
North West ◽  
Upgma Dendrogram ◽  
The North ◽  
Total Genetic Diversity ◽  
Issr Primers

The inter-simple DNA sequence repeat (ISSR) method was used to study genetic diversity in three local cattle from the north, northeast and north west of Tunisia. Twenty samples were analysed using three ISSR primers. In total, 22 bands were amplified of which 15 are polymorphic (68.18%). The total genetic diversity (Ht), genetic diversity within populations (Hs), coefficient of gene differentiation (Gst) and gene flow (Nm) were 0.2706, 0.01314, 0.8841 and 0.0656. To better visualize the structure of the population, a UPGMA dendrogram constructed from the genetic distances of NEI shows that the populations of North (Bizerte) and Northeast (Nabeul) are genetically closest while that of Northwest (Jendouba and Siliana) is the furthest from the two others.

scholarly journals Identifying Lychee (Litchi chinensis Sonn.) Cultivars and their Genetic Relationships Using Intersimple Sequence Repeat (ISSR) Markers

2003 ◽  
Vol 128 (6) ◽  
pp. 838-845 ◽  
Author(s):  
Chemda Degani ◽  
Jiusheng Deng ◽  
Avigdor Beiles ◽  
Ruth El-Batsri ◽  
Moshe Goren ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Genetic Distances ◽  
Neighbor Joining ◽  
Sequence Repeat ◽  
Issr Analysis ◽  
Simple Sequence ◽  
Issr Primers

There is widespread confusion and uncertainty concerning the identity of lychee cultivars: the same cultivar may be known under different names and different cultivars may appear under the same name. In the present study, the potential of intersimple sequence repeat (ISSR) for the identification of 66 lychee cultivars and accessions and a determination of their genetic relationships was evaluated, using 32 primers containing different simple sequence repeat motifs. Of the 194 bands produced, 124 (64%) were polymorphic. A set of six ISSR primers was sufficient to distinguish all cultivars and accessions. Thus, cultivars which are morphologically very similar and have identical isozyme profiles can be distinguished by ISSR analysis. However, seven pairs of accessions, each considered to be the same cultivar, were found to be identical by ISSR analysis. Nei and Li band-sharing distances and Nei genetic distances were calculated among the cultivars and two similarity dendrograms were generated using the neighbor-joining algorithm. Results showed that the ISSR technique is a valuable tool for identification of lychee cultivars and analysis of their genetic relationships.

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