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 Analysis of genetic relationships of genotypes of the genus Rosa L. from the collection of Nikita Botanical Gardens using ISSR and IRAP DNA markers

2020 ◽  
Vol 24 (5) ◽  
pp. 474-480
Author(s):  
I. I. Suprun ◽  
S. A. Plugatar ◽  
I. V. Stepanov ◽  
T. S. Naumenko
Keyword(s):  
Genetic Diversity ◽  
Bayesian Methods ◽  
Dna Markers ◽  
Wild Species ◽  
Genetic Similarity ◽  
Genetic Relationships ◽  
Issr Markers ◽  
The Other ◽  
Clustering Methods ◽  
Botanical Gardens

In connection with the development of breeding and the creation of new plant varieties, the problem of their genotyping and identification is becoming increasingly important, therefore the use of molecular methods to identify genetic originality and assess plant genetic diversity appears to be relevant. As part of the work performed, informative ISSR and IRAP DNA markers promising for the study of genetic diversity of the Rosa L. genus were sought and applied to analysis of genetic relationships among 26 accessions of the genus Rosa L. from the gene pool collection of Nikita Botanical Gardens. They included 18 cultivated varieties and 8 accessions of wild species. The species sample included representatives of two subgenera, Rosa and Platyrhodon. The subgenus Platyrhodon was represented by one accession of the species R. roxburghii Tratt. Cultivated roses were represented by varieties of garden groups hybrid tea, floribunda, and grandiflora. The tested markers included 32 ISSRs and 13 IRAPs. Five ISSR markers (UBC 824, ASSR29, 3A21, UBC 864, and UBC 843) and three IRAPs (TDK 2R, Сass1, and Сass2) were chosen as the most promising. They were used for genotyping the studied sample of genotypes. In general, they appeared to be suitable for further use in studying the genetic diversity of the genus Rosa L. The numbers of polymorphic fragments ranged from 12 to 31, averaging 19.25 fragments per marker. For markers UBC 864 and UBC 843, unique fingerprints were identified in each accession studied. The genetic relationships of the studied species and varieties of roses analyzed by the UPGMA, PCoA, and Bayesian methods performed on the basis of IRAP and ISSR genotyping are consistent with their taxonomic positions. The genotype of the species R. roxburghii of the subgenus Platyrhodon was determined genetically as the most distant. According to clustering methods, the representative of the species R. bengalensis did not stand out from the group of cultivated varieties. When assessing the level of genetic similarity among the cultivated varieties of garden roses, the most genetically isolated varieties were ‘Flamingo’, ‘Queen Elizabeth’, and ‘Kordes Sondermeldung’; for most of the other varieties, groups of the greatest genetic similarity were identified. This assessment reflects general trends in phylogenetic relationships, both among the studied species of the genus and among cultivated varieties.

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 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 Molecular identification and genetic relationships among coffee species (Coffea L.) inferred from ISSR and SRAP marker analyses

2011 ◽  
Vol 63 (3) ◽  
pp. 667-679 ◽  
Author(s):  
Kumar Mishra ◽  
Sandhyarani Nishani ◽  
J Jayarama
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Genetic Relationships ◽  
Resolving Power ◽  
Diversity Analysis ◽  
Srap Marker ◽  
Genetic Diversity Analysis ◽  
Species Specific ◽  
Coffee Species ◽  
Issr Primers

The identification and genetic relationships of 23 coffee species and one coffee-related species Canthium diccocum were studied using ISSR and SRAP markers. The average polymorphism information content of SRAP primers (0.81) was lower than ISSR primers (0.86), whereas the average resolving power of the SRAP primers (9.74) is higher than the ISSR primers (8.64). The genetic similarity among the species ranged from 0.30 to 0.89 using ISSR and 0.11 to 0.90 using SRAP marker systems. Based on marker analysis, all twenty three coffee species were clustered into two major groups. Both the markers amplified species-specific fragments and are useful in genetic diversity analysis of coffee.

scholarly journals Genetic diversity among asexual and sexual progenies of Phytophthora capsici detected with ISSR markers

2021 ◽  
Vol 57 (No. 4) ◽  
pp. 271-278
Author(s):  
Ping Li ◽  
Dong Liu
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Similarity ◽  
Phytophthora Capsici ◽  
Issr Markers ◽  
Similarity Coefficients ◽  
Sexual Progeny ◽  
Sexual Offspring ◽  
Issr Primers

The population structure of Phytophthora capsici among asexual and sexual progenies was analyzed using ISSR. Thirty asexual progenies of one parent and three sexual populations were assayed for genetic diversity using 5 ISSR primers and DNA from 120 offspring of P. capsici was amplified. In total, 71 reproducible ISSR fragments were obtained, of which 100% were polymorphic, revealing high polymorphism among the isolates. Among them, the percentages of polymorphism of sexual and asexual progeny isolates were 100.00 and 77.46%, respectively. Genetic similarity coefficients among all the isolates ranged from 0.54 to 0.73. The sexual offspring population showed much more variability than the asexual offspring population with 76.26% variability attributed to diversity within populations as compared with 23.74% among populations. This research reveals that the sexual progeny population of P. capsici contributes more genetic diversity than that of asexual progeny population.

scholarly journals Genetic Diversity and Relationship of China’s Bergenia Germplasm Revealed by Intersimple Sequence Repeat Markers

2021 ◽  
pp. 1-7
Author(s):  
Xiuli Lv ◽  
Yuan Guan ◽  
Jian Wang ◽  
Yanwei Zhou ◽  
Qunlu Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Phylogenetic Relationship ◽  
Theoretical Basis ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Similarity Coefficient ◽  
Sequence Repeat ◽  
Relationship Of ◽  
Selection Of

To reveal the genetic diversity and genetic relationships of China’s Bergenia germplasm, 28 Bergenia accessions from different regions in China were analyzed by 24 intersimple sequence repeat (ISSR) markers. The results showed that 318 sites were amplified in all germplasm, including 307 polymorphic sites, and the percentage of polymorphic sites was 96.54%. Cluster analysis showed that the 28 accessions were divided into three categories, with a similarity coefficient of 0.5475. Bergenia purpurascens was clustered into one category; B. scopulosa was clustered into one category; and B. tianquaninsis, B. emeiensis, B. stracheyi, and B. crassifolia were clustered into one category. The results of the cluster analysis indicated that the 28 accessions were not completely classified by origin. Using the ISSR marker technique to analyze the phylogenetic relationship of Bergenia germplasm is helpful for identifying valuable resources and providing a theoretical basis for the selection of breeding parents.

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 between Yacon Landraces from Different Countries Based on Random Amplified Polymorphic DNAs

2011 ◽  
Vol 41 (No. 2) ◽  
pp. 73-78 ◽  
Author(s):  
L. Milella ◽  
J. Salava ◽  
G. Martelli ◽  
I. Greco ◽  
E.F. Cusimamani ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Genetic Relationship ◽  
Genetic Similarity ◽  
Morphological Traits ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Similarity Coefficient ◽  
Crop Germplasm ◽  
Relationship Of

Random amplified polymorphic DNA (RAPD) markers are widely used for evaluating the genetic relationship of crop germplasm. Five different landraces of yacon (Smallantus sonchifolius (Poepp. and Hendl.) H. Robinson; Asteraceae) collected in various countries and showing different morphological traits were investigated using a total of 61 decamer primers. A total of 282 RAPD markers were scored and 28.7% of them were polymorphic at least within landraces. RAPD markers generated by one primer (OBP14) discriminated between all landraces. Markers were used to calculate genetic similarity coefficient and to build a dendrogram representing the genetic relationship between analysed landraces. The results suggest that RAPD markers could be used as a reliable tool to perform fingerprinting studies in Smallantus sonchifolius genome. This is the first report on the use of RAPDs to evaluate genetic distance and to distinguish between different landraces in yacon.  

scholarly journals An ISSR-based genetic diversity analysis of Malus sieversii in Tienshan Mountains in Xinjiang, China and Kyrgyzstan

2019 ◽  
pp. 40-48
Author(s):  
Meiling Yang ◽  
Shiyou Che ◽  
Hong Long ◽  
Guorong Yan ◽  
Weiwei Yu
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Inter Simple Sequence Repeat ◽  
Similarity Coefficient ◽  
Malus Sieversii ◽  
Long Time ◽  
Polymorphism Rate ◽  
Different Populations ◽  
Xinjiang Of China ◽  
Issr Primers

Malus sieversii constitute a valuable genetic resource in wild apple ecosystems. The aim of this study was to use inter-simple sequence repeat (ISSR) primers as an accessible tool to investigate the genetic diversity in Malus sieversii species. The experimental materials include 34 samples from Kyrgyzstan and Xinjiang of China. A total of 125 bands and 98 polymorphic bands were amplified using 47 ISSR primers. The polymorphism rate was 78.4%. The genetic similarity coefficient of Kyrgyzstan and Xinjiang of China population was 0.68; the genetic similarity coefficient of various populations in Xinjiang was 0.72~0.94. The samples in same population got into a category, but some samples in faraway geographic locations have cross clustering. Geographical isolation hindered the gene exchange of Malus sieversii in different populations for a long time, and Malus sieversii developed along the natural selection environment direction and generate genetic differentiation after that.

scholarly journals Genetic relationships in Saccharum complex germplasm collections based on morphological and molecular markers

2021 ◽  
Vol 89 (1) ◽  
Author(s):  
Wiwit Budi WIDYASARI ◽  
. DAMANHURI
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Genetic Distance ◽  
Genetic Relationship ◽  
Genetic Similarity ◽  
Genetic Relationships ◽  
Morphological Markers ◽  
Saccharum Complex ◽  
High Genetic Diversity ◽  
Germplasm Collections

and is a cross-pollinator, so information about the genetic relationship between the accessions in germplasm collections is very important for selecting the prospective parent in crossbreeding. This research aims to determine the phylogenetic relationship of 24 Saccharum complex accessions and to verify the grouping of accessions using 37 morphological and three microsatellite molecular markers. Interpretation of morphological and molecular data was obtained from the analysis using the NTYSYpc-2.02i program. The results show that within the 24 accessions analyzed using morphological markers, some accessions did not cluster as the classification at the conservation time. This difference is due to the morphological markers, descriptions of characters that do not appear are considered as the same variables though in different morphological characters, so this increases the value of genetic similarity among accessions analyzed. In contrast, the grouping of molecular markers shows that each accession was grouped according to the classification at the conservation time. These accessions had a low genetic similarity of 0.20 with a broad genetic distance of 0.80. This broad genetic distance indicates that the twenty-four accessions have a distant genetic relationship with one another, so that the genetic diversity of these accessions is relatively high. The high genetic diversity in germplasm collections improves its potential as a crossing parent to obtain a high heterosis effect.

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