scholarly journals Evaluation of genetic diversity in geranium (Geraniaceae) using RAPD marker

Genetika ◽  
2021 ◽  
Vol 53 (1) ◽  
pp. 363-378
Author(s):  
Juan Yin ◽  
Majid Khayatnezhad ◽  
Abdul Shakoor
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Morphological Characters ◽  
Mantel Test ◽  
Group Method ◽  
Plant Resources ◽  
High Genetic Diversity ◽  
Pair Group ◽  
Genetic Structure Of Populations

Genetic diversity studies are essential to understand the conservation and management of plant resources in any environment. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Geranium genetic diversity. Therefore, we collected and analyzed thirteen species from nine provinces. Overall, one hundred and twenty-five plant specimens were collected. Our aims were 1) to assess genetic diversity among Geranium species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. Unweighted pair group method with arithmetic mean and multidimensional scaling divided Geranium species into two groups. G. sylvaticum depicted unbiased expected heterozygosity (UHe) in the range of 0.11. Shannon information was high (0.38) in G. columbinum. G. sylvaticum showed the lowest value, 0.14. The observed number of alleles (Na) ranged from 0.25 to 0.55 in G. persicum and G. tuberosum. The effective number of alleles (Ne) was in the range of 1.020-1.430 for G. tuberosum and G. collinum. Gene flow (Nm) was relatively low (0.33) in Geranium. The Mantel test showed correlation (r = 0.27, p=0.0002) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Geranium 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 Geranium species.

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.

scholarly journals Molecular identification and genetic diversity in Hypericum L.: A high value medicinal plant using RAPD markers markers

Genetika ◽  
2021 ◽  
Vol 53 (1) ◽  
pp. 393-405
Author(s):  
Dezhong Bi ◽  
Dan Chen ◽  
Majid Khayatnezhad ◽  
Zohreh Hashjin ◽  
Zifa Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characters ◽  
Mantel Test ◽  
High Genetic Diversity ◽  
Genetic Structure Of Populations ◽  
Geographical Distances ◽  
Species Adaptability ◽  
Hypericum Species

Genus Hypericum (Guttiferae, Hypericoideae) is perennial, belonging to the Hypericaceae family, having 484 species in forms of trees, shrubs, and herbs, distributed in 36 taxonomic sections. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Hypericum genetic diversity. Therefore, we collected and analyzed six species from five provinces of Iran regions. Overall, seventy plant specimens were collected. Our aims were 1) to assess genetic diversity among Hypericum species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. H. dogonbadanicum depicted unbiased expected heterozygosity (UHe) in the range of 0.10. Shannon information was high (0.32) in H. perforaturm. H. dogonbadanicum showed the lowest value, 0.17. The observed number of alleles (Na) ranged from 0.22 to 0.53 in H. dogonbadanicum and H. elongaturn. Gene flow (Nm) was relatively low (0.87) in Hypericum. The Mantel test showed correlation (r = 0.45, p=0.0001) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Hypericum 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 Hypericum species.

scholarly journals Genetic diversity of Lonicera L. (Caprifoliaceae) estimated by molecular markers and morphological characters

Genetika ◽  
2021 ◽  
Vol 53 (2) ◽  
pp. 651-662
Author(s):  
Xin Ma ◽  
Huailiang Tian ◽  
Haiou Xia ◽  
Z Zeenat
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Morphological Characters ◽  
Mantel Test ◽  
High Genetic Diversity ◽  
Changing Environments ◽  
Genetic Structure Of Populations ◽  
Geographical Distances ◽  
Species Adaptability

Members of Lonicera are characterized by opposite, narrowly elliptic to obovate leaves, white, yellow, reddish, or purple-red corolla with capitate stigma and undulate calyx margin. In Flora Iranica, Wendelbo (1965) classified 19 species of the Lonicera into two subgenera (Chamaecerasus and Lonicera) and three sections, namely Isoxylosteum, Isika and Coeloxylosteum. The four studied species belong to subgenus Chamaecerasus and sections Isika and Coeloxylosteum. No detailed Random Amplified Polymorphic DNA (RAPD) studies were conducted to study Lonicera genetic diversity. Therefore, we collected and analyzed three species from 2 provinces regions. Overall, 45 plant specimens were collected. Our aims were 1) to assess genetic diversity among Lonicera species 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. The Mantel test showed correlation (r=0.66, p=0.0001) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the Lonicera 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 Lonicera species.

scholarly journals Detecting DNA polymorphism and genetic diversity in a wide pistachio germplasm by RAPD markers

Genetika ◽  
2021 ◽  
Vol 53 (2) ◽  
pp. 783-798
Author(s):  
Xiaohui Qian ◽  
Shahram Mehri
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Morphological Characters ◽  
Mantel Test ◽  
Pistacia Vera ◽  
High Genetic Diversity ◽  
Horticultural Crops ◽  
Genetic Structure Of Populations ◽  
Geographical Distances ◽  
Species Adaptability

Assessing the genetic diversity in the population is the prerequisite to start and develop plant breeding projects. Pistacia vera is considered as a commercial species of Pistacia genus. In Iran, Pistachio export is in the second place in terms of non-oil exports and in the first place among horticultural crops. Therefore, we collected and analyzed 11 pistachio genotype (Pistacia vera), from two provinces of Iran regions. Our aims were 1) to assess genetic diversity among some of Irainian pistachio cultivars 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. Akbari cultivars depicted unbiased expected heterozygosity (UHe) in the range of 0.028. Shannon information was high (0.49) in Seifadini cultivars. Akbari cultivars howed the lowest value, 0.029. The observed number of alleles (Na) ranged from 0.261 to 2.700 in Shahpasand cultivars and Kalehghoochi cultivars. The effective number of alleles (Ne) was in the range of 1.021-1.800 for Akbari cultivars and Moosaabadi cultivars .Gene flow (Nm) was relatively low (0.38) in pistachio cultivars. The Mantel test showed correlation (r = 0.33, p=0.0001) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the among some of Irainian pistachio cultivars 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 pistachio cultivars.

scholarly journals Discrimination and Genetic Diversity among Cultivated Olives of Greece Using RAPD Markers

2003 ◽  
Vol 128 (5) ◽  
pp. 741-746 ◽  
Author(s):  
N. Nikoloudakis ◽  
G. Banilas ◽  
F. Gazis ◽  
P. Hatzopoulos ◽  
J. Metzidakis
Keyword(s):  
Genetic Diversity ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Fruit Size ◽  
Similarity Index ◽  
Group Method ◽  
Poor Correlation ◽  
Pair Group ◽  
Electrophoretic Patterns

Random amplified polymorphic DNA (RAPD) markers were used to study the genetic diversity and to discriminate among 33 Greek olive (Olea europaea L.) cultivars. Three feral forms from Crete and five foreign cultivars recently introduced into Greece were also included. Nineteen primers were selected which produced 64 reproducible polymorphic bands in the 41 olive genotypes studied, with an average of 3.4 informative markers per primer. The RAPD markers resulted in 135 distinct electrophoretic patterns, with an average of 7.1 patterns per primer. Based on either unique or combined patterns, all genotypes could be identified. Genetic similarities between genotypes were estimated using the Dice similarity index and these indicated that a high degree of diversity exists within the Greek olive germplasm. Using the unweighted pair-group method (UPGMA) most cultivars were clustered into two main groups according to their fruit size or commercial use (table or olive oil). However, poor correlation was detected between clustering of cultivars and their principal area of cultivation. RAPD marker data were subjected to nonmetric multidimentional scaling (NMDS) which produced results similar to those of the UPGMA analysis. The results presented here contribute to a comprehensive understanding of cultivated Greek olive germplasm and provide information that could be important for cultural purposes and breeding programs.

scholarly journals GENETIC VARIABILITY OF INDONESIAN PAPAYA ACCESSIONS AS REVEALED BY RANDOM AMPLIFIED POLYMORPHIC DNA AND MORPHOLOGICAL CHARACTERIZATION

2019 ◽  
Vol 20 (1) ◽  
pp. 1
Author(s):  
Riry Prihatini ◽  
Tri Budiyanti ◽  
Noflindawati Noflindawati
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Principal Component ◽  
Accurate Method ◽  
Morphological Characters ◽  
Morphological Characterization ◽  
Fruit Shape ◽  
Morphological Data ◽  
Group Method ◽  
Pair Group

<p class="abstrakinggris">Diverse papaya (<em>Carica</em> sp.) accessions are found in many regions in Indonesia, but their genetic diversity have not yet been studied. Random Amplified Polymorphic DNA (RAPD) is a simple yet accurate method that can be used to examine the genetic diversity of papaya. The study aimed to examine the genetic diversity of Indonesian papaya accessions using RAPD markers and morphological characters. The RAPD was applied on 23 papaya accessions using 30 primers. The appearing bands were further analyzed with the Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and Principal Component Analysis (PCA). The molecular results were then compared to the fruit morphological data, including fruit shape, size, flesh color, texture, and flavor. The RAPD analysis revealed that the 23 papaya accessions clustered into six main clades with Dice-Sorensen coefficient similarity ranged from 0.71 to 0.98. The first group consisted of 11 accessions, including both the hybrids and local accessions. The second group consisted of eight accessions especially six Indonesian hybrids, a Mexican Hybrid and a Hawaiian hybrid. The other four groups had a single member namely Sicincin Panjang, Lokal Sumani, Cariso, and Carica. The molecular grouping, however, did not align with the fruit character grouping. Overall, it was implied that the Indonesian papaya accessions were genetically narrow, of which some accessions were closely related to Hawaiian and Mexican accessions. These results can be used as a reference on papaya crossbreeding program in Indonesia.</p>

scholarly journals Determination of genetic variations among different Trichoderma isolates using RAPD marker in Bangladesh

1970 ◽  
Vol 9 (1) ◽  
pp. 9-20 ◽  
Author(s):  
MSI Sagar ◽  
MB Meah ◽  
MM Rahman ◽  
AK Ghose
Keyword(s):  
Genetic Diversity ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Genetic Variations ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
High Level ◽  
Cluster 2

Some Trichoderma isolates were collected from different locations of Bangladesh for evaluating their bioefficiency by determining their genetic variations. PCR-based Random Amplified Polymorphic DNA (RAPD) Marker employing 3 decamer primers produced 29 scorable bands of which all (100%) were polymorphic. The co-efficient of gene differentiation (Gst) was 1.0000 reflecting the existence of high level of genetic diversity among the isolates. The Unweighted Pair Group Method of Arithmetic Means (UPGMA) dendrogram constructed from Nei’s (1972) genetic distance produced 2 main clusters (16 isolates in cluster 1 and 19 isolates in cluster 2). The result indicating their genetic diversity has opened new possibility of using the most efficient and more isolates of Trichoderma in the preparation of effective biopesticide. Keywords: Genetic diversity; Trichoderma; RAPD DOI: http://dx.doi.org/10.3329/jbau.v9i1.8738 JBAU 2011; 9(1): 9-20

Development of DNA fingerprinting keys for the identification of radish cultivars

2004 ◽  
Vol 44 (1) ◽  
pp. 95 ◽  
Author(s):  
A. Pradhan ◽  
G. Yan ◽  
J. A. Plummer
Keyword(s):  
Dna Fingerprinting ◽  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Morphological Characteristics ◽  
Group Method ◽  
Base Pairs ◽  
Difference Matrix ◽  
Pair Group ◽  
Young Leaves ◽  
Polymerase Chain

Identification of cultivars is extremely important both for cultivation and breeding of crop plants. Cultivar identification based on morphological characteristics can be difficult and complicated. Polymerase chain reaction technologies, such as random amplified polymorphic DNA (RAPD) analysis, can readily and quickly identify cultivars using seeds and young leaves. Sixty individuals representing 7 radish cultivars were examined for RAPD marker polymorphism. Based on the polymorphism generated, 5 primers were selected, out of the 14��examined, to fingerprint the cultivars. The 5 primers produced a total of 52 fragments, 6 monomorphic and 46�polymorphic fragments, ranging in size from 206 to 2258 base pairs. A total and mean character difference matrix was calculated based on the RAPD data and a dendrogram was constructed using the unweighted pair-group method with arithmetic averages (UPGMA). Three DNA fingerprinting keys were developed for the 7 cultivars and 5 markers derived from 3 primers was the minimum required to distinguish cultivars. Results demonstrated that RAPD markers could be effectively used for the identification of radish cultivars.

scholarly journals Blueberry Cultivar Identification Using Random Amplified Polymorphic DNA and Sequence-characterized Amplified Region Markers

HortScience ◽  
2017 ◽  
Vol 52 (11) ◽  
pp. 1483-1489 ◽  
Author(s):  
Kang Hee Cho ◽  
Seo Jun Park ◽  
Su Jin Kim ◽  
Se Hee Kim ◽  
Han Chan Lee ◽  
...  
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
The United States ◽  
Morphological Characters ◽  
Polymorphic Band ◽  
Group Method ◽  
Highbush Blueberry ◽  
United States Department ◽  
Scar Markers ◽  
Sequence Characterized Amplified Region ◽  
Pair Group

Blueberry cultivars have traditionally been identified based on the evaluation of sets of morphological characters; however, distinguishing closely related cultivars remains difficult. In the present study, we developed DNA markers for the genetic fingerprinting of 45 blueberry cultivars, including 31 cultivars introduced from the United States Department of Agriculture. We obtained 210 random amplified of polymorphic DNA (RAPD) markers using 43 different primers. The number of polymorphic bands ranged from three (OPG-10 and OPQ-04) to eight (OPR-16), with an average of five. A cluster analysis performed with the unweighted pair group method using arithmetic averages produced genetic similarity values among the blueberry cultivars ranging from 0.53 to 0.85, with an average similarity of 0.68. A dendrogram clustered the 45 blueberry cultivars into two main clusters, with a similarity value of 0.65. Cluster I consisted of four rabbiteye cultivars (Pink Lemonade, Alapaha, Titan, and Vernon) and the Ashworth northern highbush cultivar. Cluster II consisted of 31 northern highbush cultivars, eight southern highbush blueberry cultivars, and Northland half-highbush blueberry cultivar. Fifty five RAPD fragments selected were sequenced to develop sequence-characterized amplified region (SCAR) markers, resulting in the successful conversion of 16 of 55 fragments into SCAR markers. An amplified polymorphic band has the same size as the RAPD fragment or smaller according to the primer combinations in the 16 SCAR markers. Among these markers, a combination of 11 SCAR markers provided sufficient polymorphisms to distinguish the blueberry cultivars investigated in this study. These newly developed markers could be a fast and reliable tool to identify blueberry cultivars.

scholarly journals Assessment of Genetic Diversity in Cultivated Tomato (Solanum Lycopersicum L.) Genotypes Using Rapd Primers

2013 ◽  
Vol 21 (1) ◽  
pp. 83-89 ◽  
Author(s):  
Saida Sharifova ◽  
Sabina Mehdiyeva ◽  
Konstantinos Theodorikas ◽  
Konstantinos Roubos
Keyword(s):  
Genetic Diversity ◽  
Rapd Analysis ◽  
Diversity Index ◽  
Random Amplified Polymorphic Dna ◽  
Arithmetic Mean ◽  
Similarity Coefficient ◽  
Group Method ◽  
Solanum Lycopersicum L ◽  
Pair Group ◽  
Upgma Cluster Analysis

Abstract Random Amplified Polymorphic DNA (RAPD) analysis was carried out on 19 Azerbaijan tomato genotypes, both cultivars and local populations. A total of 26 amplified products were revealed by 6 primers. The genetic similarity among evaluated genotypes ranged from 0.188 to 1.000. The lowest similarity was observed between cultivars ‘Azerbaijan’ and ‘Shakar’ (0.188), while the highest between ‘Elnur’ and ‘Garatag’ (1.000). The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) cluster analysis based on Jaccard’s similarity coefficient divided genotypes into four main groups. The first group was the largest and consisted of 12 genotypes, while the fourth group was the smallest consisted of 1 genotype only. The most polymorphic primer was OPB-18 that presented a genetic diversity index of 0.823, while the least informative was primer OPG-17 with an index of 0.349. The average genetic diversity calculated from RAPD data was 0.665.

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