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

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

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Genetic diversity of wild sunflower (Helianthus sp.) accessions with different tolerance to mid-stalk white rot

Genetika ◽

10.2298/gensr1402331m ◽

2014 ◽

Vol 46 (2) ◽

pp. 331-342 ◽

Cited By ~ 1

Author(s):

Dragana Miladinovic ◽

Ksenija Taski-Ajdukovic ◽

Nevena Nagl ◽

Branislav Kovacevic ◽

Aleksandra Dimitrijevic ◽

...

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Random Amplified Polymorphic Dna ◽

Significance Test ◽

White Rot ◽

High Tolerance ◽

Principal Coordinates Analysis ◽

Wild Sunflower ◽

Phylogenetic Relations ◽

Principal Coordinates

Random amplified polymorphic DNA (RAPD) markers were used to detect polymorphism among accessions of wild sunflower species H?lianthus maximiliani, Helianthus tuberosus, Helianthus mollis and Helianthus rigidus with different tolerance to mid-stalk white rot and selection of potential markers for different levels of tolerance to this disease. Estimates of genetic variation showed that genetic diversity was equally distributed between Helianthus species and within them. Cluster analysis corresponded to the phylogenetic relations within the genus Helianthus. The results obtained by principal coordinates analysis (PCoA), where the first two principal coordinates accounted for 83.7% of total variation, perfectly coincided with the results of cluster analysis. Contingency coefficient significance test showed that most of the used primers generated bands associated with some level of tolerance or susceptibility to mid- stalk white rot. Furthermore, contingency analysis showed that primer C12 generated bands associated with resistance (100%) to mid-stalk white rot both in H. mollis and in all accessions, while primer X18 generated bands significantly associated with high tolerance (75%) in H. rigidus, H. mollis as well as in all tested accessions. The C15-600 bp locus was found to be significantly associated with high tolerance (75%) in all accessions, and medium tolerance (50%) in H. mollis.

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

Acta Biologica Szegediensis ◽

10.14232/abs.2019.1.15-24 ◽

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.

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Genetic Structure and Eco-Geographical Differentiation of Lancea tibetica in the Qinghai-Tibetan Plateau

Genes ◽

10.3390/genes10020097 ◽

2019 ◽

Vol 10 (2) ◽

pp. 97 ◽

Cited By ~ 2

Author(s):

Xiaofeng Chi ◽

Faqi Zhang ◽

Qingbo Gao ◽

Rui Xing ◽

Shilong Chen

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Gene Flow ◽

Tibetan Plateau ◽

Environmental Changes ◽

Restricted Gene Flow ◽

Principal Coordinates Analysis ◽

Principal Coordinates ◽

Genetic Diversity And Structure ◽

Tanggula Mountains

The uplift of the Qinghai-Tibetan Plateau (QTP) had a profound impact on the plant speciation rate and genetic diversity. High genetic diversity ensures that species can survive and adapt in the face of geographical and environmental changes. The Tanggula Mountains, located in the central of the QTP, have unique geographical significance. The aim of this study was to investigate the effect of the Tanggula Mountains as a geographical barrier on plant genetic diversity and structure by using Lancea tibetica. A total of 456 individuals from 31 populations were analyzed using eight pairs of microsatellite makers. The total number of alleles was 55 and the number per locus ranged from 3 to 11 with an average of 6.875. The polymorphism information content (PIC) values ranged from 0.2693 to 0.7761 with an average of 0.4378 indicating that the eight microsatellite makers were efficient for distinguishing genotypes. Furthermore, the observed heterozygosity (Ho), the expected heterozygosity (He), and the Shannon information index (I) were 0.5277, 0.4949, and 0.9394, respectively, which indicated a high level of genetic diversity. We detected high genetic differentiation among all sampling sites and restricted gene flow among populations. Bayesian-based cluster analysis (STRUCTURE), principal coordinates analysis (PCoA), and Neighbor-Joining (NJ) cluster analysis based on microsatellite markers grouped the populations into two clusters: the southern branch and the northern branch. The analysis also detected genetic barriers and restricted gene flow between the two groups separated by the Tanggula Mountains. This study indicates that the geographical isolation of the Tanggula Mountains restricted the genetic connection and the distinct niches on the two sides of the mountains increased the intraspecific divergence of the plants.

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

Genome ◽

10.1139/g94-143 ◽

1994 ◽

Vol 37 (6) ◽

pp. 1011-1017 ◽

Cited By ~ 37

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.

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Genetic diversity analysis using simple sequence repeat markers in soybean

Plant Genetic Resources ◽

10.1017/s1479262114000331 ◽

2014 ◽

Vol 12 (S1) ◽

pp. S87-S90 ◽

Cited By ~ 2

Author(s):

Zhenbin Hu ◽

Guizhen Kan ◽

Guozheng Zhang ◽

Dan Zhang ◽

Derong Hao ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Genetic Relationships ◽

Wild Soybean ◽

Sequence Repeat ◽

Principal Coordinates Analysis ◽

Principal Coordinates ◽

Cultivated Soybean ◽

Simple Sequence ◽

Nei's Genetic Distance

To evaluate the genetic diversity (GD) of wild and cultivated soybeans and determine the genetic relationships between them, in this study, 127 wild soybean accessions and 219 cultivated soybean accessions were genotyped using 74 simple sequence repeat (SSR) markers. The results of the study revealed that the GD of the wild soybeans exceeded that of the cultivated soybeans. In all, 924 alleles were detected in the 346 soybean accessions using 74 SSRs, with an average of 12.49 alleles per locus. In the 219 cultivated soybean accessions, 687 alleles were detected, with an average of 9.28 alleles per locus; in the 127 wild soybean accessions, 835 alleles were detected, with an average of 11.28 alleles per locus. We identified 237 wild-soybean-specific alleles and 89 cultivated-soybean-specific alleles in the 346 soybean accessions, and these alleles accounted for 35.28% of all the alleles in the sample. Principal coordinates analysis and phylogenetic analysis based on Nei's genetic distance indicated that all the accessions could be classified into two major clusters, corresponding to wild and cultivated soybeans. These results will increase our understanding of the genetic differences and relationships between wild and cultivated soybeans and provide information to develop future breeding strategies to improve soybean yield.

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Genetic diversity and relationships of Chinese donkeys using microsatellite markers

Archives Animal Breeding ◽

10.5194/aab-62-181-2019 ◽

2019 ◽

Vol 62 (1) ◽

pp. 181-187 ◽

Cited By ~ 2

Author(s):

Lulan Zeng ◽

Ruihua Dang ◽

Hong Dong ◽

Fangyu Li ◽

Hong Chen ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Genetic Relationships ◽

Mean Value ◽

Principal Coordinates Analysis ◽

Expected Heterozygosity ◽

Principal Coordinates ◽

Baseline Information ◽

Grouping Pattern ◽

The Mean

Abstract. Donkeys are one important livestock in China because of their nourishment and medical values. To investigate the genetic diversity and phylogenetic relationships of Chinese donkey breeds, a panel of 25 fluorescently labeled microsatellite markers was applied to genotype 504 animals from 12 Chinese donkey breeds. A total of 226 alleles were detected, and the expected heterozygosity ranged from 0.6315 (Guanzhong) to 0.6999 (Jiami). The mean value of the polymorphism information content, observed number of alleles, and expected number of alleles for all the tested Chinese donkeys were 0.6600, 6.890, and 3.700, respectively, suggesting that Chinese indigenous donkeys have relatively abundant genetic diversity. Although there were abundant genetic variations found, the genetic differentiation between the Chinese donkey breeds was relatively low, which displayed only 5.99 % of the total genetic variance among different breeds. The principal coordinates analysis clearly splits 12 donkey breeds into two major groups. The first group included Xiji, Xinjiang, Liangzhou, Kulun, and Guanzhong donkey breeds. In the other group, Gunsha, Dezhou, Biyang, Taihang, Jiami, Qingyang, and Qinghai donkeys were clustered together. This grouping pattern was further supported by structure analysis and neighbor-joining tree analysis. Furthermore, genetic relationships between different donkey breeds identified in this study were corresponded to their geographic distribution and breeding history. Our results provide comprehensive and precise baseline information for further research on preservation and utilization of Chinese domestic donkeys.

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Genetic Diversity of Remaining Populations of Mangaba (Hancornia speciosa Gomes) in Restingas of Brazil

Journal of Agricultural Science ◽

10.5539/jas.v9n2p46 ◽

2017 ◽

Vol 9 (2) ◽

pp. 46 ◽

Cited By ~ 1

Author(s):

Ana Veruska Cruz da Silva ◽

Julie Anne Espíndola Amorim ◽

Marília Freitas de Vasconcelos Melo ◽

Ana Da Silva Ledo ◽

Allivia Rouse Carregosa Rabbani

Keyword(s):

Genetic Diversity ◽

Genetic Relationships ◽

Issr Markers ◽

Shannon Index ◽

Conservation Strategies ◽

Principal Coordinates Analysis ◽

Fruit Species ◽

Principal Coordinates ◽

Hancornia Speciosa ◽

Brazilian Northeast

Mangaba (Hancornia speciosa Gomes) is a fruit species that is native to Brazil, and has social, economic and cultural importance. Knowledge of the genetic relationships between the remaining populations is essential in order to promote conservation strategies for these genetic resources. In the present study, it was evaluated the genetic diversity of 35 individuals from three remaining restingas areas in the states of Ceará (Iguape and Cascavel) and Pernambuco (Tamandaré), located in the Brazilian Northeast. Nine ISSR primers were used to determine the genetic variability. Sixty-one fully polymorphic fragments (100%) were generated. The largest (10) and smallest (5) number of fragments were obtained with the primers HB14 and HB12, respectively. The Shannon index (I = 0.40), the genetic diversity (H = 0.30), and the percentage of polymorphic loci (%P = 73.77%) were also estimated. Both the methods of UPGMA and the Principal Coordinates Analysis (PCoA) clustered individuals according to their place of origin. Genetic divergence was greater within population (64%) than between them (36%). This may indicate a strong genetic structure, i.e., the gene flow rate between populations is low, favoring inbreeding. ISSR markers were efficient for the analysis of genetic diversity, for the identification of clusters, and for the estimation of the genetic distance between and within populations.

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

The Journal of Agricultural Science ◽

10.1017/s002185960500554x ◽

2005 ◽

Vol 143 (5) ◽

pp. 377-384 ◽

Cited By ~ 4

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.

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

Journal of Tropical Biodiversity and Biotechnology ◽

10.22146/jtbb.44047 ◽

2019 ◽

Vol 4 (2) ◽

pp. 42 ◽

Cited By ~ 1

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.

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The Use of ISSR and RAPD Markers for Genetic Diversity among South Tunisian Barley

ISRN Agronomy ◽

10.5402/2012/952196 ◽

2012 ◽

Vol 2012 ◽

pp. 1-10 ◽

Cited By ~ 12

Author(s):

Ferdaous Guasmi ◽

Walid Elfalleh ◽

Hédia Hannachi ◽

Khadija Fères ◽

Leila Touil ◽

...

Keyword(s):

Genetic Diversity ◽

Rapd Markers ◽

Rapd Analysis ◽

Genetic Relationships ◽

Random Amplified Polymorphic Dna ◽

Resolving Power ◽

Poor Correlation ◽

Rapd And Issr ◽

South Tunisia ◽

Issr Primers

Random amplified polymorphic DNA (RAPD) and intersimple sequence repeat (ISSR) were assayed to determine the genetic diversity of 80 barley specimens from South Tunisia. The ISSR primers showed variation in the percentage of polymorphism, band informativeness (Ib), and resolving power (Rp). The percentage of polymorphism is 66.67%, the average Ib ranged from 0.24 to 0.39, while Rp ranged from 0.74 to 1.16. In RAPD analysis, three primers yielded a total of 17 scorable bands, which are all polymorphic. The three polymorphic primers exhibited variation with regard to average band informativeness (AvIb) and resolving power (Rp). RAPD and ISSR marker systems were found to be useful for the genetic diversity among the barley specimens. The two dendrograms obtained through these markers show different clustering of 80 barely specimens, but we noted that some clusters were similar in some cases. A poor correlation () was found between both sets of genetic similarity data, suggesting that both sets of markers revealed unrelated estimates of genetic relationships. Therefore, the ISSR and RAPD molecular markers show two genetic grouping of studied barely specimens.

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