Study on genetic diversity of Castanopsis phuthoensis Luong in Phu Tho province, Vietnam by RAPD markers

Castanopsis phuthoensis Luong is an endemic tree species of Phu Tho province, only distributed narrowly in forest rehabilitation in two communes belonging to Doan Hung district with density of this species is very low, only from 3.1 to 11.1 trees per hectare. Diameter distributions of the species of number of trees is characterized by curve style with a peak in 20cm or 24cm diameter classes. As it is difficult to find the seedling in the nature, research on forest structure, relations between tree species and genetic diversity is very necessary to define method of conservation for this species. In this study, we used RAPD markers to study on genetic diversity of Castanopsis phuthoensis Luong. The random amplified polymorphic DNA (RAPD) based on the polymeraze chain reaction (PCR) detects nucleotide sequence polymorphism using a single 10mer of arbitrary nucleotided sequence. The RAPD technology has quickly gained widespread acceptance and application because it providesa tool for genetic analysis that have not previously benefited the use of molecular markers. In this study, ten random primers to analyse the genetic diversity of 15 Castanopsis phuthoensis Luong samples that were collected from Phu Tho province, Vietnam. 9 RAPD primers gave DNA polymorphism and 01 RAPD primer OPA20 gave not DNA polymorphism. In the analysis region 0.25-2 kb, there were 56 DNA fragments amplified and 34 DNA fragments were polymorphic. Genetic similarity coefficients of 15 Castanopsis phuthoensis Luong samples ranged from 0.55- 0.95. The phylogenetic tree of 15 samples are divided into two main groups. As results of RAPD-PCR analysis, these samples were collected from the homologous geographical locations and the genetic diversity of 15 samples is not high. Therefore, it is necessary to conserve the "Castanopsis phuthoensis Luong".

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Genetic Diversity and Population Structure of Capirona (Calycophyllum spruceanum Benth.) from the Peruvian Amazon Revealed by RAPD Markers

Forests ◽

10.3390/f12081125 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1125

Author(s):

Carla L. Saldaña ◽

Johan D. Cancan ◽

Wilbert Cruz ◽

Mirian Y. Correa ◽

Miriam Ramos ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Molecular Markers ◽

Tree Species ◽

Rapd Markers ◽

Clustering Algorithm ◽

Random Amplified Polymorphic Dna ◽

Population Divergence ◽

Eastern Region ◽

Peruvian Amazon

Capirona (Calycophyllum spruceanum Benth.) is a tree species of commercial importance widely distributed in South American forests that is traditionally used for its medicinal properties and wood quality. Studies on this tree species have been focused mainly on wood properties, propagation, and growth. However, genetic studies on capirona have been very limited to date. Currently, it is possible to explore genetic diversity and population structure in a fast and reliable manner by using molecular markers. We here used 10 random amplified polymorphic DNA (RAPD) markers to analyze the genetic diversity and population structure of 59 samples of capirona that were sampled from four provinces located in the eastern region of the Peruvian amazon. A total of 186 bands were manually scored, generating a 59 × 186 presence/absence matrix. A dendrogram was generated using the UPGMA clustering algorithm, and, similar to the principal coordinate analysis (PCoA), it showed four groups that correspond to the geographic origin of the capirona samples (LBS, Irazola, Masisea, Iñapari). Similarly, a discriminant analysis of principal components (DAPC) and STRUCTURE analysis confirmed that capirona is grouped into four clusters. However, we also noticed that a few samples were intermingled. Genetic diversity estimation was conducted considering the four groups (populations) identified by STRUCTURE software. AMOVA revealed the greatest variation within populations (71.56%) and indicated that variability among populations is 28.44%. Population divergence (Fst) between clusters 1 and 4 revealed the highest genetic difference (0.269), and the lowest Fst was observed between clusters 3 and 4 (0.123). RAPD markers were successful and effective. However, more studies are needed, employing other molecular tools. To the best of our knowledge, this is the first investigation employing molecular markers in capirona in Peru considering its natural distribution, and as such it is hoped that this helps to pave the way towards its genetic improvement and the urgent sustainable management of forests in Peru.

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Molecular-genetic analysis of diff erent species of lace bugs (Hеteroptera: Tingidae) by RAPD-markers

Horticulture and viticulture ◽

10.31676/0235-2591-2019-6-21-25 ◽

2019 ◽

pp. 21-25

Author(s):

E. N. Besedinа ◽

V. I. Kil

Keyword(s):

Genetic Diversity ◽

Genetic Relationship ◽

Dna Polymorphism ◽

Rapd Markers ◽

Molecular Genetic ◽

Genetic Diagnosis ◽

Research Process ◽

Molecular Genetic Analysis ◽

Pcr Analysis ◽

Lace Bugs

Studying the genetics of harmful insects populations is of great importance in understanding the migratory processes of species, especially invasive ones, and the fl ow of genes between populations. In this regard, one of the priorities of the genetics of arthropod populations is to assess the genetic similarity of individuals, genetic diversity, and DNApolymorphism. Universal RAPD-primers (OPA07, OPA09 and OPA18) for lace bugs (Tingidae family) have been revealed. In order to study DNA-polymorphism and the genetic diversity of lace bugs using selected primers, a comparative PCR-analysis of four species of bugs of this family (Corythucha arcuata Say, Corythucha ciliata Say, Stephanitis pyri F., Monosteira unicostata Mulsant et Rey) was carried out. It was shown that the species Monosteara unicostata diff ered from the others in the lowest level of DNA polymorphism and genetic diversity. The high values of DNA polymorphism and genetic diversity of the other three species indicate a high migratory ability of these insect species and a signifi cant intraspecifi c gene drift. In the research process, clustering of lace bugs species based on the data obtained using RAPD-markers was carried out in order to determine their genetic relationship. Cluster analysis of the data was performed by the UPGMA-method using the Popgene program. We found out that the genetically closest species were the species of the genus Corythucha, and the most distant from others was the species Monosteira unicostata. It was shown that RAPD-PCR-method can be successfully used in the analysis of interspecifi c diff erences of insects, along with other molecular-genetic methods. The performed studies allowed us to assess the eff ectiveness of the RAPD-primers identifi ed in the work for diff erentiating the species of lace bugs and to obtain information on the genetic relationship of the Tingidae family species. The primers identifi ed in the work are also eff ective for assessing DNA-polymorphism and genetic diversity of insects of the Tingidae family. This method of molecular-genetic diagnosis allows carrying out a more eff ective monitoring of pests of this insect family.

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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 diversity in Bambara groundnut (Vigna subterranea L.) germplasm revealed by RAPD markers

Genome ◽

10.1139/g01-096 ◽

2001 ◽

Vol 44 (6) ◽

pp. 995-999 ◽

Cited By ~ 25

Author(s):

H I Amadou ◽

P J Bebeli ◽

P J Kaltsikes

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Rapd Markers ◽

Random Amplified Polymorphic Dna ◽

Geographic Origin ◽

Bambara Groundnut ◽

International Institute ◽

Tropical Agriculture ◽

Vigna Subterranea ◽

Ibadan Nigeria

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic diversity in Bambara groundnut (Vigna subterranea L.) germplasm using 25 African accessions from the collection in the International Institute for Tropical Agriculture, Ibadan, Nigeria. Fifty random decamer primers were screened to assess their ability to detect polymorphism in bambara; 17 of them were selected for this study. Considerable genetic diversity was found among the V. subterranea accessions studied. The relationships among the 25 accessions were studied by cluster analysis. The dendrograms showed two main groups of accessions mainly along the lines of their geographic origin. It is concluded that RAPD can be used for germplasm classification in bambara groundnut and hence for improving this crop.Key words: germplasm, PCR, RAPD, Vigna subterranea.

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Detection of genetic diversity in tea (Camellia sinensis) using RAPD markers

Genome ◽

10.1139/g95-025 ◽

1995 ◽

Vol 38 (2) ◽

pp. 201-210 ◽

Cited By ~ 89

Author(s):

F. N. Wachira ◽

R. Waugh ◽

W. Powell ◽

C. A. Hackett

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Southeast Asia ◽

Camellia Sinensis ◽

Rapd Markers ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Systematic Assessment ◽

Tree Crop ◽

Taxonomic Relationships

Camellia sinensis is a beverage tree crop native to Southeast Asia and introductions have been made into several nonindigenous countries. No systematic assessment of genetic variability in tea has been done anywhere. In this study, random amplified polymorphic DNA (RAPD) analysis was used to estimate genetic diversity and taxonomic relationships in 38 clones belonging to the three tea varieties, assamica, sinensis, and assamica ssp. lasiocalyx. Extensive genetic variability was detected between species, which was partitioned into between and within population components. Seventy percent of the variation was detected within populations. Analyses based on band sharing separated the three populations in a manner consistent with both the present taxonomy of tea and with the known pedigrees of some clones. RAPD analysis also discriminated all of the 38 commercial clones, even those which cannot be distinguished on the basis of morphological and phenotypic traits.Key words: genetic diversity, RAPDs, Camellia sinensis.

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Genetic Diversity of Salvia Species Assessed by ISSR and RAPD Markers

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha44210391 ◽

2016 ◽

Vol 44 (2) ◽

pp. 431-436 ◽

Cited By ~ 6

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. Neiâ€™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.

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ANALYSIS OF GENETIC DIVERSITY OF 26 CASSAVA VARIETIES (Manihot esculenta CRANTZ) WITH DIFFERENT RESPONSES TO WATERLOGGING CONDITIONS BY USING RAPD MARKERS

Journal of Science Natural Science ◽

10.18173/2354-1059.2021-0058 ◽

2021 ◽

Vol 66 (3) ◽

pp. 170-179

Author(s):

Sengsoulichan Dethvongsa ◽

Vu Nguyen Anh ◽

Van Tran Khanh

Keyword(s):

Genetic Diversity ◽

Phylogenetic Tree ◽

Manihot Esculenta ◽

Rapd Markers ◽

Flood Tolerance ◽

Randomly Amplified Polymorphic Dna ◽

Manihot Esculenta Crantz ◽

Rapd Pcr ◽

Cassava Production ◽

Cassava Varieties

RAPD (Randomly Amplified Polymorphic DNA) is an indicator for high and stable polymorphism, widely used in the study of the diversity of cassava. In this paper, the results of using 20 polymorphic primers OPK combined with the establishment of the phylogenetic tree to analyze the genetic diversity of 26 cassava varieties with different responses to waterlogging conditions by using the RAPD-PCR technique were presented. The purpose of this experiment was to show the genetic relevance of the studied cassava varieties. The results showed that the flood tolerance of cassava was not related to the polymorphism and branching characteristics of the stem. This information may be use as a basis for selecting flood-tolerant cassava varieties for cassava production, as well as the basis for selecting genetically different parents for breeding.

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