scholarly journals GENETIC DIVERSITY EEL Anguilla marmorata BY RAPD IN THUA THIEN HUE PROVINCE, VIETNAM

2021 ◽  
Vol 130 (2B) ◽  
Author(s):  
Kiều Thị Huyền ◽  
Hà Thị Huệ ◽  
Nguyễn Quang Linh
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Molecular Marker ◽  
Genetic Similarity ◽  
Economic Value ◽  
Similarity Coefficient ◽  
Similarity Coefficients ◽  
Random Primer ◽  
Anguilla Marmorata ◽  
Random Amplification

Anguilla marmorata is a species with high economic value and increasingly interested by organizations and scientists. So far, many of the eel's biological characteristics remain mysterious, and they are often classified according to morphological features such as pigmentation patches, number of vertebrae, ... It is even difficult to distinguish one individual from another in some species, especially in the larval stage. In this study, the Random amplification of polymorphic DNA (RAPD) molecular marker was used to evaluate the genetic diversity of 48 eels collected in Thua Thien Hue province. Results showed that the genetic diversity of individuals in the Eel population studied is quite high. With 8 random primers via PCR, 77 DNA tapes with 76 polymorphic tapes were obtained, the tape size ranged from 170-2,500 bp, in which primer S10 showed the highest diversity with an average Ho value of 0.563, followed by primer S8 (Ho = 0.558). The lowest diversity was in the OPD5 primer (Ho = 0.300). The OPG17 primer is the primer that produces the most polymorphic tapes (13/13 tapes) and the S3 primer for the least amplified tapes polymorphism (9/10 DNA tapes). The diversity coefficient in each random primer ranged from about 0.300 to 0.563, with an average of 0.433. The genetic variation in the Eel population is random. Genetic variation can be attributed mainly to different eel breeding conditions and origins. Genetic similarity coefficients among the Eels varied from 0.660 to 0.910 and were divided into two main groups in genetic similarity coefficient 0.660.

scholarly journals GENETIC DIVERSITY AMONG NATURAL POPULATIONS OF Keteleeria evelyniana Mast. IN CENTRAL HIGLANDS OF VIETNAM USING SSR MARKERS

2018 ◽  
Vol 56 (3) ◽  
pp. 275
Author(s):  
Tran Thi Lieu ◽  
Dinh Thi Phong ◽  
Vu Thi Thu Hien
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Similarity ◽  
Natural Populations ◽  
Similarity Coefficient ◽  
Similarity Matrix ◽  
Analysis Of Molecular Variance ◽  
Molecular Variance ◽  
Private Alleles ◽  
Softwood Species

Keteleeria evelyniana Mast. is a big softwood species with high economic values. Therefore, the number of these trees are rapidly decreasing due to rampant exploitation as well as its habitat loss and recently, the species is considered vulnerablein Vietnam. In this study, we assessed the genetic variation among seventy K. evelyniana samples of three natural populations in Lam Dong, Dak Lak and Kon Tum using 16 microsatellite markers. The results showed that thirteen markers were polymorphic. A total 39 DNA fragments were amplified, among them, thirty – five were polymorphic (accounting for 89.74%). Among studied populations, the level of genetic diversity at Lam Dong (Na = 2.063; Ne = 1.730; Ap = 0.375; I = 0.558; Ho = 0.459 and He = 0.367) was the highest. Analysis of molecular variance (AMOVA) showed that the total level of molecular changes between populations was 34.65% and between individuals in the same population was 65.35%. Private alleles (Ap) and inbreeding values (Fis) of K. evelyniana species were founded of all three populations in Lam Dong, Dak Lak and Kon Tum (0.375 and -0.234; 0.188 and -0.065; 0.063 and -0.047, respectively). The gene flow (Nm) also occurred among the K. evelyniana populations with the average of Nm = 5.423. A dendrogram (UPGMA) constructed based on the similarity matrix of 70 K. evelyniana samples divided into two main groups with their genetic similarity coefficient ranged from 76.5% (Ke26 and Ke44) to 99% (Ke23 and Ke25). The obtained results indicated the importance of conserving the genetic resources of K. evelyniana species in Tay Nguyen.

scholarly journals Analisis Keragaman Genetik Acremonium yang Berasosiasi dengan Tanaman Gaharu Menggunakan Teknik Random Amplified Polymorphic DNA (RAPD)

2016 ◽  
Vol 5 (2) ◽  
pp. 65
Author(s):  
Dewi Rahmawati ◽  
Nurita Toruan-Mathius
Keyword(s):  
Cluster Analysis ◽  
Genetic Variation ◽  
Genetic Similarity ◽  
Random Amplified Polymorphic Dna ◽  
Economic Value ◽  
Similarity Index ◽  
Similarity Coefficients ◽  
West Sumatra ◽  
High Degree ◽  
Geographical Locations

<p>Agarwood<br />or gaharu is a plant that has a high economic value in Asia,<br />due to its use for production of incense and traditional<br />medicines. The agarwood formation occurs in the trunk and<br />roots of trees that have been infected by a fungus, such as<br />Acremonium spp. Various fungi were associated with the<br />agarwood formation. Acremonium is generally considered as<br />highly polyphyletic, contains distantly related fungi. A study<br />was done to identify genetic diversities in 10 isolates of<br />Acremonium spp. from four different areas in Indonesia that<br />are associated with Aquilaria and Gyrinops verstigii using the<br />Random Amplified Polymorphic DNA (RAPD) technique.<br />Eight RAPD primers, i.e., OPA 02, OPB 04, OPB 07, OPB 17,<br />OPC 11, OPD 03, OPD 05, and OPE 07 were used in the<br />analyses. The results indicated that similarity index values of<br />the genetic variation ranged from 0.21 to 0.97. Based on the<br />Nei and Li’s similarity coefficients, these values indicating<br />the presence of high degree of genetic variability. The lowest<br />degree of genetic similarity were found between isolates F<br />(Acremonium spp., which is associated with G. verstigii from<br />Mataram, Nusa Tenggara Barat), and LM2 from south coastal<br />area of West Sumatra. The highest genetic similarity value<br />(0.97) was found between isolates Sr2 and Sr4 from Sorong,<br />Papua. Results from the cluster analysis indicated that the<br />isolates could be grouped into two major clusters that were<br />associated with their geographical locations.</p>

Population genetic diversity of Phytophthora infestans from China as revealed by SSRs and RAPDs

2009 ◽  
Vol 6 (2) ◽  
pp. 161-170 ◽  
Author(s):  
Li Ben-Jin ◽  
Lv Xin ◽  
Chen Qing-He ◽  
Lan Cheng-Zhong ◽  
Zhao Jian ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phytophthora Infestans ◽  
Inner Mongolia ◽  
Genetic Similarity ◽  
Similarity Coefficient ◽  
The North ◽  
Random Amplification ◽  
Ssr Primers ◽  
Polymorphic Bands ◽  
Simple Sequence

AbstractSimple sequence repeats (SSR) and random amplification of polymorphic DNA (RAPD) molecular markers were used to assess the genetic diversity of 80 isolates of Phytophthora infestans in potato (Solanum tuberosum) from Fujian, Heilongjiang, Hebei and Inner Mongolia Provinces in China. Polymorphism was identified by 13 SSR primers and 14 RAPD primers in the isolates of P. infestans in potato. A total of 76 bands were amplified by SSRs, with the percentage of polymorphic bands (PPB) being 78.9% and the similarity coefficient ranging between 0.00 and 0.42. A total of 189 bands were amplified by RAPDs, with the percentage of polymorphic bands being 95.2% and the similarity coefficient ranging between 0.04 and 0.66. Analysis of genetic diversity showed that there exists higher genetic variation in the Fujian population in comparison to the populations of Heilongjiang, Hebei and Inner Mongolia. Nei's genetic identity analysis indicates that the genetic similarity between populations of Heilongjiang and Inner Mongolia is the highest and that between Fujian and Hebei is the lowest. A cluster analysis revealed that isolates from Fujian, in the south of China, are distantly related to those from Heilongjiang, Hebei and Inner Mongolia in the north, and the Fujian population is distributed among more groups than the other three, exhibiting a higher genetic diversity.

Genetic Diversity of Phalaris arundinacea Linn Germplasm Detected by SRAP Markers

2013 ◽  
Vol 726-731 ◽  
pp. 4494-4503
Author(s):  
Kai Kai Cheng ◽  
Juan Du ◽  
Yan Hua Huang ◽  
Casler Michael ◽  
Yun Wei Zhang
Keyword(s):  
Genetic Diversity ◽  
Molecular Marker ◽  
Information Content ◽  
Polymorphism Information Content ◽  
Genetic Similarity ◽  
Phalaris Arundinacea ◽  
Similarity Coefficient ◽  
Ecological Environment ◽  
The Usa ◽  
Polymorphic Bands

Sequence-related amplified polymorphism (SRAP) molecular marker was used to detect the genetic diversity of 25 accessions of Phalaris arundinacea Linn that collected from the USA, Russia, Kazakhstan, Canada, LanZhou and HuBei. The following results were obtained: 1) Sixteen primer pairs produced 131 polymorphic bands, with an average of 8.19 bands per primer pair. The percentage of polymorphic bands on average was 89.25%. The polymorphism information content (PIC) ranged from 0.784 to 0.9069, with an average of 0.8696. 2) The Neis genetic similarity coefficient of the tested accessions ranged from 0.5959 to 0.8425, and the average of Neis coefficient was 0.7422. These results suggested that there was rich genetic diversity among the resources of Phalaris arundinacea Linn. 3) Twenty-five accessions were clustered into five groups. Moreover, the accessions from the same or similar origin frequently clustered into one group. The findings implied that the correlation among the resources, geographical and ecological environment.

scholarly journals EVALUATION OF GENETIC DIVERSITY IN CACAO COLLECTED FROM KOLAKA, SOUTHEAST SULAWESI, USING SSR MARKERS

2016 ◽  
Vol 16 (2) ◽  
pp. 71
Author(s):  
Rubiyo Rubiyo ◽  
Nur Kholilatul Izzah ◽  
Indah Sulistiyorini ◽  
Cici Tresniawati
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Gel Electrophoresis ◽  
Genetic Similarity ◽  
Similarity Coefficient ◽  
Breeding Program ◽  
New Variety ◽  
Average Value ◽  
The Third ◽  
Ctab Method

Kolaka, which is located in Southeast Sulawesi, has long been known as one of cacao production centers in Indonesia. Therefore, many different cacao germplasms can be found in this region. The study aimed to evaluate genetic diversity and relationships of 12 cacao genotypes collected from Kolaka. Genomic DNA was extracted by using a modified CTAB method. Meanwhile, genetic diversity was analyzed based on 16 SSR markers, which then separated by 6% non-denaturing polyacryl-amide gel electrophoresis. The result showed that all of those markers, 14 markers exhibited polymorphism and subsequently used for data analysis using NTSYS and PowerMarker program. About 70 different alleles were generated from 12 cacao genotypes analyzed with an average of 5 alleles per locus. Average value of polymorphism information content (PIC) resulted in this study was 0.59. The cluster analysis using UPGMA method based on the genetic similarity coefficient revealed that all cacao genotypes were separated into three major groups. The first group consisted of five cacao genotypes, the second one held four cacao genotypes, whereas the third group contained three genotypes. This result indicates that three genotypes that clustered separately from the others could be used as a good clonal candidate for cacao breeding program. The information resulted from this present study would be useful for future cacao breeding program, especially in efforts to release a new variety.

scholarly journals Genetic Diversity of Vitis davidii Accessions Revealed Using Microsatellite and Sequence-related Amplified Polymorphism Markers

HortScience ◽  
2018 ◽  
Vol 53 (3) ◽  
pp. 283-287
Author(s):  
Xiu Cai Fan ◽  
Hai Sheng Sun ◽  
Ying Zhang ◽  
Jian Fu Jiang ◽  
Min Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Similarity ◽  
Similarity Coefficient ◽  
Srap Markers ◽  
Average Percentage ◽  
Allele Number ◽  
Ssr Primers ◽  
Vitis Davidii ◽  
Simple Sequence

In this study, simple sequence repeat (SSR) and sequence-related amplified polymorphism (SRAP) markers were used to analyze the genetic diversity of 48 wild Vitis davidii accessions. A total of 78 distinct alleles were amplified by 11 SSR primers, and the average allele number was 8.8. The average observed heterozygosity (Ho) and expected heterozygosity (He) values were 0.785 and 0.814, respectively. The effective allele numbers ranged from 3.92 to 9.61. The average polymorphism information content (PIC) was 0.798. Twelve of 169 SRAP primer combinations were selected for SRAP analysis. A total of 188 bands were produced, and the average was 15.7 bands per primer combination; the average percentage of polymorphic bands was 84.0%. The average PIC was 0.76. The results of the clustering analysis based on SSR markers showed that the 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient level of 0.68. The dendrogram obtained from the SRAP data showed that 48 wild V. davidii accessions could be classified into five main clusters and had a genetic similarity coefficient of 0.72. SSR and SRAP markers differentiated all accessions studied including those with a similar pedigree. We speculated on the origin of Ciputao 0941♀, Ciputao 0940♂, and Fu’an-ci-01 using SSR markers and used both SSR and SRAP markers to resolve homonymy. The result will be valuable for further management and protection of V. davidii germplasm resources.

scholarly journals Comparison of Genetic Variation of Anthurium (Anthurium andraeanum) Cultivars Using SCoT, CDDP and RAPD Markers

2018 ◽  
Vol 28 (2) ◽  
pp. 171-182 ◽  
Author(s):  
Abbas Saidi ◽  
Zahra Daneshvar ◽  
Zohreh Hajibarat
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Genetic Variation ◽  
Molecular Markers ◽  
Rapd Markers ◽  
Start Codon ◽  
Similarity Matrix ◽  
Random Amplification ◽  
Anthurium Andraeanum ◽  
Rapd Polymorphism

To evaluate the genetic diversity among 10 cultivars of anthurium were performed using three molecular markers such as Start Codon Targeted (SCoT) and Conserved DNA-derived Polymorphism (CDDP), and Random Amplification of Polymorphic DNA (RAPD). Polymorphism index content (PIC) was calculated 0.39, 0.42 and 0.37 for RAPD, SCoT and CDDP, respectively. This result showed all the three molecular markers had almost an identical potential in estimating genetic diversity. Cluster analysis using SCoT, CDDP and RAPD divided the cultivars to three distinct clusters. The similarity matrix obtained through SCoT and CDDP was positively significantly correlated (r = 0.76, p < 0.01). This is the first report in which the efficiency of two targeted DNA region molecular markers (SCoT and CDDP) together with RAPD technique have been compared with each other in a set of anthurium cultivras. Results suggested that SCOT, CDDP and RAPD fingerprinting techniques are of sufficient ability to detect polymorphism in anthurium cultivars. Plant Tissue Cult. & Biotech. 28(2): 171-182, 2018 (December)

Conservation genetics and ecology of the endangered rainforest shrub, Triunia robusta, from the Sunshine Coast, Australia

2002 ◽  
Vol 50 (1) ◽  
pp. 93 ◽  
Author(s):  
Alison Shapcott
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Gene Flow ◽  
Conservation Genetics ◽  
Population Size ◽  
Genetic Similarity ◽  
Small Region ◽  
Geographic Proximity ◽  
Close Proximity ◽  
The Mean

Triunia robusta, which until recently was thought to be extinct, is now classified nationally as endangered. It is an understorey species restricted to the subcoastal rainforests in a small region of the Sunshine Coast, Queensland. The project involved sampling the genetic variation and measuring the population size and size distribution of T. robusta and its geographically closest congener T. youngiana, which occurs further south and has a wider geographic distribution. A total of 877 T. robusta plants were recorded across the 11 populations, approximately half (56.8&percnt;) of these were juveniles less than 1 m tall, whereas in T. youngiana only about 36.4&percnt; of a population was composed of juveniles. Genetic diversity was similar but significantly higher for T. robusta than T. youngiana if the very small T. robusta populations (2 or 3 plants) were excluded from analysis (P &lt; 0.05). The mean percentage of polymorphic loci among populations was high for both species. Triunia robusta is not, on average, more inbred than the more common T. youngiana. There was more differentiation between the T. robusta populations, which were in close proximity, than between the more geographically separated T. youngiana populations. Thus, there is evidence of more gene flow between populations of T. youngiana than between those of T. robusta. However, there was no geographic relationship between genetic similarity and geographic proximity in T. robusta

scholarly journals Genetic diversity among 24 clones of robusta coffee in Lampung based on RAPD markers

2021 ◽  
Vol 22 (6) ◽  
Author(s):  
Sri Ramadiana ◽  
Dwi Hapsoro ◽  
Rusdi Evizal ◽  
Kukuh Setiawan ◽  
Agus Karyanto ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Similarity ◽  
Rapd Markers ◽  
Breeding Program ◽  
Similarity Coefficients ◽  
Robusta Coffee ◽  
Genomic Dnas ◽  
Polymerase Chain ◽  
Group Ii ◽  
Group 1

Abstract. Ramadiana S, Hapsoro D, Evizal R, Setiawan K, Karyanto A, Yusnita. 2021. Genetic diversity among 24 clones of robusta coffee in Lampung based on RAPD markers. Biodiversitas 22: 3122-3129. This study aimed to estimate the genetic diversity among 24 clones of Robusta coffee from Lampung, Indonesia, by use of RAPD markers. The clones consisted of 18 local and 6 BP clones. These BP clones were developed from a breeding program of The Indonesian Coffee and Cocoa Research Institute. Genomic DNAs extracted from these clones were subjected to polymerase chain reaction and the amplified products were run using gel electrophoresis. Eleven random primers produced clear, reproducible, scorable bands. Fifty-four of 86 bands showed polymorphism and were used to construct a dendrogram based on UPGMA Jaccard's Similarity Coefficients. The genetic base of the population was narrow (average genetic similarity 68.4%), ranging from 26-93%. The genetic similarity of the local clones was higher than that of BP clones. The clones were clustered into five groups. Group 1 contained one clone (BP 534), while each of Group II-V contained more than one clone. The average genetic similarity of BP 534 to each clone of Group II-V was 41%. The genetic similarity of clones in Group II, III, IV, and V were 55.5%, 43.0%, 81.1%, and 80.1%, respectively. This research should be very useful for selecting parents in a breeding program to produce better clones of Robusta coffee.

scholarly journals Evaluation of genetic diversity and DNA fingerprinting of 19 standard reference rice varieties using SSR markers

2020 ◽  
Vol 16 (4) ◽  
pp. 603-609
Author(s):  
Tran Long ◽  
Luu Minh Cuc ◽  
Nguyen Quang Sang ◽  
Pham Xuan Hoi
Keyword(s):  
Genetic Diversity ◽  
Dna Fingerprinting ◽  
Genetic Similarity ◽  
Similarity Coefficient ◽  
International Union ◽  
Rice Varieties ◽  
Reference Marker ◽  
High Uniformity ◽  
New Varieties ◽  
Group 2

Molecular markers are advanced-tools for identifying new varieties at DNA levels. According to the International Union for the Protection of New Varieties ofPlants,  new breeded varieties need to be tested for the Distinctness, Uniformity and Stability (DUS), before being recognized as the new ones. Traditional DUS criteria based on 62 - 65 morphological and biochemical characteristics, which evaluated on comparison of new varieties with 19 standard reference varieties for traits of interest.  Study on the genotypic polymorphism of 19 standard reference rice varieties provides genotypic information of these varieties for the evaluation of new rice varieties based on genotyping analysis.  The reference marker set (30 markers) was used to evaluate the genetic diversity and DNA fingerprinting of 19 standard reference rice varieties. The results showed the similarity coefficient of 19 varieties varied from 0.04 to 0.548. At the genetic similarity coefficient of 0.1, the 19 rice varieties divided into two main groups. Group one included 3 varieties: DH1, DH5, DH13. Group 2 included the remaining 16 varieties. Inside group two, phylogenetic tree divided into two main branches at the genetic similarity coefficient of 0.3. Branch 1 includes 5 varieties including DH2, DH6, DH10, DH11 and DH7. The 11 remaining varieties were in the branch 2. The most closely varieties were DH6 and DH10 with the genetic similarity coefficient of 0.548. This study shows that, the standard reference varieties have high uniformity and high genotypic polymorphism, could used for testing new varieties based on genotyping by DNA fingerprinting combining with phenotype.

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