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

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

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

HUE UNIVERSITY JOURNAL OF SCIENCE TECHNIQUES AND TECHNOLOGY ◽

10.26459/hueunijtt.v130i2b.6132 ◽

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.

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Determine The Genetic Variation of Phenotypic Groups of Quail (Different With Feathers Color ) Using The Chain Polymerase Reaction Technique (PCR)

IOP Conference Series Earth and Environmental Science ◽

10.1088/1755-1315/910/1/012110 ◽

2021 ◽

Vol 910 (1) ◽

pp. 012110

Author(s):

Majid A. S. Al-Neemy ◽

Esraa Mohammed Tawfeq ◽

Haitham Mohammed Sabeeh Hadi

Keyword(s):

Genetic Variation ◽

Genetic Similarity ◽

Agricultural Research ◽

Genetic Difference ◽

Similarity Index ◽

Research Station ◽

A Value ◽

Hereditary Variation ◽

The City ◽

Geographical Locations

Abstract The main objective of this research was to specify the hereditary variation associated with the plumage color in three local genotypes of Japanese quail which bred in two geographical locations. The birds distributed on six treatments with five birds for each depending on the feather's color and geographical locations. DNA extraction was executed from the blood samples of each treatment and amplified by thermo cycler apparatus and the electrophoresis was done using 1.5% agarose gel for DNA bands exhibiting. Genotype influence has been shown that the black color quail B1 of the agricultural research station in the city of Mosul showed maximum genetic similarity with the Black quail B2 of Tikrit University with a value of 0.9549, the highest genetic similarity between different colors found between B1 and W2 that amounted to 0.9391 based on the similarity index (band sharing). While, the least genetic similarity observed between B2 and W1, which went down to 0.8468. Genetic difference values among studied quail groups showed that the groups B2 and W1 in the higher genetic variation, whereas the least genetic difference found between B1 and B2 groups. The average of dissimilarities for each group with all others varied between the values 0.1203 - 0.0851. The present work prove that the effectiveness of RAPD markers in knowing the similarity and specify the inherited relationship within the quail varieties.

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Phylogenetic relationships of five morphological groups of hexaploid wheat (Triticum aestivum L. em Thell.) based on RAPD analysis

Genome ◽

10.1139/g00-030 ◽

2000 ◽

Vol 43 (4) ◽

pp. 724-727 ◽

Cited By ~ 16

Author(s):

Wenguang Cao ◽

G Scoles ◽

P Hucl ◽

R N Chibbar

Keyword(s):

Hexaploid Wheat ◽

Phylogenetic Relationships ◽

Genetic Similarity ◽

Rapd Analysis ◽

Genetic Relationships ◽

Random Amplified Polymorphic Dna ◽

Triticum Aestivum L ◽

Similarity Coefficients ◽

Morphological Classification ◽

Wild Wheat

The genetic relationships among the five groups of hexaploid wheat: common, spelta, macha, vavilovii, and semi-wild wheat (SWW) are not clear. Random amplified polymorphic DNA (RAPD) analysis was used to assess phylogenetic relationships among these five morphological groups of hexaploid wheat. RAPD data were analyzed using the NTSYS-PC computer program to generate Jaccard genetic similarity coefficients. A dendrogram based on RAPD analysis grouped 15 accessions into five distinct clusters. These results are in agreement with those based on morphological classification, suggesting that common wheat is most closely related to SWW, followed by spelta, vavilovii, and macha.Key words: RAPD, macha, spelta, vavilovii, semi-wild wheat, phylogenetic relationships.

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Genetic Variation Analysis of Hevea brasiliensis Genotype Population of In Vitro Micro-Cutting Culture by RAPD Marker

Jurnal Sumberdaya Hayati ◽

10.29244/jsdh.4.2.57-62 ◽

2020 ◽

Vol 4 (2) ◽

pp. 57-62

Author(s):

IRFAN MARTIANSYAH ◽

NURHAIMI HARIS ◽

TATI HUSNIYATI ◽

EDI DJAUHARI PURWAKUSUMAH

Keyword(s):

Genetic Similarity ◽

Growth Response ◽

Random Amplified Polymorphic Dna ◽

Rapd Marker ◽

Culture Technique ◽

Similarity Coefficients ◽

Micro Cutting ◽

Explant Source ◽

Dna Fragment

The rubber seeds are insufficient for producing rootstocks to rubber grafting. It can be overcome by an in vitro micro-cutting culture technique developed in the Indonesian Research Institute for Biotechnology and Bioindustry (IRIBB). However, the origin clone of 57 rubber genotypes used as an explant source in vitro micro-cutting culture is not recognized. The study was to investigate the 57 genotypes that came from mixed GT 1, PB 260, and RRIM 600 as parent clones. We investigated using seven primers of Random Amplified Polymorphic DNA (RAPD), i.e., OPA 02, OPA 07, OPA 15, OPB 04, OPC 05, OPC 11, and OPC 20. The qualitative analyzed by electrophoresis 1% gel agarose. A total of 47 DNA fragments produced with an average of 7 fragments per primer. OPA 02 generated of 13 fragments, whereas OPB 04 only one fragment. The DNA fragment pattern shows the presence of polymorphism. The genetic similarity coefficients obtained in the range of 62-96%. The highest genetic similarity (96%) is genotype 70 and 78. It recognized that 42 genotypes from 57 rubber genotypes had the closest relationship with PB 260 clones. Furthermore, six genotypes had a significant growth response as an explant in vitro micro-cutting culture.

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Rapd variation of late-maturing sorghum [ Sorghum bicolor (L.) Moench] landraces from Ethiopia

Acta Agronomica Hungarica ◽

10.1556/aagr.55.2007.3.14 ◽

2007 ◽

Vol 55 (3) ◽

pp. 375-382 ◽

Cited By ~ 3

Author(s):

S. Mamo ◽

A. Ayana ◽

T. Tesso

Keyword(s):

Genetic Variation ◽

Genetic Distance ◽

Sorghum Bicolor ◽

Rapd Markers ◽

Diversity Index ◽

Random Amplified Polymorphic Dna ◽

The Mean ◽

Polymorphic Bands ◽

High Degree ◽

Sorghum Bicolor L

A study on the extent and pattern of genetic variability in late-maturing sorghum [ Sorghum bicolor (L.) Moench] landraces collected from the Wello and Hararge areas of Ethiopia was conducted using random amplified polymorphic DNA (RAPD) markers for 70 individuals representing 14 populations. Four oligonucleotide primers generated a total of 55 polymorphic bands with 13–19 bands per primer and a mean of 16 bands across the 70 individuals. The value of the Shannon diversity index among the populations (0.26) and between the two regions (0.24) was low to moderate, despite the high degree of polymorphic bands per primer. The mean genetic distance (0.25) between the populations was found to be low. The low genetic variation may be due to the reduced population size of late-maturing sorghum landraces in the two regions of Ethiopia because of farmers’ decisions in the process of planting, managing, harvesting and processing their crops. Partitioning of the genetic variation into variation between and within the population revealed that 92.9% and 7.10% of the variation was found to be between and within the populations, respectively. Cluster analysis of genetic distance estimates further confirmed a low level of differentiation in late-maturing sorghum populations both between and within the regions. The implications of the results for genetic conservation purposes are discussed.

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Analysis of intra-population variability of bald cypress (Taxodium distichum L. Rich.) in seed stand near Backa Palanka using RAPD markers

Genetika ◽

10.2298/gensr1502571p ◽

2015 ◽

Vol 47 (2) ◽

pp. 571-580

Author(s):

Vladan Popovic ◽

Aleksandar Lucic ◽

Danijela Ristic ◽

Ljubinko Rakonjac ◽

Sabahudin Hadrovic ◽

...

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Dna Markers ◽

Genetic Similarity ◽

Rapd Markers ◽

Rapd Analysis ◽

Genetic Distances ◽

Similarity Coefficients ◽

Bald Cypress ◽

Seed Stand

The analysis of Bald cypress genetic variability at the level of test trees was performed using RAPD (Random Amlified Polymorphic DNA) markers. RAPD analysis was performed on 20 test trees with 13 primers. A total of ten primers gave a clear picture while three primers amplified weakly. 60 is a total number of detected bands obtained by RAPD analysis with 10 selected primers, and the average number of bands is 6. Based on presence/absence of RAPD fragments among all 20 Bald cypress test trees were calculated similarity coefficients by Dice and they range from 0.73 to 1. Based on similarity coefficients was performed the cluster analysis and results were presented as a dendrogram. All 20 test trees were grouped into two sub-clusters. Test trees 1, 4 and 11 were grouped in the first sub-cluster while other test trees were grouped in the second sub-cluster. By analysis of relations within every sub-cluster and sub-sub-cluster the existence of genetic distances between observed test trees can be noticed. The greatest similarity is between test trees 2, 12, 15 and 18. The results of genetic similarity and distance between observed test trees indicate the overwhelming presence of genetic diversity.

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Genetic Similarity of Commerson’s Anchovy across Segara Anakan Cilacap Assessed Using Randomly Amplified Polymorphic DNA (RAPD) Markers

Jurnal Biota ◽

10.19109/biota.v7i1.7201 ◽

2021 ◽

Vol 7 (1) ◽

pp. 42-50

Author(s):

Muhammad Khoerol Anam ◽

Adi Amurwanto ◽

Kusbiyanto Kusbiyanto ◽

Hendro Pramono ◽

M Husein Sastranegara ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Similarity ◽

Rapd Markers ◽

Random Amplified Polymorphic Dna ◽

Genetic Differences ◽

Population Genetic Study ◽

Randomly Amplified Polymorphic Dna ◽

High Genetic Diversity ◽

Impressive Result

Segara Anakan areas can be divided into three different regions according to their salinity. Salinity differences suggested that Commerson’s anchovy population in that area can be divided into three subpopulations due to genetic differences. Genetic differences among subpopulation can be assessed through a population genetic study using random amplified polymorphic DNA. This study aims to evaluate the genetic variation and differences of Commerson's anchovy (Stolephorus commersonnii) collected at three different water salinities in Segara Anakan estuary Cilacap Indonesia. Total genomic DNA was isolated using the Chelex method. Genetic diversity and differences were assessed using RAPD markers and were analyzed statistically using an analysis of molecular variance, as implemented in Arlequin software. The results showed that high genetic diversity was observed within the subpopulations. However, no significant genetic differences were observed among subpopulations which indicate genetic similarity. A high number of offspring are likely to cause high genetic variation within subpopulations. Adult and larvae migration is the cause of genetics similarity across Segara Anakan. Another impressive result is that water salinity did not affect the genetic characteristic of Commerson,s anchovy. Genetic similarity of Commerson’s anchovy indicates that Segara Anakan forms a single genetic conservation unit.

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Genetic fingerprinting of Australian cotton cultivars with RAPD markers

Genome ◽

10.1139/g95-132 ◽

1995 ◽

Vol 38 (5) ◽

pp. 1005-1008 ◽

Cited By ~ 42

Author(s):

D. S. Multani ◽

B. R. Lyon

Keyword(s):

Cluster Analysis ◽

Gossypium Hirsutum ◽

Dna Markers ◽

Genetic Similarity ◽

Rapd Markers ◽

Random Amplified Polymorphic Dna ◽

Pairwise Comparisons ◽

Breeding Line ◽

Genetic Fingerprinting ◽

Broad Agreement

RAPD (random amplified polymorphic DNA) markers generated by 30 random decamer primers were used to fingerprint 12 released cultivars and a breeding line of Gossypium hirsutum and 1 cultivar of G. barbadense presently under cultivation in Australia. Among a total of 453 developed markers, 69 (15.2%) were only present (unique) in the G. barbadense cultivar Pima S-7. Of the remaining markers, 128 (33.3%) were fixed in all 13 G. hirsutum cultivars. In pairwise comparisons of the degree of band sharing, nine closely-related cultivars showed 92.1–98.9% genetic similarity. Cluster analysis of genetic distance estimates between each of the cultivars revealed phylogenetic relationships in broad agreement with the known lineage of the cultivars. Ten of the G. hirsutum cultivars can be characterized individually based upon cultivar-specific RAPD markers, thus making it possible to differentiate closely related cultivars by molecular markers.Key words: RAPD, DNA fingerprinting, Gossypium hirsutum, Gossypium barbadense, cotton cultivars.

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Genetic diversity of blaKPC-gene-containing IncF plasmids from epidemiologically related and unrelated Enterobacteriaceae

10.1101/2020.11.01.362400 ◽

2020 ◽

Author(s):

Joep J.J.M. Stohr ◽

Marjolein F. Q. Kluytmans-van den Bergh ◽

Veronica A.T.C. Weterings ◽

John W. A. Rossen ◽

Jan A. J. W. Kluytmans

Keyword(s):

Genetic Similarity ◽

Sequence Data ◽

Sequence Similarity ◽

Similarity Index ◽

Pairwise Comparisons ◽

Phylogenetic Distance ◽

Limited Information ◽

Hospital Outbreak ◽

Long Read ◽

High Degree

AbstractBackgroundLimited information is available on whether blaKPC-containing plasmids from isolates in a hospital outbreak can be differentiated from epidemiologically unrelated blaKPC-containing plasmids based on sequence data.ObjectiveThis study aimed to evaluate the performance of three approaches to distinguish epidemiologically related from unrelated blaKPC-containing IncF plasmids.MethodEpidemiologically related isolates, were short- and long-read whole genome sequenced on an Illumina MiSeq and MinION sequencer. A hybrid assembly was performed and plasmid sequences were extracted from the assembly graph. Epidemiologically unrelated plasmid sequences were extracted from the GenBank. Pairwise comparisons were performed of epidemiologically related and unrelated plasmids based on SNP differences using snippy, phylogenetic distance using Roary and using a similarity index that penalizes size differences between plasmids (Stoesser-index). The percentage of pairwise comparisons misclassified as genetically related or as clonally unrelated was determined using different genetic thresholds for genetic relatedness for all three comparison methods.ResultsDespite the median number of SNP differences, Roary phylogenetic distance, and Stoesser-index differed between the epidemiologically related and unrelated plasmids, the range of differences overlapped between the two comparison groups for all three comparison methods. When using a genetic similarity threshold that classified 100% of epidemiologically related plasmid pairs as genetically related, the percentages of plasmids misclassified as epidemiologically related ranged from 6.7% (Roary) to 20.8% (Stoesser-index).DiscussionAlthough epidemiologically related plasmids can be distinguished from unrelated plasmids based on genetic similarity, epidemiologically related and unrelated blaKPC-containing IncF plasmids show a high degree of sequence similarity. The phylogenetic distance as determined using Roary showed the highest degree of discriminatory power between the epidemiologically related and unrelated plasmids.Impact statementAccurately distinguishing epidemiologically related from unrelated plasmids is essential to detect nosocomial plasmid transmission in outbreaks. However, limited information is available on whether blaKPC-containing plasmids from isolates in a hospital outbreak can be differentiated from epidemiologically unrelated blaKPC-containing plasmids based on sequence data. This study aimed to evaluate the performance of three approaches to distinguish epidemiologically related from unrelated blaKPC-containing IncF plasmids. Pairwise comparisons were performed of epidemiologically related and unrelated plasmids based on SNP differences using snippy, phylogenetic distance using Roary and using a similarity index that penalizes size differences between plasmids (Stoesser-index). Based on our results, epidemiologically related plasmids can be distinguished from unrelated plasmids based on genetic similarity. Despite this, epidemiologically related and unrelated blaKPC-containing IncF plasmids show a high degree of sequence similarity and judgements on the horizontal transfer of these plasmids during hospital outbreaks based on genetic identity should be made with caution. The phylogenetic distance determined using Roary showed the highest discriminatory power between the epidemiologically related and unrelated plasmids.Data summaryShort-and long-read sequence data of the epidemiologically related Enterobacteriaceae isolates included in this study are available from the publicly available European Nucleotide Archive of the European Bioinformatics Institute under study accession number: PRJEB41009. The authors confirm that all supporting data have been provided within the article and through the supplementary data files.

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Keragaman Genetik Beberapa Genotipe Teh Berdasarkan Penanda RAPD (Random Amplified Polymorphic DNA)

Jurnal Tanaman Industri dan Penyegar ◽

10.21082/jtidp.v1n1.2014.p1-6 ◽

2014 ◽

Vol 1 (1) ◽

pp. 1 ◽

Cited By ~ 1

Author(s):

Budi Martono ◽

Laba Udarno

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Camellia Sinensis ◽

Genetic Similarity ◽

Rapd Markers ◽

Dna Marker ◽

Random Amplified Polymorphic Dna ◽

Rapd Marker ◽

Plant Breeding Program ◽

Marker Loci

Informasi keragaman genetik dan ketersediaan plasma nutfah teh (Camellia sinensis) diperlukan dalam perakitan varietas unggul. Keragaman genetik berdasarkan penanda DNA dapat memberikan hasil yang lebih konsisten karena tidak dipengaruhi lingkungan. Dalam penelitian ini sebanyak 9 genotipe teh dianalisis keragamannya menggunakan enam penanda RAPD (OPA 03, OPA 05, OPB 04, OPB 06, OPC 06, dan OPD 08). Penelitian dilakukan mulai bulan Maret sampai Mei 2013 di Laboratorium Terpadu Biotrop Bogor. Perhitungan koefisien kesamaan genetik dan analisis gerombol dilakukan dengan menggunakan perangkat lunak NTSYSpc versi 2.02. Sebanyak 54 lokus penanda RAPD berhasil diamplifikasi menggunakan enam primer dan 47 lokus di antaranya memiliki alel yang polimorfik (87,04%). Hasil analisis gerombol berdasarkan kesamaan genetiknya mengelompokkan 9 genotipe ke dalam enam kelompok. Empat kelompok (I, II, IV, V) masing-masing terdiri atas satu genotipe, sementara dua kelompok yang lain yaitu kelompok III dan VI masing-masing beranggotakan tiga dan dua genotipe.Kata Kunci: Camellia sinensis, diversitas genetik, penanda RAPDThe availability of diverse tea (Camellia sinensis) germplasms as well as the information about their genetic diversity is required for plant breeding program. Genetic diversity analysis based on DNA marker is known to be more effective since the markers provide more consistent results. In this study, nine tea genotypes were evaluated for their genetic diversity using six Random Amplified Polymorphic DNA (RAPD) markers (OPA 03, OPA 05, OPB 04, OPB 06, OPC 06, and OPD 08). The study was conducted from March to May 2013 in the Integrated Laboratory of Biotrop Bogor. The estimation of genetic similarity and the cluster analysis were done using NTSYSpc version 2.02. Of the six RAPD markers used in this study, a total of 54 RAPD marker loci have been successfully amplified. In which, 47 loci (87.04%) were polymorphic and subsequently used for the evaluation of tea genotypes. The results of cluster analysis showed that those tea genotypes were clustered into six groups. Each of four groups (I, II, IV, V) consisted of only one genotype. Meanwhile, the other two groups (III and VI) had three and two genotypes, respectively.

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