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

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.

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

Genome ◽  
2000 ◽  
Vol 43 (4) ◽  
pp. 724-727 ◽  
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.

scholarly journals Virulence profile of ten Paracoccidioides brasiliensis isolates: association with morphologic and genetic patterns

2005 ◽  
Vol 47 (5) ◽  
pp. 257-262 ◽  
Author(s):  
Cilmery S. Kurokawa ◽  
Catalina R. Lopes ◽  
Maria F. Sugizaki ◽  
Eiko E. Kuramae ◽  
Marcello F. Franco ◽  
...  
Keyword(s):  
Genetic Similarity ◽  
Paracoccidioides Brasiliensis ◽  
Random Amplified Polymorphic Dna ◽  
Cell Recovery ◽  
Fungal Virulence ◽  
Genetic Patterns ◽  
Extreme Phenotypes ◽  
High Virulence ◽  
Outbred Mice

Ten isolates of Paracoccidioides brasiliensis were examined for differences in virulence in outbred mice intravenously inoculated with the fungus, associated with mycelial morphology, and genetic patterns measured by random amplified polymorphic DNA (RAPD). Virulence was evaluated by viable yeast cell recovery from lungs and demonstration of histopathologic lesions in different organs. The results showed that the isolates presented four virulence degrees: high virulence, intermediate, low and non-virulence. RAPD clustered the isolates studied in two main groups with 56% of genetic similarity. Strains with low virulence, Pb265 or the non-virulent, Pb192, showed glabrous/cerebriform morphology and high genetic similarity (98.7%) when compared to the other isolates studied. The same was observed with Bt79 and Bt83 that shared 96% genetic similarity, cottony colonies and high virulence. The RAPD technique could only discriminate P. brasiliensis isolates according to glabrous/cerebriform or cottony colonies, and also high from low virulence strains. Isolates with intermediate virulence such as Pb18, Pb18B6, Bt32 and Bt56 showed variability in their similarity coefficient suggesting that RAPD was able to detect genetic variability in this fungal specie. Virulence profile of P. brasiliensis demonstrated that both mycelial morphologic extreme phenotypes may be associated with fungal virulence and their in vitro subculture time. Thus, RAPD technique analysis employed in association with virulence, morphologic and immunologic aspects might prove adequate to detect differences between P. brasiliensis isolates.

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>

scholarly journals Identifikasi Molekuler dan Analisis Kekerabatan Aksesi Nenas Menggunakan Marka RAPD Menunjang Perakitan Varietas Unggul Baru

2019 ◽  
Vol 28 (1) ◽  
pp. 1
Author(s):  
Sri Hadiati ◽  
Riry Prihatini ◽  
Ellina Mansyah
Keyword(s):  
Molecular Identification ◽  
Genetic Similarity ◽  
Rapd Marker ◽  
Computer Software ◽  
Similarity Coefficient ◽  
Ananas Comosus ◽  
Similarity Coefficients ◽  
Tropical Fruit ◽  
New Varieties ◽  
Polymorphism Level

<p><strong>(</strong><em><strong>Molecular Identification and Relationships Among Several Pineapple Accessions Using RAPD Marker to Support the Assembling New Varieties</strong></em><strong>)</strong></p><p>Produksi dan produktivitas nenas dapat ditingkatkan antara lain melalui penggunaan varietas unggul. Dalam perakitan varietas, dibutuhkan informasi hubungan kekerabatan antartetuanya agar diperoleh efek heterosis yang tinggi melalui kegiatan identifikasi secara molekuler. Penelitian bertujuan (1) mengetahui tingkat polimorfisme primer yang digunakan,(2) mengidentifikasi fragmen DNA spesifik yang membedakan individu atau kelompok individu nenas, dan (3) mengetahui hubungan kekerabatan antarspesies dan aksesi nenas. Penelitian dilaksanakan mulai bulan Mei–Desember 2014 di Laboratorium Uji Mutu Benih dan Molekuler Balai Penelitian Tanaman Buah Tropika. Sampel yang digunakan sebanyak 19 aksesi dari empat spesies nenas (Ananas comosus, A. bracteatus, A. lucidus, dan A. nanus). Sebanyak 20 marka rapid amplified polymorphism DNA (RAPD) digunakan dalam analisis. Data diskor secara biner kemudian dianalisis menggunakan program NTSYSpc 2,1x. Hasil analisis menunjukkan bahwa polimorfisme 20 primer yang diuji berkisar 33–100% dengan rata-rata 87%. Primer dengan tingkat polimorfisme 100%, yaitu RAPD3, OPA13, OPAV3, OPC12, OPC16, dan OPY15. Kelompok Cayenne dicirikan oleh marka RAPD1 ukuran1.000 base-pair (bp) dan OPAV3 700 bp. Kelompok Queen dapat diidentifikasikan oleh marka RAPD3 ukuran 700 bp, kelompok Spanish dengan marka RAPD2 dan RAPD3 ukuran 1.500 bp. Analisis kluster menunjukkan bahwa 19 aksesi yang diuji terpisah menjadi enam kelompok pada koefisien kesamaan genetik 0,75, yaitu kelompok Queen, Cayenne, Spanish, A. bracteatus, A. lucidus, dan A. nanus. Aksesi yang diuji mempunyai keragaman genetik yang luas dengan koefisien kesamaan genetik berkisar 0,41–0,85. Aksesi yang mempunyai kesamaan genetik tertinggi, yaitu antara N-73 dengan BB (0,85) dan terkecil, yaitu antara N-94 (A. nanus) dengan N-18 (Green Spanish) sebesar 0,41. Implikasi hasil penelitian adalah aksesi yang mempunyai kesamaan genetik tinggi salah satunya dapat dieliminasi untuk efisiensi dalam pengelolaan plasma nutfah, sedangkan aksesi-aksesi yang memiliki kesamaan genetik kecil, baik digunakan sebagai tetua persilangan agar diperoleh variabilitas genetik yang luas dan efek heterosis yang tinggi.</p><p><strong>Keywords</strong></p><p><em>Ananas</em> spp.; Identifikasi; Karakterisasi; Kekerabatan genetik; Molekuler.</p><p><strong>Abstract</strong></p><p>Pineapple production and productivity can increased by the use of superior variety. Pertaining to variety assembling, the relationship information among parents are needed to gain heterosis effect through molecular identification activity. This research was aimed to (1) determine the level of polymorphism primers used, (2) identify specific DNA fragments which discrete individual or group of pineapple, and (3) reveal genetic relationship among pineapple species and accessions. The experiment was conducted on May to December 2014 in Seeds Quality Testing and Molecular Laboratory of Indonesian Tropical Fruit Research Institute. Nineteen accessions from four species (Ananas comosus, A. brachteatus, A. lucidus, and A. nanus) of pineapple were used as samples. Twenty rapid amplified polymorphism DNA (RAPD) markers were used on molecular analysis. The data were scored binary and then they were analyzed using NTSYSpc 2.1x computer software. The analysis showed that the 20 primers had 33–100%  polymorphic with 87% in average. Primers with 100% polymorphism level were RAPD3, OPA13, OPAV3, OPC12, OPC16, and OPY15. Cayenne group could be denoted with RAPD1 and OPAV3 markers by 1,000 base-pairs (bp) and 700 bp band, respectively. Meanwhile the Queen group can be identified by 700 bp band  RAPD3 marker. The Spanish group can be specified by1,500 bp band RAPD2 and RAPD3 markers. Based on cluster analysis the 19  accessions were separated  into six groups with 0.75 genetic similarity coefficient i.e., Queen, Cayenne, Spanish, A. bracteatus, A. lucidus, and A. nanus. These accessions had a wide genetic diversity with 0.41 to (0.85) genetic similarity coefficients. The highest genetic similarity coefficient (0.85) was determined between N-73 and BB, whereas the lowest value down to 0.41 was indicated on N-94 (A. nanus) and N-18 (Green Spanish). The implications of this research are that one of two accessions that have high genetic similarities can be eliminated for efficiency in the management of germplasm. While accessions which  have little genetic similarity are both used as crosses parent in order to obtain wide genetic variability and high heterosis effects.</p>

scholarly journals Identification of a gene encoding adaptin-like protein in the Paracoccidioides brasiliensis genome by random amplified polymorphic DNA analysis

2007 ◽  
Vol 56 (7) ◽  
pp. 884-887 ◽  
Author(s):  
Patrícia Ferrari Andreotti ◽  
Juliana Leal Monteiro da Silva ◽  
Elaine Cristina Teixeira ◽  
Maria Célia Bertolini ◽  
Christiane Pienna Soares ◽  
...  
Keyword(s):  
Dna Analysis ◽  
Paracoccidioides Brasiliensis ◽  
Random Amplified Polymorphic Dna ◽  
Genotypic Differences ◽  
Gene Encoding ◽  
Two Samples ◽  
Yeast Phase ◽  
Dna Fragment ◽  
Micro Organisms

Paracoccidioides brasiliensis isolates are not homogeneous in their patterns of pathogenicity in animals and adhesion to epithelial cells. During this investigation, genotypic differences were observed between two samples of P. brasiliensis strain 18 yeast phase (Pb18) previously cultured many times, one taken before (Pb18a) and the other after (Pb18b) animal inoculation. Random amplified polymorphic DNA analysis using the primer OPJ4 distinguished Pb18b from Pb18a by one 308 bp DNA fragment, which after cloning and sequencing was shown to encode a polypeptide sequence homologous to the protein β-adaptin. It is suggested, by comparison to other micro-organisms, that this protein might play an important role in the virulence of P. brasiliensis. This result demonstrates the influence of in vitro subculturing on the genotype of this organism.

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

2014 ◽  
Vol 1 (1) ◽  
pp. 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

<p>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.</p><p>Kata Kunci: Camellia sinensis, diversitas genetik, penanda RAPD</p><p>The 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.</p>

scholarly journals Taxonomic variation among Schinus molle L. plants associated with a slight change in elevation

2017 ◽  
Vol 24 (2) ◽  
pp. 205-214
Author(s):  
Abeer Al-Andal ◽  
Mahmoud Moustafa ◽  
Suliman Alruman
Keyword(s):  
Genetic Similarity ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Dna Fingerprints ◽  
Similarity Coefficients ◽  
Tree Analysis ◽  
Schinus Molle ◽  
Plant Taxon ◽  
Maximum Similarity ◽  
Rapd And Issr

This study examined the degree of variations in DNA fingerprints associated with slight altitudinal change of Schinus molle grown in Abha region, Saudi Arabia. Seven populations from Schinus molle plants located at 2193.0, 2246.0, 2197.7, 2441.0, 2372.0, 2250.6 and 2175.0 meters had been investigated. The degree of genetic variability was evaluated using random amplified polymorphic DNA (RAPD), mixed RAPD and intersimple sequence repeat markers (ISSR). The genetic similarity coefficients from RAPD analysis revealed the maximum similarity value (89.9%) was between population at 2250.6 m and population at 2175.0 m. The genetic similarity coefficients from mixed RAPD primers displayed the highest similarity value (87.6%) between population at 2246.0 m and population at 2197.7 m. Similarity coefficients from ISSR analysis revealed the highest similarity value (86.2%) among populations at 2193.0 m, 2246.0 m, 2441.0 m and at 2250.6 m. Super tree analysis (RAPD + mixed RAPD + ISSR) showed the highest similarity value (85.5%) between population at 2441.0 m and population at 2250.6 m. In conclusion, marker systems including RAPD, mixed RAPD and ISSR, alone or combined can be effectively used in determining the genetic relationship among Schinus molle plants even at very close populations.Bangladesh J. Plant Taxon. 24(2): 205–214.

Assessment of factors on shoot proliferation potential of nodal explants of Phyllanthus fraternus and assessment of genetic fidelity of micropropagated plants using RAPD marker

Biologia ◽  
2014 ◽  
Vol 69 (12) ◽  
Author(s):  
Richa Upadhyay ◽  
Sarvesh Kashyap ◽  
Chandrashekhar Singh ◽  
Kavindra Tiwari ◽  
Karuna Singh ◽  
...  
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Rapd Marker ◽  
Carbon Sources ◽  
Germplasm Conservation ◽  
Genetic Fidelity ◽  
Axillary Shoots ◽  
Micropropagated Plants ◽  
The Media ◽  
Phyllanthus Fraternus

AbstractPhyllanthus fraternus is an important medicinal plant, popularly known for its hepatoprotective and antiviral activities since ancient times. Various physiological factors like carbon sources, concentration of agar, pH of the media and effect of season of explants collection were optimized for high frequency regeneration of P. fraternus. The frequency of regeneration, average number and length of shoots were highly influenced by the type and concentration of carbon sources (monosaccharides and disaccharides, 1 to 4%), agar concentration (0.2 to 1%) and pH (4.5 to 6.8) of the media. Media containing 3% sucrose, 0.6% agar at pH 5.8 was best for regeneration. Seasonal variation of explants collection significantly affected the axillary shoots proliferation from explants and best proliferation was observed from explants collected during April to June. Genetic fidelity of regenerated plants was assessed by random amplified polymorphic DNA markers. No polymorphism was detected in micropropagated plants and the mother plant, revealing the genetic homogeneity of the in vitro raised plantlets. This is the first report regarding establishment of genetic fidelity of micropropagated P. fraternus plants, which could be successfully applied for the mass multiplication, germplasm conservation and further genetic transformation assays to meet the ever increasing demand of this medicinally potent plant for industrial and pharmaceutical uses.

scholarly journals The growth response of rice (Oryza sativa L. var. FARO 44) in vitro after inoculation with bacterial isolates from a typical ferruginous ultisol

2021 ◽  
Vol 45 (1) ◽  
Author(s):  
Musa Saheed Ibrahim ◽  
Beckley Ikhajiagbe
Keyword(s):  
16S Rrna ◽  
Bacillus Cereus ◽  
Proteus Mirabilis ◽  
Growth Response ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rice Seedlings ◽  
Rrna Gene Sequencing

Abstract Background Rice forms a significant portion of food consumed in most household worldwide. Rice production has been hampered by soil factors such as ferruginousity which has limited phosphorus availability; an important mineral component for the growth and yield of rice. The presence of phosphate-solubilizing bacteria (PSB) in soils has been reported to enhance phosphate availability. In view of this, the present study employed three bacteria species (BCAC2, EMBF2 and BCAF1) that were previously isolated and proved P solubilization capacities as inocula to investigate the growth response of rice germinants in an in vitro setup. The bacteria isolates were first identified using 16S rRNA gene sequencing and then applied as inoculum. The inolula were prepared in three concentrations (10, 7.5 and 5.0 ml) following McFarland standard. Viable rice (var. FARO 44) seeds were sown in petri dishes and then inoculated with the three inocula at the different concentrations. The setup was studied for 28 days. Results 16S rRNA gene sequencing identified the isolates as: isolate BCAC2= Bacillus cereus strain GGBSU-1, isolate BCAF1= Proteus mirabilis strain TL14-1 and isolate EMBF2= Klebsiella variicola strain AUH-KAM-9. Significant improvement in rice germination, morphology, physiology and biomass parameters in the bacteria-inoculated setups was observed compared to the control. Germination percentage after 4 days was 100 % in the inoculated rice germinants compared to 65% in the control (NiS). Similarly, inoculation with the test isolates enhanced water-use efficiency by over 40%. The rice seedlings inoculated with Bacillus cereus strain GGBSU-1 (BiS) showed no signs of chlorosis and necrosis throughout the study period as against those inoculated with Proteus mirabilis strain TL14-1 (PiS) and Klebsiella variicola strain AUH-KAM-9 (KiS). Significant increase in chlorophyll-a, chlorophyll-b and alpha amylase was observed in the rice seedlings inoculated with BiS as against the NiS. Conclusion Inoculating rice seeds with Bacillus cereus strain GGBSU-1, Proteus mirabilis strain TL14-1 and Klebsiella variicola strain AUH-KAM-9 in an in vitro media significantly improved growth parameters of the test plant. Bacillus cereus strain GGBSU-1 showed higher efficiency due to a more improved growth properties observed.

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