scholarly journals Optimasi Konsentrasi DNA dan MgCl2 pada Reaksi Polymerase Chain Reaction-Random Amplified Polymorphic DNA untuk Analisis Keragaman Genetik Tanaman Faloak (Sterculia quadrifida R.Br) (Optimization of DNA and MgCl2 Concentrations in Polymerase Chain Reacti

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Uslan Uslan ◽  
Made Pharmawati
Keyword(s):  
Genetic Diversity ◽  
Polymerase Chain Reaction ◽  
Random Amplified Polymorphic Dna ◽  
Optimum Conditions ◽  
Chain Reaction ◽  
Dna Templates ◽  
Clear Band ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Pcr Conditions

Abstrak Faloak  merupakan tanaman yang tumbuh di lahan kritis. Sebagai upaya mendukung pemuliaan dan konservasi tanaman faloak diperlukan informasi keragaman genetiknya. Salah satu metode analisis keragaman genetik adalah menggunakan penanda DNA yang berbasis PCR. Untuk itu diperlukan kondisi PCR (Polymerase Chain Reaction) yang tepat sehingga diperoleh hasil yang dapat dianalisis lebih lanjut. Penelitian ini bertujuan menentukan kondisi optimum PCR-RAPD (Polymerase Chain Reaction-Random Amplified Polymorphic DNA) tanaman faloak. Ekstraksi DNA dilakukan dengan metode CTAB. Optimasi dilakukan dengan menggunakan beberapa konsentrasi DNA cetakan dan MgCl2. Kondisi optimum PCR-RAPD tanaman faloak yang menghasilkan pita produk PCR yang jelas diperoleh  menggunakan 50 ng/ul DNA, 3 mM MgCl2 serta jumlah siklus termal 45 x. Kata kunci : PCR-RAPD, optimasi, tanaman faloak Abstract Faloak is a plant that grows on critical lands. In an effort to support breeding and conservation of faloak, information about its genetic diversity is required. One of the methods of genetic diversity analysis is using PCR-based DNA markers. For that purpose, proper PCR conditions is needed in order to obtain results that can be further analyzed. This study aimed to determine the optimum conditions for PCR-RAPD of faloak plants. DNA extraction was conducted using CTAB. Optimization was done by using several concentrations of DNA templates and MgCl2. The optimum conditions of PCR-RAPD of faloak plants that produce clear band of PCR products were obtained using 50 ng/ ul DNA, 3 mM MgCl2 and 45x thermal cycles Keywords : PCR-RAPD, optimization, faloak plant

scholarly journals Optimization of RAPD-PCR conditions for the study of genetic diversity in Nepal’s Swertia chirayita (Roxb. Ex Fleming) H. Karst

2011 ◽  
Vol 6 (8) ◽  
pp. 35-40
Author(s):  
Sangita Shrestha ◽  
Jaishree Sijapati ◽  
Neesha Rana ◽  
Diwa Malla ◽  
Prabha Regmi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Polymerase Chain Reaction ◽  
Random Amplified Polymorphic Dna ◽  
Molecular Genetic ◽  
Molecular Diagnostic ◽  
Chain Reaction ◽  
Natural Habitats ◽  
Molecular Genetic Diversity ◽  
Rapd Pcr ◽  
Polymerase Chain

Of the 30 species (including five varieties) of the genus Swertia in Nepal, nine have been reported to possess medicinal properties. Among these, S. chirayita is the most valuable species, with high demand in domestic and international markets. Nepal’s S. chirayita and related species are being recklessly exploited for commercial purposes. Two problems that have emerged with this lucrative market are (a) adulteration and fraudulent labeling of S. chirayita, and (b) depletion of S. chirayita and allied species from their natural habitats. To address the problem of adulteration and conservation, we studied molecular genetic diversity in S. chirayita populations and developed a molecular diagnostic tool for the purposes of authentication. We studied intra-specific genetic diversity in S. chirayita using Polymerase Chain Reaction (PCR)-based Random Amplified Polymorphic DNA (RAPD) technique. As a preliminary step, we identified optimal RAPD-PCR reaction and cycling conditions by varying PCR reaction parameters such as concentration of template DNA, MgCl2, dNTPs, primer, Taq DNA polymerase and RAPD-PCR programs. The optimized PCR reaction and cycling conditions were then used in subsequent RAPD profiling experiments for the study of genetic diversity within S. chirayita populations from various geographical locations. Genetic diversity characterization of S. chirayita populations at the molecular level would furnish information with significant applications in the conservation and sustainable utilization of S. chirayita and its allied species in Nepal. Key words: Polymerase Chain Reaction, Random Amplified Polymorphic DNA, DNA fingerprinting, genetic diversity DOI: http://dx.doi.org/10.3126/hjs.v6i8.2699 Himalayan Journal of Sciences Vol.6 Issue 8 2010 pp.35-40

Effect of vegetation on the presence and genetic diversity ofBacillus thuringiensisin soil

2013 ◽  
Vol 59 (1) ◽  
pp. 28-33 ◽  
Author(s):  
Ana Paula Scaramal Ricieto ◽  
Fernanda Aparecida Pires Fazion ◽  
Celso Duarte Carvalho Filho ◽  
Laurival Antonio Vilas-Boas ◽  
Gislayne Trindade Vilas-Bôas
Keyword(s):  
Genetic Diversity ◽  
Polymerase Chain Reaction ◽  
Riparian Forest ◽  
Random Amplified Polymorphic Dna ◽  
Soil Samples ◽  
High Rate ◽  
Bacillus Species ◽  
Cry Genes ◽  
Chain Reaction ◽  
Polymerase Chain

Bacillus thuringiensis isolates were obtained from soil samples collected at different sites located in the same region but with different vegetation. The sites showed different frequencies of B. thuringiensis, depending on the type of vegetation. Strains of B. thuringiensis were found to be less common in samples of riparian forest soil than in soil of other types of vegetation. The rate of occurrence of B. thuringiensis in the samples also varied according to the vegetation. These results show that whenever this bacterium was found, it showed a high rate of occurrence, indicating that this species could be better adapted to using soil as a reservoir than other Bacillus species. The presence of cry genes was analyzed by polymerase chain reaction, and genes that exhibited activity against Diptera species were the most commonly found. The isolates obtained were characterized by random amplified polymorphic DNA, and 50% were clustered into clonal groups. These results demonstrated the possible occurrence of a high number of genetically similar strains when samples are collected from the same region, even if they are from locations with different vegetation.

scholarly journals A Comparative Study of 5S rDNA Non-Transcribed Spacers in Elaeagnaceae Species

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 4
Author(s):  
Oleg S. Alexandrov ◽  
Olga V. Razumova ◽  
Gennady I. Karlov
Keyword(s):  
Polymerase Chain Reaction ◽  
Molecular Markers ◽  
Dna Markers ◽  
5S Rdna ◽  
Chain Reaction ◽  
Closely Related Species ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Species Specific ◽  
Shepherdia Canadensis

5S rDNA is organized as a cluster of tandemly repeated monomers that consist of the conservative 120 bp coding part and non-transcribed spacers (NTSs) with different lengths and sequences among different species. The polymorphism in the 5S rDNA NTSs of closely related species is interesting for phylogenetic and evolutional investigations, as well as for the development of molecular markers. In this study, the 5S rDNA NTSs were amplified with universal 5S1/5S2 primers in some species of the Elaeagnaceae Adans. family. The polymerase chain reaction (PCR) products of five Elaeagnus species had similar lengths near 310 bp and were different from Shepherdia canadensis (L.) Nutt. and Sh. argentea (Pusch.) Nutt. samples (260 bp and 215 bp, respectively). The PCR products were cloned and sequenced. An analysis of the sequences revealed that intraspecific levels of NTS identity are high (approximately 95–96%) and similar in the Elaeagnus L. species. In Sh. argentea, this level was slightly lower due to the differences in the poly-T region. Moreover, the intergeneric and intervarietal NTS identity levels were studied and compared. Significant differences between species (except E. multiflora Thunb. and E. umbellata Thunb.) and genera were found. Herein, a range of the NTS features is discussed. This study is another step in the investigation of the molecular evolution of Elaeagnaceae and may be useful for the development of species-specific DNA markers in this family.

Inheritance of random amplified polymorphic DNA markers in an interspecific cross in the genus Stylosanthes

Genome ◽  
1993 ◽  
Vol 36 (1) ◽  
pp. 50-56 ◽  
Author(s):  
Kemal Kazan ◽  
John M. Manners ◽  
Don F. Cameron
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequences ◽  
Rapd Markers ◽  
Dna Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Interspecific Cross ◽  
Parental Origin ◽  
Chain Reaction ◽  
Stylosanthes Hamata ◽  
Polymerase Chain

The inheritance of random amplified polymorphic DNA (RAPD) markers generated via the polymerase chain reaction amplification of genomic DNA sequences in an F2 family of an interspecific cross between Stylosanthes hamata and S. scabra was investigated. An initial comparison between the parental species, S. hamata cv. Verano and S. scabra cv. Fitzroy, demonstrated that 34% of detected RAPD bands were polymorphic. Of 90 primers tested, 35 showed relatively simple and reliably scorable polymorphisms and were used for segregation analysis. Sixty F2 individuals were scored for the segregation of 73 RAPD markers and 55 of these markers fit a 3:1 ratio. Segregation of eight other RAPD markers deviated significantly from a 3:1 ratio. There was no bias in the inheritance of RAPD markers regarding parental origin of the segregating RAPD markers. Linkage analysis revealed 10 linkage groups containing a total of 44 RAPD loci. Another 10 RAPD markers (7 of maternal origin) that were polymorphic between the parents did not segregate in the F2 population. One of the maternally inherited RAPD bands hybridized to chloroplast DNA. Analysis of RAPD loci by DNA hybridization indicated that mainly repeated sequences were amplified. These data indicate that RAPDs are useful genetic markers in Stylosanthes spp. and they may be suitable for genetic mapping.Key words: genetic mapping, molecular markers, polymerase chain reaction, Stylosanthes hamata, Stylosanthes scabra.

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