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Journal ArticleDOI

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

Uslan Uslan1, Made Pharmawati
28 Feb 2015-Vol. 5, Iss: 1

TL;DR: 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 MgCl 2 and 45x thermal cycles.

AbstractAbstrak Faloak  merupakan tanaman yang tumbuh di lahan kritis . Sebagai upaya mendukung pemuliaan dan konservasi tanaman faloak diperlukan informasi keragaman genetik nya. 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 MgCl 2 . Kondisi optimum PCR-RAPD tanaman faloak yang menghasilkan pita produk PCR yang jelas diperoleh  menggunakan 50 ng/ul DNA, 3 mM MgCl 2 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 i s required . One of the methods of genetic diversity analysis is using PCR-based DNA markers. For that purpose, proper PCR conditions i s 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 MgCl 2. 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 MgCl 2 and 45x thermal cycles Keywords : PCR-RAPD, optimization, faloak plant

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TL;DR: Based on the results of the dendrogram analysis, the R. mucronata population in Timor Island correlated with its geographical location, and the adjacent populations have a tendency to form one subgroup.
Abstract: . Ihwan, Uslan, Widodo, Hakim L. 2019. Genetic diversity of Rhizophora mucronata in eastern region of Timor Island, Indonesia as revealed by RAPD. Biodiversitas 20: 3364-3371. Mangrove ecosystems have essential functions in producing organic materials, protecting against erosion, and supporting the area between land and sea. Rhizophora mucronata is a dominant mangrove species in all coastal areas of Timor Island, East Nusa Tenggara, Indonesia. Recent reports suggest that mangroves have been affected by anthropogenic pressure and natural disasters. The aim of this study was to determine the genetic diversity of R. mucronata in the east region of Timor Island. This study is important in supporting mangrove protected management planning in the region. The sampling was carried out in six mangrove vegetation sites, DNA was isolated from the leaves and used for PCR-RAPD using six primers. Dendrogram analysis of the species was determined based on UPGMA (unweighted pair group method) and the similarity coefficient from Nei and Li using the MVSP program. The results showed that the six primers used generated a DNA length of 270-1345 bp, with the number of bands being 22-27. The percentage of polymorphism ranged from 73.91% to 86.96% in all primers used, with a polymorphic information content (PIC) value of 0.94. Thus, it can be concluded that the value of genetic diversity (He) from the R. mucronata mangrove population in Timor Island has a value of 0.666. The R. mucronata population in Abudenok and Tanjung Bastian has the highest genetic diversity with a value of 0.667, while the population in Tanjung Tuamese has the lowest genetic diversity with a value of 0.664. Based on the results of the dendrogram analysis, the R. mucronata population in Timor Island correlated with its geographical location. The adjacent populations have a tendency to form one subgroup.

3 citations


Cites methods from "Optimasi Konsentrasi DNA dan MgCl2 ..."

  • ...Pellets were dried, and 100 μL of sterile ddH2O was added (Uslan and Pharmawati 2015)....

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Journal Article
Abstract: The mangroveRhizophoramucronatathat grows on the western coast of Timor Island is undertreated by various anthropogenic activities, such as logging for firewood and other household needs, which require a strategy for sustainable development. Information on the genetic diversity of the species is important to plan for coastal management and conservation of the mangrove. Therefore, we conducted a study on mangrove genetic diversityon the western coast of Timor Island. Mangrove leaf samples were collected from 10 locations. Samples underwent DNA isolation and random amplified polymorphic DNA testing using six primers. The R. mucronatapopulation formed three main groups and 12 subgroups with a similarity coefficient value of 0.42, and the genetic proximity among populations is not related to geographical distance. Further analysis suggested that the genetic diversity of R. mucronataon Timor Island can be classified as moderate. The highest degree of genetic diversity was found in Sumlili (Ne = 2.999, Na = 11.167, He = 0.667), whereas the lowest genetic diversity was found in Sulamu (Ne = 2.967, Na = 11.833, He = 0.663). The environmental stress and dry climate condition might be a factor in the genetic diversity of the mangrove at the moderate level.

1 citations


Cites methods from "Optimasi Konsentrasi DNA dan MgCl2 ..."

  • ...The pellets were dried and then resuspended in 100 μL of sterile H2O (Uslan and Pharmawati, 2015)....

    [...]