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All Journal MANAJEMEN HUTAN TROPIKA Journal of Tropical Forest Management Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan (Journal of Natural Resources and Environmental Management)
Arrofaha, Nawwall
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Agriculture, Biological Sciences & Forestry Earth & Planetary Sciences Environmental Science

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Optimizing DNA Extraction and Selecting Suitable Regions for Biodiversity Assessment: A Study on Shorea leprosula Rachmat, Henti Hendalastuti; Yulita, Kusumadewi Sri; Dwiyanti, Fifi Gus; Susilowati, Arida; Arrofaha, Nawwall; Susila, Susila; Kamal, Irsyad; Siregar, Iskandar Zulkarnaen
Jurnal Manajemen Hutan Tropika Vol. 30 No. 1 (2024)
Publisher : Institut Pertanian Bogor (IPB University)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.7226/144

Abstract

The extraction method plays a crucial role in obtaining high-quality DNA samples, which is indispensable for various molecular biology techniques and analyses, enabling a deeper comprehension of genetic information and biological processes. The objectives of the study were: a) to optimize the chloroplast DNA extraction protocol by comparing modified CTAB methods and GeneAid for both leaf and wood samples of Shorea leprosula, a major commercial timber species, and b) to identify a suitable cpDNA region that exhibits variability and universality across taxa. Total DNA was analyzed by gel electrophoresis followed by Sanger sequencing to determine the amplification success. The results revealed that trnL intron, trnL-trnF, and trnG yielded readable sequences of the expected length (maximum 586 bp, 480 bp, and 908 bp, respectively), while the rps 16 intron failed to assemble a contig. The petL-psbE region provided long readability for reverse sequences (769 bp) but not for the forward sequence (195 bp). Higher successful DNA extraction was achieved from the leaves compared to the woods. The lower sequencing quality may be attributed to suboptimal primer design, the structural features of the regions resulting from extensive repetitive sequences, and the suboptimal condition of the extraction method in eliminating wood chemical compounds.
Optimizing DNA Extraction Methods from Leaf and Wood Tissues to Support Dipterocarp Conservation and Sustainable Forest Management Arrofaha, Nawwall; Rachmat, Henti Hendalastuti; Dwiyanti, Fifi Gus; Adinugroho, Wahyu Catur; Siregar, Iskandar Zulkarnaen; Kamal, Irsyad; Syaputra, Dhika; Salamah, Andi
Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan (Journal of Natural Resources and Environmental Management) Vol 16 No 1 (2026): Jurnal Pengelolaan Sumberdaya Alam dan Lingkungan (JPSL)
Publisher : Pusat Penelitian Lingkungan Hidup, IPB (PPLH-IPB) dan Program Studi Pengelolaan Sumberdaya Alam dan Lingkungan, IPB (PS. PSL, SPs. IPB)

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/jpsl.16.1.13

Abstract

Dipterocarpaceae are economically important, contributing over 85% of Indonesia's timber exports. However, this crucial resource is increasingly threatened by illegal logging, habitat destruction, and the illegal timber trade, which jeopardize dipterocarp population. Furthermore, conservation efforts utilizing genetic and forensic techniques often encounter substantial challenges due to the complexities in DNA extraction protocol. To address this, the study aimed to enhance the efficiency of DNA extraction methodologies by comparing two methods: the modified cetyltrimethylammonium bromide (CTAB) and the Genomic DNA Mini Kit (Plant) from Geneaid Biotech Ltd. The research focused on leaf and wood samples from two species, spesifically Rubroshorea leprosula (Miq.) P.S.Ashton & J.Heck and Shorea laevis Ridl. For each of these species, five leaf and five wood samples were extracted using both methods. The quality of the DNA extraction was evaluated using electrophoresis and quantified with a Qubit fluorometer. Higher DNA concentrations were obtained with the modified CTAB method compared to the GeneAid kit for both R. leprosula and S. laevis, particularly in leaf tissue. The GeneAid kit consistently exhibited low DNA yield efficiency compared to the modified CTAB method for both species. Additionally, PCR amplification of both leaf and wood samples confirmed that the extracted DNA was suitable formolecular analyses. These findings not only contributed to laboratory applications but also served as practical tools for species identification and genetic conservation for sustainable forest management and law enforcement.
Co-Authors Adinugroho, Wahyu Catur Andi Salamah Arida Susilowati Iswanto Fifi Gus Dwiyanti Irsyad Kamal ISKANDAR ZULKARNAEN SIREGAR KUSUMADEWI SRI YULITA Rachmat, Henti Hendalastuti Susila, Susila Syaputra, Dhika