I. L. G. Nurtjahjaningsih, AYPBC Widyatmoko, Liliek Haryjanto, Yuliah Yuliah, Yayan Hadiyan


Aquilaria malaccensis (agarwood) is a native species to Indonesia, it produces fragrance. Aim in this study was to assess genetic diversity and structure of A. malaccensis in order to manage seed stand to produce high quality and quantity seeds/seedlings. Leaf samples for DNA template were collected from  populations at western Bangka i.e. Air Gantang, Pelangas, and Simpang Gong. Amplifications of 14 RAPD markers were confirmed; 42 DNA samples of A. malaccensis were analysed using RAPD markers. Parameters of genetic diversity within population i.e. private alleles (PA) and expected heterozygosity (H) were calculated using GeneAlex software. Genetic structure among populations were determined as genetic distance (Da), Analysis Molecular of Variance (AMOVA), a neighbor-joining tree, were calculated using GeneAlex and PopTrew software. Eleven out of 14 RAPD markers were produced 104 stable and polymorphic alleles; Pwere found at Air Gantang and Pelangas, 1 and 2 alleles, respectively. The H ranged between 0.133 (Simpang Gong) and 0.328 (Pelangas). The Da was moderate (0.099). AMOVA showed significant genetic diversity among populations (14%). A neighbor-joining tree showed the populations divided into two clusters with high boostrap value, and concordance with their geographical positions. Restricted gene flow might cause a high genetic relationship among populations. Low HEin Simpang Gong caused this population was priored to being conserved; Air Gantang and Pelangas should be designed as different conservation units due to the population contained different private alleles.


expected heterozygosity; genetic relationship; private allele; RAPD markers


Bekku, Y. S., Kurokochi, H., Matsuku, Y., Nishi, N., & Lian, C. (2019). Genetic structure of Pinus parviflora on Mt. Fuji in relation to the hoarding behavior of the Japanese nutcracker. Ecophere, 10(4), 1–13.

Beseega, C., Pometti, C., Campos, C., Saidman, B., & Vilardi, J. (2017). Implications of mating system and pollen dispersal indicates for management and conservation of the semi-arid species Prosopis flexuosa (Leguminosae). Forest Ecology and Management, 400, 218–227.

Borrell, J. S., Wang, N., Nichols, R. A., Buggs, R. J. A., & Richard J.A. Buggs. (2018). Genetic diversity maintained among fragmented populations of a tree undergoing range contraction. Heredity, 121, 304–318.

Dea. (2018). Cerita pengusaha kayu gaharu: Sekilo gaharu bisa seharga Rp 800 juta,. Tribunbanjarmasin.Com.

Excoffier, L., Smouse, P. E., & Quattro, J. M. (1992). Analysis of molecular variance inferred from matric distnaces among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479–491.

Kang, K. S., Bila, A. D., Harju, A. M., & Lindgren, D. (2003). Estimation of fertility variation in forest tree populations. Forestry, 76, 329–343.

Komar, T. E., Wardani, M., Hardjanti, F. I., & Ramdhania, N. (2014). In situ and Ex situ conservation of Aquilaria and Gyrinops: A review (Bismark, E. Santoso, & A. P. Tampubolon (eds.)). Center for Conservation and Rehabilitation Research and Development International Tropical Timber Organization (ITTO) – CITES Phase II Project.

Lian, L. C. S., Leong, L. ., Hoo, L. K., Ting, L. C., Hong, N. ., & Siong, K. N. K. (2016). Conservation action plant for the threated agarwood species Aquilaria malaccensis (Thymelaeaceae) in peninsular Malaysia.

Nurtjahjaningsih, I. L. G., Herawan, T., Rachma, R. P., & Rimbawanto, A. (2018). Pengujian penanda Random Amplified Polymorphism DNA untuk mengetahui kestabilan genetik klon jati (Tectona grandis). Jurnal Pemuliaan Tanaman Hutan, 12(2), 105–135.

Nurtjahjaningsih, I. L. G., Saito, Y., Tsuda, Y., & Ide, Y. (2007). Genetic diversity of parental and offspring populations in a Pinus merkusii seedling seed orchard detected by microsatellite markres. Bulletin-Tokyo University Forest, 118, 1–14.

Nurtjahjaningsih, I. L. G., Sukartiningsih, Saranti, A., Sulistyawati, P., & Rimbawanto, A. (2017). Kekerabatan genetik anakan alam ulin (Eusideroxylon zwageri TEIJSM. & BINN.) menggunakan penanda Random Amplified Polymorphism DNA. Jurnal Pemuliaan Tanaman Hutan, 11(1), 25–31.

Nurtjahjaningsih, I. L. G., Sulistyawati, P., Widyatmoko, A., & Rimbawanto, A. (2012). Karakteristik pembungaan dan sistem perkawinan nyamplung (Calophyllum inophyllum) pada hutan tanaman di Watusipat, Gunung Kidul. Jurnal Pemuliaan Tanaman Hutan, 6(2), 65–80.

Peakall, R., & Smouse, P. (2012). GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics, 28(19).

Rimbawanto, A., & Widyatmoko, A. (2011). Identifikasi Aquilaria malaccensis dan A. microcarpa menggunakan penanda RAPD. Jurnal Pemuliaan Tanaman Hutan, 5(1), 23–30.

Robledo-Arnuncio, J. J., Alia, R., & Gil, L. (2004). Increased selfing and correlated paternity in a small population of a predominantly outcrossing conifer, Pinus sylvestris. Molecular Ecology, 13, 2567–2577.

Sork, V. L. (2016). Gene flow and natural selection shape spatial patterns of genes in tree populations: implication for evolutionary processes and applications. Evolutionary Application, 9, 291–310.

Takesaki, N., Nei, M., & Tamura, K. (2014). POPTREEW: Web version of POPTREE for Constructing Population Trees from Allele Frequency Data and Computing Some Other Quantities. Molecular Biology Evolution, 31(6), 1622–1624.

Widyatmoko, A., Harijanto, L., Yuliah, & Nurtjahjaningsih, I. L. G. (2020). Laporan Hasil Penelitian.



  • There are currently no refbacks.

Copyright (c) 2020 Jurnal Pemuliaan Tanaman Hutan

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

Jurnal Pemuliaan Tanaman Hutan Indexed By:


Copyright of Jurnal Pemuliaan Tanaman Hutan (JPTH)

eISSN : 2527-8665   pISSN : 1693-7147