Hostname: page-component-76fb5796d-r6qrq Total loading time: 0 Render date: 2024-04-30T02:38:26.401Z Has data issue: false hasContentIssue false
  • English
  • Français

Utilization of the internal transcribed spacer (ITS) DNA sequence to trace the geographical sources of Aquilaria malaccensis Lam. populations

Published online by Cambridge University Press:  16 February 2017

Shiou Yih Lee ,
Rozi Mohamed ,
Ibrahim Faridah-Hanum  and
Dhilia Udie Lamasudin
Shiou Yih Lee
Affiliation:
Forest Biotech Laboratory, Department of Forest Management, Faculty of Forestry, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
Rozi Mohamed*
Affiliation:
Forest Biotech Laboratory, Department of Forest Management, Faculty of Forestry, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
Ibrahim Faridah-Hanum
Affiliation:
Department of Forest Management, Faculty of Forestry, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
Dhilia Udie Lamasudin
Affiliation:
Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia Halal Products Research Institute, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
*
*Corresponding author. E-mail: rozimohd@upm.edu.my
Get access Rights & Permissions [Opens in a new window]

Abstract

Overexploitation in search of its valuable non-wood fragrance product has put pressure on the survival of the endangered Aquilaria trees in the wild. In this study, the pattern of genetic variation among wild populations was measured to aid in designing useful strategies for in situ conservation. We sequenced the internal transcribed spacer (ITS) of the nuclear region of 19 wild Aquilaria malaccensis populations from different states in Peninsular Malaysia, and compared the sequence with the same species residing outside of Malaysia, mainly from the Assam region in India and Sumatra in Indonesia. This widely distributed species is found in the Indomalesian region and is a major source of agarwood. In addition, we included five wild Aquilaria hirta populations for semblance purposes. Intraspecific variations were not found within A. malaccensis and A. hirta populations in Peninsular Malaysia. Interestingly, Single Nucleotide polymorphisms (SNPs) were identified when comparing A. malaccensis from three geographical regions, with a total of 25 SNPs detected. We imply that geographical segregation is a contributing factor toward genetic variation in A. malaccensis. This is the first report on utilizing the ITS region for analysing genetic variation in A. malaccensis of various geographical regions. The molecular information obtained in this study will serve as a useful reference in designing in situ programmes for this endangered species.

Keywords

agarwoodAquilaria hirtaAquilaria malaccensisconservationgenetic variation
Type
Research Article
Information
Plant Genetic Resources , Volume 16 , Issue 2 , April 2018 , pp. 103 - 111
Copyright
Copyright © NIAB 2017 

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Alvarez, I and Wendel, JF (2003) Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29: 417–434.Google Scholar
Baldwin, BG (1992) Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plants: an example from the Compositae. Molecular Phylogenetics and Evolution 1: 3–16.Google Scholar
Baldwin, BG, Sanderson, MJ, Porter, JM, Wojciechowski, MF, Campbell, CS and Donoghue, MJ (1995) The ITS region of nuclear ribosomal DNA: a valuable source of evidence on angiosperm phylogeny. Annals of the Missouri Botanical Garden 82: 247–277.Google Scholar
Barden, A, Anak, NA, Mulliken, T and Song, M (2000) Heart of the Matter: Agarwood use and Trade and CITES Implementation for Aquilaria malaccensis. Cambridge: Traffic International.Google Scholar
Faridah-Hanum, I, Mustapa, MZ, Lepun, P, Tuan Marina, TI, Nazre, M, Alan, R and Mohamed, R (2009) Notes on the distribution and ecology of Aquilaria Lam.(Thymelaeaceae) in Malaysia. Malaysian Forester 72: 247–259.Google Scholar
Gao, Q, Zhang, D, Duan, Y, Zhang, F, Li, Y, Fu, P and Chen, S (2012) Intraspecific divergences of Rhodiola alsia (Crassulaceae) based on plastid DNA and internal transcribed spacer fragments. Botanical Journal of the Linnean Society 168: 204–215.Google Scholar
Gregory, TR (2004) Insertion–deletion biases and the evolution of genome size. Gene 324: 15–34.Google Scholar
Hou, D (1960) Thymelaeaceae. In: Van Steenis, CGGJ (ed.) Flora Malesiana, Series 1, vol. 6–1. Netherlands: Wolters-Noordhoff Publishing, pp. 1–59.Google Scholar
Jiao, L, Yin, Y, Chen, Y and Jiang, X (2013) DNA barcoding for identification of the endangered species Aquilaria sinensis: comparison of data from heated or aged wood samples. Holzforschung 68: 487–494.Google Scholar
Kimura, M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111–120.Google Scholar
Lee, SY, Weber, JS and Mohamed, R (2011) Genetic variation and molecular authentication of selected Aquilaria species from natural populations in Malaysia using RAPD and SCAR marker. Asian Journal of Plant Science 10: 202–211.Google Scholar
Mabberley, DJ (2008) Mabberley's Plant-Book: A Portable Dictionary of Plants, Their Classifications, and Uses. Cambridge: Cambridge University Press.Google Scholar
Mohamad, A, Azhari, MH, Ismail, SN and Parween, KSAS (2013) Optimization of ISSR markers for molecular DNA fingerprinting in Aquilaria sp. Nuclear Technical Convention 2013, Bangi, Malaysia. 2013, 8–10 October. Available at https://inis.iaea.org/search/search.aspx?orig_q=RN:45097341 Google Scholar
Neves, SS and Forrest, LL (2011) Plant DNA sequencing for phylogenetic analyses: from plants to sequences. In: Cagney, G and Emili, A (eds) Network Biology. New York: Humana Press, pp. 183–235.Google Scholar
Niu, XL, Ji, KP and Lu, GQ (2010) Preliminary studies on identification of Aquilaria sinensis (L.) Gilg by the PCR product of rDNA ITS sequencing. Guangdong Nong Ye Ke Xue 37: 167–169.Google Scholar
Paoli, GD, Peart, DR, Leighton, M and Samsoedin, I (2001) An ecological and economic assessment of the non-timber product gaharu wood in Gunung Palung National Park, West Kalimantan, Indonesia. Conservation Biology 15: 1721–1732.CrossRefGoogle Scholar
Shen, YJ, Yan, P, Zhao, X, Pang, QH and Zhao, SJ (2008) Application of ISSR marker and ITS sequence to investigation of genetic variation of Aquilaria sinensis . Journal of South China University of Technology (Natural Science Edition) 36: 128–132.Google Scholar
Tamura, K, Stecher, G, Peterson, D, Filipski, A and Kumar, S (2013) MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution 30: 2725–2729.CrossRefGoogle ScholarPubMed
The Plant List (2013) Version 1.1. Available at http://www.theplantlist.org (accessed 17 July 2015).Google Scholar
Tnah, LH, Lee, CT, Lee, SL, Ng, KKS, Ng, CH, Nurul-Farhanah, Z, Lau, H and Chua, LSL (2012) Isolation and characterization of microsatellite markers for an important tropical tree, Aquilaria malaccensis (Thymelaeaceae). American Journal of Botany 99: e431–433. doi: 10.3732/ajb.1200165.Google Scholar
UNEP-WCMC (Comps.) (2015) The Checklist of CITES Species Website. CITES Secretariat, Geneva, Switzerland. Compiled by UNEP-WCMC, Cambridge, UK. Available at http://checklist.cites.org (accessed 17 July 2015).Google Scholar
Whitmore, TC (1973) Thymelaeaceae. Order 28: Myrtiflorae. Tree Flora of Malaya – A Manual for Foresters. Selangor: Longman, pp 1:18, 2: 383–391.Google Scholar
Zhou, M, Xia, Z, Lu, C, Wang, H, Ji, J, Wang, W (2012) Genetic diversity and differentiation of Aquilaria sinensis (Lour.) Gilg revealed by ISSR and SRAP markers. Crop Science 52: 2304–2313.Google Scholar
Supplementary material: File

Lee supplementary material

Supplementary Figure

Download Lee supplementary material(File)
File 1.8 MB