AGARWOOD BIBLIOGRAPHY A COMPILATION OF ABSTRACTS ON AGARWOOD STUDIES
AGARWOOD BIBLIOGRAPHY
A COMPILATION OF ABSTRACTS
ON AGARWOOD STUDIES
Compiled by:
Adi Susilo
Denny
Ministry of Forestry
Forestry Research and Development
Center for Conservation and Rehabilitation Research and Development
in cooperation with
International Tropical Timber Organization
(ITTO) – CITES Phase II Project
Bogor – Indonesia, 2014
AGARWOOD BIBLIOGRAPHY:
A COMPILATION OF ABSTRACTS ON AGARWOOD STUDIES
Compiled by:
Adi Susilo
Denny
Editors:
Maman Turjaman
Agustinus P. Tampubolon
Atok Subiakto
Desain Cover:
Agustina Dwi Setyowati
Copyright © 2014 Center for Conservation and Rehabilitation Research and
Development
in cooperation with International Tropical Timber Organization (ITTO) – CITES
Phase II Project
ISBN 978-602-1681-22-0
Published by
Center for Conservation and Rehabilitation Research and Development
International Tropical Timber Organization (ITTO) – CITES Phase II Project
Jl. Gunung Batu No. 5 Bogor, Indonesia
Telp. +62-251-8633234, Fax. +62-251-8638111
Printed by: IPB Press
Bogor, Desember 2014
This work was made possible by a grant from ITTO under its collaborative program with CITES ‘Support
to ITTO: CITES Implementation for Tree Species and Trade/Market Transparency (TMT)’. Donors to this
collaborative program include the EU (primary donor), the USA, Germany, the Netherlands and Norway. The
project was implemented by Center for Conservation and Rehabilitation Research and Development.
Preface
“Agarwood Bibliography: A compilation of Abstract on Agarwood studies” is one of
the outputs of the “Promoting Conservation of Plant Genetic Resources of Aquilaria
and Gyrinops Species in Indonesia”, funded by ITTO.
The Bibliography covers 126 references of agarwood on ecology, genetic,
silviculture, agarwood formation, chemical compound, and social economy that
were published from 2000 to 2014. Included references range from published
document, theses, dissertation, journal articles, to project reports and conference
papers. The bibliography represents the collection of information concerning the
progress of agarwood technology from various scientific publications.
We hope that Agarwood bibliography will serve as a useful source of references to
researcher, scientists and anyone who is interested in agarwood research.
Director of CCR
Ir. Adi Susmianto, M.Sc
Tabel of Content
Preface .................................................................................................................................iii
Table of Content ................................................................................................................... v
Executive Summary.............................................................................................................vii
A. Ecology .......................................................................................................................... 1
B. Genetic........................................................................................................................... 8
C. Silviculture.................................................................................................................... 18
D. Agarwood Formation.................................................................................................... 38
E. Chemical Compound ................................................................................................... 56
F. Social and Economy .................................................................................................... 72
G. References................................................................................................................... 82
Index ................................................................................................................................... 95
Executive Summary
Agarwood, resinous dark-colored heartwood, is an economically important natural product
to produce incense, perfumes and traditional medicines. The most important agarwoodproducing trees are Aquilaria spp. and Gyrinops spp. on Thymelaeaceae. Because of the
increasing agarwood demand, Aquilaria spp. and Gyrinops spp. has become very rare in
the wild. As consequences Aquilaria and Gyrinops species were listed on Appendix II of the
Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES)
to control commercial agarwood trade.
This book, Agarwood bibliography, is a compilation abstract of published scientific research
carried out by research institutions and universities in Indonesia and overseas. With the
help of librarians from library of Ministry of Environment and Forestry (Ardikusuma Library),
Ministry of Agriculture, Bogor Agriculture University (IPB: Institut Pertanian Bogor) and
Indonesian Institute of Science (LIPI: Lembaga Ilmu Pengetahuan Indonesia) published
research studies of agarwood were collected. Further more, online database such as
Proquest, Science direct, Google scholar and Infotract were also accessed to enrich the
collected result. Keywords used were agarwood, Aquilaria and Gyrinops. With this method,
126 scientific publications were collected covering aspect of ecology, silviculture, genetic,
agarwood formation, chemical compound, and social economy. Included references range
from published document, theses, journal articles, to project reports and conference papers
that were published from 2000 to 2014. Entries are arranged alphabetically by author and
year of publication in each of topic classification.
Gyrinops was poorly studied. From 126 collected scientific publications only 15 discussed
on Gyrinops, 105 discussed on Aquilaria and the rest of 6 discussed both. In term of subject
the most popular one was silviculture (29) followed by chemical compound (28), agarwood
formation (27), Genetic (15), social economy (15) and Ecology (12). The bibliography
represents the collection of information regarding the progress of agarwood technology.
1
A. Ecology
_________________________________________________________________
Soehartono T, Newton AC. 2000. Conservation and Sustainable Use of Tropical
Trees in the Genus Aquilaria I. Status and distribution in Indonesia Biological
Conservation 96 (2000): 83-94
Tropical trees in the genus Aquilaria Lam. are the principal source of gaharu, one
of the most valuable forest products traded internationally. Although these species
are the focus of increasing conservation concern, information on their status and
distribution is lacking. Information from herbarium accessions, a national forest
inventory (NFI), field surveys and gaharu traders was used to assess the distribution
of Aquilaria species in Indonesia, indicating population concentrations in Sumatra
and eastern Kalimantan. Analysis of NFI data indicated that population densities are
relatively low, with values generally 3.18 cm diameter at
breast height = DBH), saplings and seedlings, respectively. This pattern of density
distribution (seedlings > saplings > trees) indicates good regeneration status of the
species in homegardens. On the other hand, out of the eight selected homegardens,
seven showed good regeneration status, whereas, one showed fair regeneration
status for the species. Seasonal survival rate of A. malaccensis saplings was
significantly different among the eight selected homegardens during all the four
seasons (each season of three months) of the year but that of seedlings and trees
did not differ significantly. Average seasonal growth rate of A. malaccensis (in terms
of collar diameter for seedlings and saplings, and DBF for trees) varied significantly
among the eight selected home gardens as well as between the tour seasons. The
findings of the present study suggest that homegardens can save the species from
the risk of extinction.
Keywords: Agarwood, Basal cover, Coppice regeneration, Density, Growth
survival
_______________________________________________________________
Saikia P, Khan ML. 2014. Ecological Features of Cultivated Stands of Aquilaria
malaccensis Lam. (Thymelaeaceae), a Vulnerable Tropical Tree Species in
Assamese Homegardens. International Journal of Forestry Research.
Research was conducted in twenty-seven selected villages located in Jorhat and
Golaghat districts of upper Assam, northeast India, for population estimation,
quantitative ecological analysis, and evaluation of Aquilaria malaccensis
(Thymelaeaceae). Vegetation sampling was done by quadrat method and A.
malaccensis is the most dominant tree species in all twenty-seven different study
sites of upper Assam contributing 10-54% of the total tree density with a mean of 34
% ± 2. Density of the species varied from 6,236 individuals ha-1 to 429 individuals
ha-1 with a mean of 1,609 individuals ha-1 ± 217, whereas frequency of occurrence
is very high ranging from 93% to 100% with a mean of 98 % ± 0.53 in different study
sites. Distribution of A. malaccensis is found contagious in all twenty-six study sites
on the basis of abundance to frequency ratio except in KBG, Golaghat, where its
distribution is random with 0.04 abundance to frequency ratio. The widespread
cultivation of A. malaccensis in upper Assam, northeast India, offers a potential ex
situ reservoir for the future conservation and management of this threatened tree.
Keywords: Aquilaria malaccensis, Quadrat method, Assam Northeast India
_______________________________________________________________
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B. gENETIc
_________________________________________________________________
Eurlings MCM, Gravendeel B. 2005. TrnL-trnF Sequence Data Imply Paraphyly
of Aquilaria and Gyrinops (Thymelaeaceae) and Provide New Perspectives
for Agarwood Identification. Plant Systematics and Evolution 254(1): 1-12
The genera Aquilaria and Gyrinops (Thymelaeaceae, Malvales) are well known for
the production of agarwood which is a highly wanted forest product of substantial
economic value. The taxonomic status of Aquilaria and Gyrinops as separate
genera is doubted as they are only distinguished by the number of stamens. We
investigated their status by conducting phylogenetic analyses of DNA sequences
from the plastid trnL-trnF spacer. Control of international trade of agarwood is
currently hampered by the failure of traditional methods such as microscopy to
identify samples to species level. We therefore evaluated the potential of molecular
identification of agarwood by searching for species- and region-specific plastid
DNA polymorphisms. DNA sequences were obtained from 31 Thymelaeaceae
accessions encompassing 20 different species in six genera. Aquilaria and Gyrinops
appear to be paraphyletic. Success in sequencing wood samples demonstrates
that molecular markers provide new perspectives for agarwood identification.
Keywords: Aquilaria, gaharu, Gyrinops, phylogeny, trnL- trnF
_________________________________________________________________
Azwin. 2007. Evaluasi Stabilitas Genetik Tanaman Gaharu (Aquilaria
malaccensis Lamk.) Hasil Kultur In Vitro. Skripsi IPB (Bogor Agricultural
University)
Gaharu (A. malaccensis Lamk.) adalah salah satu tanaman hutan tropis penghasil
resin yang bernilai ekonomi tinggi. Meningkatnya permintaan gaharu dari tahun ke
tahun menyebabkan terjadinya penebangan liar dari hutan alam tidak terkontrol.
Untuk mengatasi permasalahan ini, perlu dilakukan pengembangan tanaman gaharu.
Teknik kultur jaringan adalah suatu metode alternatif yang dapat menghasilkan
bibit secara genetik lebih baik dimasa yang akan datang. Keuntungan kultur
jaringan dapat menghasilkan planlet dalam jumlah yang banyak dan dalam waktu
yang singkat. Disamping itu, dengan teknik ini juga dapat menghasilkan tanaman
yang homogen dan bebas penyakit. Meskipun demikian, teknik kultur jaringan juga
dapat menyebabkan terjadinya variasi genetik atau variasi somaklonal. Tujuan
penelitian ini adalah (1) untuk mengetahui perbedaan stabilitas genetik tanaman
gaharu hasil kultur in vitro baik eksplan yang berasal dari tunas aksilar maupun
eksplan dari tunas adventif, dan (2) untuk mendapatkan konsentrasi optimum zat
pengatur tumbuh BAP atau TDZ untuk menginduksi tunas gaharu dalam kultur
in vitro. Media dasar yang digunakan adalah media MS (Murashige and Skoog,
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1962). Rancangan percobaan yang digunakan adalah rancangan acak lengkap
(RAL) dengan perlakuan konsentrasi BAP (kontrol; 0,50 ppm; 0,75 ppm; 1,0 ppm)
atau TDZ (kontrol; 0,25 ppm; 0,50 ppm; 0,75 ppm), dengan 3 ulangan, setiap
ulangan terdiri dari 4 botol, setiap botol ditanam satu eksplan yang berasal dari
tunas aksilar atau tunas adventif. Teknik Random Amplified Polymorphic DNA
(RAPD) telah digunakan untuk mengetahui variasi genetik dari pohon induk dan
bibit (sebelum kultur) dan variasi somaklonal tunas aksilar dan tunas adventif (hasil
kultur). Hasil penelitian ini menunjukkan bahwa dua jenis eksplan yang ditanam
secara in vitro pada media MS yang diberi perlakuan BAP 0,50 ppm atau TDZ 0,25
ppm menghasilkan jumlah tunas, panjang tunas dan jumlah daun yang terbaik.
Hasil evaluasi stabilitas genetik tanaman gaharu hasil kultur in vitro menggunakan
penanda RAPD menunjukkan bahwa keragaman genetik sebelum kultur (0,0729),
hasil kultur (planlets) (0,0833), sub kultur I (0,0903) dan sub kultur II (0,0382),
sedangkan keragaman genetik pohon induk sebesar 0,2454.
Kata Kunci: Genetik, Gaharu, Aquilaria malaccensis
_________________________________________________________________
Rahmawati D, Toruan-Mathius N. 2009. Analisis Keragaman Genetik Acremonium
yang Berasosiasi dengan Tanaman Gaharu Menggunakan Teknik Random
Amplified Polymorphic DNA (RAPD). Jurnal Agro Biogen 5 (2): 65-70
Agarwood or gaharu is a plant that has a high economic value in Asia, due to its
use for production of incense and traditional medicines. The agarwood formation
occurs in the trunk and roots of trees that have been infected by a fungus, such
as Acremonium spp. Various fungi were associated with the agarwood formation.
Acremonium is generally considered as highly polyphyletic, contains distantly related
fungi. A study was done to identify genetic diversities in 10 isolates of Acremonium
spp. from four different areas in Indonesia that are associated with Aquilaria
and Gyrinops versteegii using the Random Amplified Polymorphic DNA (RAPD)
technique. Eight RAPD primers, i.e., OPA 02, OPB 04, OPB 07, OPB 17, OPC 11,
OPD 03, OPD 05, and OPE 07 were used in the analyses. The results indicated
that similarity index values of the genetic variation ranged from 0.21 to 0.97. Based
on the Nei and Li’s similarity coefficients, these values indicating the presence
of high degree of genetic variability. The lowest degree of genetic similarity were
found between isolates F (Acremonium spp., which is associated with G. verstegii
from Mataram, Nusa Tenggara Barat), and LM2 from south coastal area of West
Sumatra. The highest genetic similarity value (0.97) was found between isolates
Sr2 and Sr4 from Sorong, Papua. Results from the cluster analysis indicated that
the isolates could be grouped into two major clusters that were associated with their
geographical locations.
Key words: Agarwood, genetic diversity, Acremonium spp., RAPD.
_________________________________________________________________
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Siburian RHS. 2009. Keragaman Genetik Gyrinops versteegii asal Papua
Berdasarkan RAPD dan Mikrosatelit. Skripsi Fakultas Matematika dan Ilmu
Pengetahuan Alam (IPB)
Gyrinops versteegii merupakan salah satu tanaman penghasil gaharu yang berasal
dari Papua. Gyrinops versteegii yang dijumpai di alam memiliki morfologi daun
yang agak berbeda, terutama pada daerah dengan ketinggian tempat tumbuh yang
berbeda. Perbedaan morfologi ini menunjukkan tingkat keragaman genetik seperti
yang umum dijumpai pada berbagai jenis tumbuhan lain. Informasi keragaman
genetik, berupa tingkat dan distribusi keragaman yang ada pada suatu jenis sangat
penting untuk diketahui berkaitan dengan penyusunan strategi pemuliaan (breeding)
dan juga konservasinya. Keragaman genetik yang ada merupakan sumberdaya
yang dapat memberikan peluang untuk dilakukannya rekombinasi, evaluasi dan
seleksi. Informasi keragaman genetik dapat diperoleh dengan melakukan kegiatan
inventarisasi genetik baik melalui pengujian lapangan (field trial) ataupun analisis
dengan bantuan penanda genetik.
Penelitian ini bertujuan untuk mengetahui variasi genetik tanaman Gyrinops
versteegii yang berasal dari dataran rendah dan tinggi (Manokwari dan Kebar)
dengan menggunakan penanda DNA RAPD dan Mikrosatelit. Nilai keragaman
genetik Gyrinops versteegii dalam populasi dengan menggunakan metode RAPD
menunjukkan keragaman genetik populasi Kebar (He = 0,2944) lebih tinggi
dibanding populasi Manokwari. (He = 0,2357). Hasil AMOVA menunjukkan bahwa
sumbangan keragaman terbesar diberikan oleh keragaman antar individu yakni
sebesar 89% dari total ragam. Analisis dendogram berdasarkan jarak genetik,
menunjukkan bahwa populasi induk dan anakan dalam satu lokasi membentuk satu
kelompok dengan jarak genetik yang kecil, sedang antar populasi induk Manokwari
dan Kebar memiliki jarak genetik yang besar. Hal ini menggambarkan kedua
kelompok tersebut terpisah dan diduga hal ini menjadi penghalang terjadinya aliran
gen. Informasi keragaman genetik ini diharapkan dapat menjadi dasar strategi
pengembangan konservasi dan pemuliaan.
Kata kunci: Genetik, Gyrinops versteegii, RAPD, Mikrosatelit
_________________________________________________________________
Fujino H, Kadota S, Katoh Y, Kenmotsu Y, Kurosaki F, Ogita S. 2011. Methyl
Jasmonate-induced Enhancement of Expression Activity of AmFaPS-1, a Putative Farnesyl Diphosphate Synthase Gene from Aquilaria
microcarpa. Journal of Natural Medicines 65(1): 194-197
A cDNA clone, designated Am-FaPS-1 (1310 bp), was isolated from callus culture
derived from the leaf tissues of Aquilaria microcarpa. This gene contains an open
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reading frame encoding the protein of 342 amino acid residues with high homology
to farnesyl diphosphate synthase from various plant sources. An appreciable
increase in the transcriptional level of Am-FaPS-1 was reproducibly observed by
the exposure of the cell culture to methyl jasmonate. The expression activity of
the gene was also elevated when the cells were treated with yeast extract and
Ca.sup.2+-ionophore A23187. These results suggest that Am-FaPS-1 and its
translate play roles in methyl jasmonate- and yeast extract-induced responses
of A. microcarpa, and Ca.sup.2+ functions as an important messenger molecule
in these processes. This set of the results would support our hypothesis that the
activation of Ca.sup.2+-cascade evoked by the elevation of cytoplasmic Ca.sup.2+
concentration is an essential early event in methyl jasmonate-induced responses
of higher plant cells.
Keywords: Methyl jasmonate, Farnesyl diphosphate synthase, Sesquiterpene
biosynthesis, Agarwood,Aquilaria microcarpa
_________________________________________________________________
Ito M, Kumeta Y. 2011. Genomic Organization of [delta]-guaiene Synthase
Genes in Aquilaria crassna and its Possible Use for the Identification of
Aquilaria species. Journal of Natural Medicines 65 (3-4): 508-513
The resinous portions of Aquilaria plants, called agarwood, have been used as
medicines and incenses. Agarwood contains a great variety of sesquiterpenes,
and a study using cultured cells of Aquilaria crassna showed that the production
of sesquiterpenes ([alpha]-guaiene, [alpha]-humulene, and [delta]-guaiene) was
induced by treatment with methyl jasmonate, which led to the cloning of [delta]guaiene synthases. In the present study, analyses of genomic organization and
Southern blotting of [delta]-guaiene synthase in A. crassna were performed in
order to examine the genomic background of [delta]-guaiene synthases in Aquilaria
plants. Genomic cloning and sequencing revealed five types of sequence in putative
[delta]-guaiene synthases sharing more than 96% identity in exon regions, and that
these enzymes belonged to the class III TPS subfamily with seven exons and six
introns. Furthermore, Southern blotting revealed that at least five copies of [delta]guaiene synthase existed in A. crassna. The hybridization of digested DNA of A.
crassna and A. sinensis with probes made with a [delta]-guaiene synthase cDNA
fragment resulted in different banding patterns for these two species. It may be
possible to identify Aquilaria species by restriction fragment length polymorphism
analyses with [delta]-guaiene synthase cDNA probes.
Keywords: Aquilaria crassna, Agarwood, Sesquiterpenes
_________________________________________________________________
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Gao ZH, W JH, Yang Y, Zhang Z, Zao WT. 2012. Selection and Validation
of Reference Genes for Studying Stress-related Agarwood Formation of
Aquilaria sinensis. Plant Cell Reports 31 (9): 1759-68
Agarwood is a high-valued woody material for medicine, perfume, and incense
production in Asia, Middle East, and Europe. The wild resources of agarwoodproducing tree species, e.g., Aquilaria sinensis have been greatly threatened. The
formation of agarwood is considered to be associated with the plant stress and
defensive responses, thus it would be urgent and significant to investigate the
molecular mechanism of these species responding to a variety of stresses. This
is the first report regarding the reference gene selection of Aquilaria species for
studying the molecular mechanism of stress-related agarwood production. Candidate
reference genes were selected according to previous reports and the sequences
were obtained from the 454 EST library of A. sinensis. To obtain the robust genes,
we applied three independent programs depending on distinct assumptions and
combined these results by a rank aggregation algorithm. The result supports tubulin,
ribosomal protein, and glyceraldehyde-3-phosphate dehydrogenase to be the most
stable reference genes for quantification of target gene expression in the overall
samples examined. Validation of these genes through normalizing the expression of
a terpene synthase demonstrated that these three genes are reliable. The selective
usage of three algorithms based on their characteristics was underlined. However,
more robust genes could be identified if the results of all algorithms were combined
by a proper method such as the rank aggregation algorithm.
Keywords: Quantitative genes expression, Reference gene, Aquilaria sinensis,
Agawood, Strees
_________________________________________________________________
Kenmotsu Y, Yamamura Y, Kurosaki F. 2012. Expression of Specific Calmodulin
Genes Isolated from Tissue Cultured Cells of AquilariaMicrocarpa in Response
to Methyl Jasmonate and Yeast Extract. In Vitro Cellular & Developmental Biology
48(6):627-631
We found that the early cellular events which lead to the activation of secondary
metabolism in appropriately stimulated plant cells, such as gene expression
of monomeric GTP-binding proteins and their intracellular translocation, occur
very rapidly, and are sometimes terminated within 30 min after the stimulation
(Mitamura et al. 2011). Together with the results obtained in the present study, the
physiological roles of plant CAM appear to be regulated by various mechanisms,
such as differential transcriptional control of specific CAM paralogues and posttranslational modification followed by intracellular translocation of the protein.
Keywords : Aquilaria microcarpa, Calmodulin genes
_________________________________________________________________
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Laswi I. 2012. Genetic Variation of Planted and Natural Agarwood Assessed
by Microsatellite. Skripsi Bogor Agriculture University (IPB)
Agarwood is one of the valuable Non Timber Forest Products (NTFPs) that contain
resin with a specific fragrance, and is often used as raw materials of perfumes,
pharmaceuticals, cosmetics, incense, preservatives as well as religious activities.
Over exploitation of agarwood has resulted in scarcity of agarwood in the nature
leading to the losses of trees of superior genotypes. This scarcity has led agarwood
to be included into the CITES Appendix II list in which a quota system is imposed
for trading activities. However, this quota still does not distinguish clearly between
natural or cultivated agarwood, opening opportunities for illegal trading practices.
It is therefore necessary to provide an effective attempts to control of the origin
of. Nowdays, the use of DNA markers gains significant importance in the forensic
activities such as verification of the origin of timber and plant materials. This tool
is difficult to be manipulated. Therefore, a study was carried with aims to 1) cross
amplify Aquilaria crassna microsatellite primers into other agarwood species
(transferability study), and 2) to infer the origin of agarwoodbeing traded in the
market. Materials for research were populations of agarwood from natural and
planted forests and agarwood pieces of unknown origin. A.crassna microsatellite
primers were used, namely 6pa18 (180-210 bp), 10pa17 (152-156 bp), 16pa17 (143155 bp), and 71pa17 (152-224 bp). Results showed that agarwood samples from
both natural forests and plantations could cross amplify with expected fragment size
ranges. Result showed that genetic diversity (He) in the planted forest was 0.5443
a slighty higher than that of natural forest (He=0.4642). Information on the level of
genetic diversities can be used as scientific basis for conservation program. Cluster
analysis showed different groupings of agarwood originated from plantations and
natural forests. Futher analysis showed that agarwood timbers with unclear origins
clustered into agarwood group from natural forests indicating common existence of
traded natural agarwood.
Keywords: Agarwood, Cross amplification, Microsatellite, CITES, genetic
diversity
_________________________________________________________________
Tnah LH, Lee CT, Lee SL, Ng KKS, Ng CH, Nurul-Farhanah Z, Lau KH, Chua LSL.
2012. Isolation and Characterization of Microsatellite Markers for an Important
Tropical Tree, Aquilaria malaccensis (Thymelaeaceae). American Journal of
Botany 99 (11): e431-433
Aggressive collections and trade activities in recent decades have resulted in heavy
pressure on the natural stands of Aquilaria malaccensis and concerns over its longterm survival potential. To aid DNA profiling and assessment of its genetic diversity,
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microsatellite markers were developed for the species. Seventeen polymorphic
microsatellite markers were developed for A. malaccensis using an enrichment
protocol. The markers were screened on 24 samples from a natural population. The
number of alleles ranged from two to 11, and the observed heterozygosity ranged
from 0.042 to 0.957. No significant deviation from Hardy-Weinberg equilibrium was
detected after conservative Bonferroni correction. This is the first report on the
development of microsatellite markers in A. malaccensis. The markers will be used
to establish a DNA profiling database and to estimate the genetic diversity and
population genetic structure of the species.
Keywords: Microsatellite
microsatellite
markers,
Aquilaria
malaccensis,
Polymorphic
_________________________________________________________________
Kenmotsu Y, Asano K, Yamamura Y, Kurosaki F. 2013. Cloning and Expression
of Putative Rac/Rop GTPase Genes, Am- rac1 and Am- rac2, Involved in Methyl
Jasmonate-induced Transcriptional Activation of Farnesyl Diphosphate
Synthase in Cell Cultures of Aquilaria microcarpa. Plant Molecular Biology
Reporter 31 (3): 539-546
A homology-based cloning strategy yielded two cDNA clones presumably
encoding Rac/Rop GTPases, Am- rac1 and Am- rac2, from callus cultures of
Aquilaria microcarpa. Transcriptional levels of Am- rac1, measured using reverse
transcription polymerase chain reaction, remained steady, while those of Amrac2 increased dramatically following treatment of cultured cells with either a
yeast extract or methyl jasmonate. These results suggested that Am- rac1 was a
constitutively expressed homologue, while Am- rac2 was induced in A. microcarpa
cells. Moreover, a farnesyl diphosphate synthase gene of A. microcarpa, AmFaPS1, was transcriptionally activated in A. microcarpa cells grown in the presence
of methyl jasmonate; however, expression levels were markedly lowered in the
presence of various signal transduction-related inhibitors involved in Ca-, Rap/Rop
GTPase-, or ubiquitin-dependent signaling processes. Whereas, expression of AmFaPS1 was markedly increased, even in the absence of methyl jasmonate in A.
microcarpa cells over-expressing Am- rac2. These findings suggested that Rac/
Rop GTPase proteins played important roles in jasmonate-induced enhancement
of terpenoid metabolism in A. microcarpa.
Keywords: Aquilaria microcarpa, Farnesyl diphosphate synthase, Methyl
jasmonate, Signal transduction
_________________________________________________________________
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Xu Y, Zheng Z, Mengxi W, Wei J, Hongjiang C, Zhihui G, Chun S, Hongmei L,
Xingli Z, Yun Y, Hui M, Li W. 2013. Identification of Genes Related to Agarwood
Formation: Transcriptome Analysis of Healthy and Wounded Tissues of
Aquilariasinensis. BMC Genomics 14(1): 1-16
Agarwood is an expensive resinous heartwood derived from Aquilaria plants that
is widely used in traditional medicines, incense and perfume. Only wounded trees
can produce agarwood, and the huge demand for the agarwood products has led
all Aquilaria spp. being endangered and listed in the Appendix II of the CITES
(http://www.cites.org). The major components of agarwood are sesquiterpenes
and phenylethyl chromones. Owing to a lack of genomic information, the molecular
basis of wound-induced sesquiterpenes biosynthesis and agarwood formation
remains unknown. Results: To identify the primary genes that maybe related to
agarwood formation, we sequenced 2 cDNA libraries generated from healthy and
wounded A.sinensis (Lour.) Gilg. A total of 89,137 unigenes with an average length
of 678.65 bp were obtained, and they were annotated in detail at bioinformatics
levels. Of those associated with agarwood formation, 30 putatively encoded
enzymes in the sesquiterpene biosynthesis pathway, and a handful of transcription
factors and protein kinases were related to wound signal transduction. Three fulllength cDNAs of sesquiterpene synthases (ASS1-3) were cloned and expressed in
Escherichiacoli, and enzyme assays revealed that they are active enzymes, with
the major products being δ-guaiene. A methyl jasmonate (MJ) induction experiment
revealed that the expression of ASS was significantly induced by MJ, and the
production of sesquiterpenes was elevated accordingly. The expression of some
transcription factors and protein kinases, especially MYB4, WRKY4, MPKK2 and
MAPK2, was also induced by MJ and coordinated with ASS expression, suggesting
they maybe positive regulators of ASS. Conclusions: This study provides extensive
transcriptome information for Aquilaria spp. and valuable clues for elucidating the
mechanism of wound-induced agarwood sesquiterpenes biosynthesis and their
regulation.
Keywords: Agarwood; GC-MS; Sesquiterpenes; Transcriptome; Wound signal
transduction
_________________________________________________________________
Chen C, Kuo TC, Yang M, Chien T, Chu M, Huang L, Chen C, Lo H, Jeng S, Chen
L. 2014. Identification of cucurbitacins and assembly of a draft genome for
Aquilaria agallocha. Genomics 15:578
Agarwood is derived from Aquilaria trees, the trade of which has come under strict
control with a listing in Appendix II of the Convention on International Trade in
Endangered Species of Wild Fauna and Flora. Many secondary metabolites of
agarwood are known to have medicinal value to humans, including compounds
that have been shown to elicit sedative effects and exhibit anti-cancer properties.
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16
However, little is known about the genome, transcriptome, and the biosynthetic
pathways responsible for producing such secondary metabolites in agarwood. In
this study, we present a draft genome and a putative pathway for cucurbitacin E
and I, compounds with known medicinal value, from in vitro Aquilaria agallocha
agarwood. DNA and RNA data are utilized to annotate many genes and protein
functions in the draft genome. The expression changes for cucurbitacin E and I
are shown to be consistent with known responses of A. agallocha to biotic stress
and a set of homologous genes in Arabidopsis thaliana related to cucurbitacin biosynthesis is presented and validated through qRT-PCR. This study is the first
attempt to identify cucurbitacin E and I from in vitro agarwood and the f
A COMPILATION OF ABSTRACTS
ON AGARWOOD STUDIES
Compiled by:
Adi Susilo
Denny
Ministry of Forestry
Forestry Research and Development
Center for Conservation and Rehabilitation Research and Development
in cooperation with
International Tropical Timber Organization
(ITTO) – CITES Phase II Project
Bogor – Indonesia, 2014
AGARWOOD BIBLIOGRAPHY:
A COMPILATION OF ABSTRACTS ON AGARWOOD STUDIES
Compiled by:
Adi Susilo
Denny
Editors:
Maman Turjaman
Agustinus P. Tampubolon
Atok Subiakto
Desain Cover:
Agustina Dwi Setyowati
Copyright © 2014 Center for Conservation and Rehabilitation Research and
Development
in cooperation with International Tropical Timber Organization (ITTO) – CITES
Phase II Project
ISBN 978-602-1681-22-0
Published by
Center for Conservation and Rehabilitation Research and Development
International Tropical Timber Organization (ITTO) – CITES Phase II Project
Jl. Gunung Batu No. 5 Bogor, Indonesia
Telp. +62-251-8633234, Fax. +62-251-8638111
Printed by: IPB Press
Bogor, Desember 2014
This work was made possible by a grant from ITTO under its collaborative program with CITES ‘Support
to ITTO: CITES Implementation for Tree Species and Trade/Market Transparency (TMT)’. Donors to this
collaborative program include the EU (primary donor), the USA, Germany, the Netherlands and Norway. The
project was implemented by Center for Conservation and Rehabilitation Research and Development.
Preface
“Agarwood Bibliography: A compilation of Abstract on Agarwood studies” is one of
the outputs of the “Promoting Conservation of Plant Genetic Resources of Aquilaria
and Gyrinops Species in Indonesia”, funded by ITTO.
The Bibliography covers 126 references of agarwood on ecology, genetic,
silviculture, agarwood formation, chemical compound, and social economy that
were published from 2000 to 2014. Included references range from published
document, theses, dissertation, journal articles, to project reports and conference
papers. The bibliography represents the collection of information concerning the
progress of agarwood technology from various scientific publications.
We hope that Agarwood bibliography will serve as a useful source of references to
researcher, scientists and anyone who is interested in agarwood research.
Director of CCR
Ir. Adi Susmianto, M.Sc
Tabel of Content
Preface .................................................................................................................................iii
Table of Content ................................................................................................................... v
Executive Summary.............................................................................................................vii
A. Ecology .......................................................................................................................... 1
B. Genetic........................................................................................................................... 8
C. Silviculture.................................................................................................................... 18
D. Agarwood Formation.................................................................................................... 38
E. Chemical Compound ................................................................................................... 56
F. Social and Economy .................................................................................................... 72
G. References................................................................................................................... 82
Index ................................................................................................................................... 95
Executive Summary
Agarwood, resinous dark-colored heartwood, is an economically important natural product
to produce incense, perfumes and traditional medicines. The most important agarwoodproducing trees are Aquilaria spp. and Gyrinops spp. on Thymelaeaceae. Because of the
increasing agarwood demand, Aquilaria spp. and Gyrinops spp. has become very rare in
the wild. As consequences Aquilaria and Gyrinops species were listed on Appendix II of the
Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES)
to control commercial agarwood trade.
This book, Agarwood bibliography, is a compilation abstract of published scientific research
carried out by research institutions and universities in Indonesia and overseas. With the
help of librarians from library of Ministry of Environment and Forestry (Ardikusuma Library),
Ministry of Agriculture, Bogor Agriculture University (IPB: Institut Pertanian Bogor) and
Indonesian Institute of Science (LIPI: Lembaga Ilmu Pengetahuan Indonesia) published
research studies of agarwood were collected. Further more, online database such as
Proquest, Science direct, Google scholar and Infotract were also accessed to enrich the
collected result. Keywords used were agarwood, Aquilaria and Gyrinops. With this method,
126 scientific publications were collected covering aspect of ecology, silviculture, genetic,
agarwood formation, chemical compound, and social economy. Included references range
from published document, theses, journal articles, to project reports and conference papers
that were published from 2000 to 2014. Entries are arranged alphabetically by author and
year of publication in each of topic classification.
Gyrinops was poorly studied. From 126 collected scientific publications only 15 discussed
on Gyrinops, 105 discussed on Aquilaria and the rest of 6 discussed both. In term of subject
the most popular one was silviculture (29) followed by chemical compound (28), agarwood
formation (27), Genetic (15), social economy (15) and Ecology (12). The bibliography
represents the collection of information regarding the progress of agarwood technology.
1
A. Ecology
_________________________________________________________________
Soehartono T, Newton AC. 2000. Conservation and Sustainable Use of Tropical
Trees in the Genus Aquilaria I. Status and distribution in Indonesia Biological
Conservation 96 (2000): 83-94
Tropical trees in the genus Aquilaria Lam. are the principal source of gaharu, one
of the most valuable forest products traded internationally. Although these species
are the focus of increasing conservation concern, information on their status and
distribution is lacking. Information from herbarium accessions, a national forest
inventory (NFI), field surveys and gaharu traders was used to assess the distribution
of Aquilaria species in Indonesia, indicating population concentrations in Sumatra
and eastern Kalimantan. Analysis of NFI data indicated that population densities are
relatively low, with values generally 3.18 cm diameter at
breast height = DBH), saplings and seedlings, respectively. This pattern of density
distribution (seedlings > saplings > trees) indicates good regeneration status of the
species in homegardens. On the other hand, out of the eight selected homegardens,
seven showed good regeneration status, whereas, one showed fair regeneration
status for the species. Seasonal survival rate of A. malaccensis saplings was
significantly different among the eight selected homegardens during all the four
seasons (each season of three months) of the year but that of seedlings and trees
did not differ significantly. Average seasonal growth rate of A. malaccensis (in terms
of collar diameter for seedlings and saplings, and DBF for trees) varied significantly
among the eight selected home gardens as well as between the tour seasons. The
findings of the present study suggest that homegardens can save the species from
the risk of extinction.
Keywords: Agarwood, Basal cover, Coppice regeneration, Density, Growth
survival
_______________________________________________________________
Saikia P, Khan ML. 2014. Ecological Features of Cultivated Stands of Aquilaria
malaccensis Lam. (Thymelaeaceae), a Vulnerable Tropical Tree Species in
Assamese Homegardens. International Journal of Forestry Research.
Research was conducted in twenty-seven selected villages located in Jorhat and
Golaghat districts of upper Assam, northeast India, for population estimation,
quantitative ecological analysis, and evaluation of Aquilaria malaccensis
(Thymelaeaceae). Vegetation sampling was done by quadrat method and A.
malaccensis is the most dominant tree species in all twenty-seven different study
sites of upper Assam contributing 10-54% of the total tree density with a mean of 34
% ± 2. Density of the species varied from 6,236 individuals ha-1 to 429 individuals
ha-1 with a mean of 1,609 individuals ha-1 ± 217, whereas frequency of occurrence
is very high ranging from 93% to 100% with a mean of 98 % ± 0.53 in different study
sites. Distribution of A. malaccensis is found contagious in all twenty-six study sites
on the basis of abundance to frequency ratio except in KBG, Golaghat, where its
distribution is random with 0.04 abundance to frequency ratio. The widespread
cultivation of A. malaccensis in upper Assam, northeast India, offers a potential ex
situ reservoir for the future conservation and management of this threatened tree.
Keywords: Aquilaria malaccensis, Quadrat method, Assam Northeast India
_______________________________________________________________
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B. gENETIc
_________________________________________________________________
Eurlings MCM, Gravendeel B. 2005. TrnL-trnF Sequence Data Imply Paraphyly
of Aquilaria and Gyrinops (Thymelaeaceae) and Provide New Perspectives
for Agarwood Identification. Plant Systematics and Evolution 254(1): 1-12
The genera Aquilaria and Gyrinops (Thymelaeaceae, Malvales) are well known for
the production of agarwood which is a highly wanted forest product of substantial
economic value. The taxonomic status of Aquilaria and Gyrinops as separate
genera is doubted as they are only distinguished by the number of stamens. We
investigated their status by conducting phylogenetic analyses of DNA sequences
from the plastid trnL-trnF spacer. Control of international trade of agarwood is
currently hampered by the failure of traditional methods such as microscopy to
identify samples to species level. We therefore evaluated the potential of molecular
identification of agarwood by searching for species- and region-specific plastid
DNA polymorphisms. DNA sequences were obtained from 31 Thymelaeaceae
accessions encompassing 20 different species in six genera. Aquilaria and Gyrinops
appear to be paraphyletic. Success in sequencing wood samples demonstrates
that molecular markers provide new perspectives for agarwood identification.
Keywords: Aquilaria, gaharu, Gyrinops, phylogeny, trnL- trnF
_________________________________________________________________
Azwin. 2007. Evaluasi Stabilitas Genetik Tanaman Gaharu (Aquilaria
malaccensis Lamk.) Hasil Kultur In Vitro. Skripsi IPB (Bogor Agricultural
University)
Gaharu (A. malaccensis Lamk.) adalah salah satu tanaman hutan tropis penghasil
resin yang bernilai ekonomi tinggi. Meningkatnya permintaan gaharu dari tahun ke
tahun menyebabkan terjadinya penebangan liar dari hutan alam tidak terkontrol.
Untuk mengatasi permasalahan ini, perlu dilakukan pengembangan tanaman gaharu.
Teknik kultur jaringan adalah suatu metode alternatif yang dapat menghasilkan
bibit secara genetik lebih baik dimasa yang akan datang. Keuntungan kultur
jaringan dapat menghasilkan planlet dalam jumlah yang banyak dan dalam waktu
yang singkat. Disamping itu, dengan teknik ini juga dapat menghasilkan tanaman
yang homogen dan bebas penyakit. Meskipun demikian, teknik kultur jaringan juga
dapat menyebabkan terjadinya variasi genetik atau variasi somaklonal. Tujuan
penelitian ini adalah (1) untuk mengetahui perbedaan stabilitas genetik tanaman
gaharu hasil kultur in vitro baik eksplan yang berasal dari tunas aksilar maupun
eksplan dari tunas adventif, dan (2) untuk mendapatkan konsentrasi optimum zat
pengatur tumbuh BAP atau TDZ untuk menginduksi tunas gaharu dalam kultur
in vitro. Media dasar yang digunakan adalah media MS (Murashige and Skoog,
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9
1962). Rancangan percobaan yang digunakan adalah rancangan acak lengkap
(RAL) dengan perlakuan konsentrasi BAP (kontrol; 0,50 ppm; 0,75 ppm; 1,0 ppm)
atau TDZ (kontrol; 0,25 ppm; 0,50 ppm; 0,75 ppm), dengan 3 ulangan, setiap
ulangan terdiri dari 4 botol, setiap botol ditanam satu eksplan yang berasal dari
tunas aksilar atau tunas adventif. Teknik Random Amplified Polymorphic DNA
(RAPD) telah digunakan untuk mengetahui variasi genetik dari pohon induk dan
bibit (sebelum kultur) dan variasi somaklonal tunas aksilar dan tunas adventif (hasil
kultur). Hasil penelitian ini menunjukkan bahwa dua jenis eksplan yang ditanam
secara in vitro pada media MS yang diberi perlakuan BAP 0,50 ppm atau TDZ 0,25
ppm menghasilkan jumlah tunas, panjang tunas dan jumlah daun yang terbaik.
Hasil evaluasi stabilitas genetik tanaman gaharu hasil kultur in vitro menggunakan
penanda RAPD menunjukkan bahwa keragaman genetik sebelum kultur (0,0729),
hasil kultur (planlets) (0,0833), sub kultur I (0,0903) dan sub kultur II (0,0382),
sedangkan keragaman genetik pohon induk sebesar 0,2454.
Kata Kunci: Genetik, Gaharu, Aquilaria malaccensis
_________________________________________________________________
Rahmawati D, Toruan-Mathius N. 2009. Analisis Keragaman Genetik Acremonium
yang Berasosiasi dengan Tanaman Gaharu Menggunakan Teknik Random
Amplified Polymorphic DNA (RAPD). Jurnal Agro Biogen 5 (2): 65-70
Agarwood or gaharu is a plant that has a high economic value in Asia, due to its
use for production of incense and traditional medicines. The agarwood formation
occurs in the trunk and roots of trees that have been infected by a fungus, such
as Acremonium spp. Various fungi were associated with the agarwood formation.
Acremonium is generally considered as highly polyphyletic, contains distantly related
fungi. A study was done to identify genetic diversities in 10 isolates of Acremonium
spp. from four different areas in Indonesia that are associated with Aquilaria
and Gyrinops versteegii using the Random Amplified Polymorphic DNA (RAPD)
technique. Eight RAPD primers, i.e., OPA 02, OPB 04, OPB 07, OPB 17, OPC 11,
OPD 03, OPD 05, and OPE 07 were used in the analyses. The results indicated
that similarity index values of the genetic variation ranged from 0.21 to 0.97. Based
on the Nei and Li’s similarity coefficients, these values indicating the presence
of high degree of genetic variability. The lowest degree of genetic similarity were
found between isolates F (Acremonium spp., which is associated with G. verstegii
from Mataram, Nusa Tenggara Barat), and LM2 from south coastal area of West
Sumatra. The highest genetic similarity value (0.97) was found between isolates
Sr2 and Sr4 from Sorong, Papua. Results from the cluster analysis indicated that
the isolates could be grouped into two major clusters that were associated with their
geographical locations.
Key words: Agarwood, genetic diversity, Acremonium spp., RAPD.
_________________________________________________________________
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Siburian RHS. 2009. Keragaman Genetik Gyrinops versteegii asal Papua
Berdasarkan RAPD dan Mikrosatelit. Skripsi Fakultas Matematika dan Ilmu
Pengetahuan Alam (IPB)
Gyrinops versteegii merupakan salah satu tanaman penghasil gaharu yang berasal
dari Papua. Gyrinops versteegii yang dijumpai di alam memiliki morfologi daun
yang agak berbeda, terutama pada daerah dengan ketinggian tempat tumbuh yang
berbeda. Perbedaan morfologi ini menunjukkan tingkat keragaman genetik seperti
yang umum dijumpai pada berbagai jenis tumbuhan lain. Informasi keragaman
genetik, berupa tingkat dan distribusi keragaman yang ada pada suatu jenis sangat
penting untuk diketahui berkaitan dengan penyusunan strategi pemuliaan (breeding)
dan juga konservasinya. Keragaman genetik yang ada merupakan sumberdaya
yang dapat memberikan peluang untuk dilakukannya rekombinasi, evaluasi dan
seleksi. Informasi keragaman genetik dapat diperoleh dengan melakukan kegiatan
inventarisasi genetik baik melalui pengujian lapangan (field trial) ataupun analisis
dengan bantuan penanda genetik.
Penelitian ini bertujuan untuk mengetahui variasi genetik tanaman Gyrinops
versteegii yang berasal dari dataran rendah dan tinggi (Manokwari dan Kebar)
dengan menggunakan penanda DNA RAPD dan Mikrosatelit. Nilai keragaman
genetik Gyrinops versteegii dalam populasi dengan menggunakan metode RAPD
menunjukkan keragaman genetik populasi Kebar (He = 0,2944) lebih tinggi
dibanding populasi Manokwari. (He = 0,2357). Hasil AMOVA menunjukkan bahwa
sumbangan keragaman terbesar diberikan oleh keragaman antar individu yakni
sebesar 89% dari total ragam. Analisis dendogram berdasarkan jarak genetik,
menunjukkan bahwa populasi induk dan anakan dalam satu lokasi membentuk satu
kelompok dengan jarak genetik yang kecil, sedang antar populasi induk Manokwari
dan Kebar memiliki jarak genetik yang besar. Hal ini menggambarkan kedua
kelompok tersebut terpisah dan diduga hal ini menjadi penghalang terjadinya aliran
gen. Informasi keragaman genetik ini diharapkan dapat menjadi dasar strategi
pengembangan konservasi dan pemuliaan.
Kata kunci: Genetik, Gyrinops versteegii, RAPD, Mikrosatelit
_________________________________________________________________
Fujino H, Kadota S, Katoh Y, Kenmotsu Y, Kurosaki F, Ogita S. 2011. Methyl
Jasmonate-induced Enhancement of Expression Activity of AmFaPS-1, a Putative Farnesyl Diphosphate Synthase Gene from Aquilaria
microcarpa. Journal of Natural Medicines 65(1): 194-197
A cDNA clone, designated Am-FaPS-1 (1310 bp), was isolated from callus culture
derived from the leaf tissues of Aquilaria microcarpa. This gene contains an open
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11
reading frame encoding the protein of 342 amino acid residues with high homology
to farnesyl diphosphate synthase from various plant sources. An appreciable
increase in the transcriptional level of Am-FaPS-1 was reproducibly observed by
the exposure of the cell culture to methyl jasmonate. The expression activity of
the gene was also elevated when the cells were treated with yeast extract and
Ca.sup.2+-ionophore A23187. These results suggest that Am-FaPS-1 and its
translate play roles in methyl jasmonate- and yeast extract-induced responses
of A. microcarpa, and Ca.sup.2+ functions as an important messenger molecule
in these processes. This set of the results would support our hypothesis that the
activation of Ca.sup.2+-cascade evoked by the elevation of cytoplasmic Ca.sup.2+
concentration is an essential early event in methyl jasmonate-induced responses
of higher plant cells.
Keywords: Methyl jasmonate, Farnesyl diphosphate synthase, Sesquiterpene
biosynthesis, Agarwood,Aquilaria microcarpa
_________________________________________________________________
Ito M, Kumeta Y. 2011. Genomic Organization of [delta]-guaiene Synthase
Genes in Aquilaria crassna and its Possible Use for the Identification of
Aquilaria species. Journal of Natural Medicines 65 (3-4): 508-513
The resinous portions of Aquilaria plants, called agarwood, have been used as
medicines and incenses. Agarwood contains a great variety of sesquiterpenes,
and a study using cultured cells of Aquilaria crassna showed that the production
of sesquiterpenes ([alpha]-guaiene, [alpha]-humulene, and [delta]-guaiene) was
induced by treatment with methyl jasmonate, which led to the cloning of [delta]guaiene synthases. In the present study, analyses of genomic organization and
Southern blotting of [delta]-guaiene synthase in A. crassna were performed in
order to examine the genomic background of [delta]-guaiene synthases in Aquilaria
plants. Genomic cloning and sequencing revealed five types of sequence in putative
[delta]-guaiene synthases sharing more than 96% identity in exon regions, and that
these enzymes belonged to the class III TPS subfamily with seven exons and six
introns. Furthermore, Southern blotting revealed that at least five copies of [delta]guaiene synthase existed in A. crassna. The hybridization of digested DNA of A.
crassna and A. sinensis with probes made with a [delta]-guaiene synthase cDNA
fragment resulted in different banding patterns for these two species. It may be
possible to identify Aquilaria species by restriction fragment length polymorphism
analyses with [delta]-guaiene synthase cDNA probes.
Keywords: Aquilaria crassna, Agarwood, Sesquiterpenes
_________________________________________________________________
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Gao ZH, W JH, Yang Y, Zhang Z, Zao WT. 2012. Selection and Validation
of Reference Genes for Studying Stress-related Agarwood Formation of
Aquilaria sinensis. Plant Cell Reports 31 (9): 1759-68
Agarwood is a high-valued woody material for medicine, perfume, and incense
production in Asia, Middle East, and Europe. The wild resources of agarwoodproducing tree species, e.g., Aquilaria sinensis have been greatly threatened. The
formation of agarwood is considered to be associated with the plant stress and
defensive responses, thus it would be urgent and significant to investigate the
molecular mechanism of these species responding to a variety of stresses. This
is the first report regarding the reference gene selection of Aquilaria species for
studying the molecular mechanism of stress-related agarwood production. Candidate
reference genes were selected according to previous reports and the sequences
were obtained from the 454 EST library of A. sinensis. To obtain the robust genes,
we applied three independent programs depending on distinct assumptions and
combined these results by a rank aggregation algorithm. The result supports tubulin,
ribosomal protein, and glyceraldehyde-3-phosphate dehydrogenase to be the most
stable reference genes for quantification of target gene expression in the overall
samples examined. Validation of these genes through normalizing the expression of
a terpene synthase demonstrated that these three genes are reliable. The selective
usage of three algorithms based on their characteristics was underlined. However,
more robust genes could be identified if the results of all algorithms were combined
by a proper method such as the rank aggregation algorithm.
Keywords: Quantitative genes expression, Reference gene, Aquilaria sinensis,
Agawood, Strees
_________________________________________________________________
Kenmotsu Y, Yamamura Y, Kurosaki F. 2012. Expression of Specific Calmodulin
Genes Isolated from Tissue Cultured Cells of AquilariaMicrocarpa in Response
to Methyl Jasmonate and Yeast Extract. In Vitro Cellular & Developmental Biology
48(6):627-631
We found that the early cellular events which lead to the activation of secondary
metabolism in appropriately stimulated plant cells, such as gene expression
of monomeric GTP-binding proteins and their intracellular translocation, occur
very rapidly, and are sometimes terminated within 30 min after the stimulation
(Mitamura et al. 2011). Together with the results obtained in the present study, the
physiological roles of plant CAM appear to be regulated by various mechanisms,
such as differential transcriptional control of specific CAM paralogues and posttranslational modification followed by intracellular translocation of the protein.
Keywords : Aquilaria microcarpa, Calmodulin genes
_________________________________________________________________
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Laswi I. 2012. Genetic Variation of Planted and Natural Agarwood Assessed
by Microsatellite. Skripsi Bogor Agriculture University (IPB)
Agarwood is one of the valuable Non Timber Forest Products (NTFPs) that contain
resin with a specific fragrance, and is often used as raw materials of perfumes,
pharmaceuticals, cosmetics, incense, preservatives as well as religious activities.
Over exploitation of agarwood has resulted in scarcity of agarwood in the nature
leading to the losses of trees of superior genotypes. This scarcity has led agarwood
to be included into the CITES Appendix II list in which a quota system is imposed
for trading activities. However, this quota still does not distinguish clearly between
natural or cultivated agarwood, opening opportunities for illegal trading practices.
It is therefore necessary to provide an effective attempts to control of the origin
of. Nowdays, the use of DNA markers gains significant importance in the forensic
activities such as verification of the origin of timber and plant materials. This tool
is difficult to be manipulated. Therefore, a study was carried with aims to 1) cross
amplify Aquilaria crassna microsatellite primers into other agarwood species
(transferability study), and 2) to infer the origin of agarwoodbeing traded in the
market. Materials for research were populations of agarwood from natural and
planted forests and agarwood pieces of unknown origin. A.crassna microsatellite
primers were used, namely 6pa18 (180-210 bp), 10pa17 (152-156 bp), 16pa17 (143155 bp), and 71pa17 (152-224 bp). Results showed that agarwood samples from
both natural forests and plantations could cross amplify with expected fragment size
ranges. Result showed that genetic diversity (He) in the planted forest was 0.5443
a slighty higher than that of natural forest (He=0.4642). Information on the level of
genetic diversities can be used as scientific basis for conservation program. Cluster
analysis showed different groupings of agarwood originated from plantations and
natural forests. Futher analysis showed that agarwood timbers with unclear origins
clustered into agarwood group from natural forests indicating common existence of
traded natural agarwood.
Keywords: Agarwood, Cross amplification, Microsatellite, CITES, genetic
diversity
_________________________________________________________________
Tnah LH, Lee CT, Lee SL, Ng KKS, Ng CH, Nurul-Farhanah Z, Lau KH, Chua LSL.
2012. Isolation and Characterization of Microsatellite Markers for an Important
Tropical Tree, Aquilaria malaccensis (Thymelaeaceae). American Journal of
Botany 99 (11): e431-433
Aggressive collections and trade activities in recent decades have resulted in heavy
pressure on the natural stands of Aquilaria malaccensis and concerns over its longterm survival potential. To aid DNA profiling and assessment of its genetic diversity,
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microsatellite markers were developed for the species. Seventeen polymorphic
microsatellite markers were developed for A. malaccensis using an enrichment
protocol. The markers were screened on 24 samples from a natural population. The
number of alleles ranged from two to 11, and the observed heterozygosity ranged
from 0.042 to 0.957. No significant deviation from Hardy-Weinberg equilibrium was
detected after conservative Bonferroni correction. This is the first report on the
development of microsatellite markers in A. malaccensis. The markers will be used
to establish a DNA profiling database and to estimate the genetic diversity and
population genetic structure of the species.
Keywords: Microsatellite
microsatellite
markers,
Aquilaria
malaccensis,
Polymorphic
_________________________________________________________________
Kenmotsu Y, Asano K, Yamamura Y, Kurosaki F. 2013. Cloning and Expression
of Putative Rac/Rop GTPase Genes, Am- rac1 and Am- rac2, Involved in Methyl
Jasmonate-induced Transcriptional Activation of Farnesyl Diphosphate
Synthase in Cell Cultures of Aquilaria microcarpa. Plant Molecular Biology
Reporter 31 (3): 539-546
A homology-based cloning strategy yielded two cDNA clones presumably
encoding Rac/Rop GTPases, Am- rac1 and Am- rac2, from callus cultures of
Aquilaria microcarpa. Transcriptional levels of Am- rac1, measured using reverse
transcription polymerase chain reaction, remained steady, while those of Amrac2 increased dramatically following treatment of cultured cells with either a
yeast extract or methyl jasmonate. These results suggested that Am- rac1 was a
constitutively expressed homologue, while Am- rac2 was induced in A. microcarpa
cells. Moreover, a farnesyl diphosphate synthase gene of A. microcarpa, AmFaPS1, was transcriptionally activated in A. microcarpa cells grown in the presence
of methyl jasmonate; however, expression levels were markedly lowered in the
presence of various signal transduction-related inhibitors involved in Ca-, Rap/Rop
GTPase-, or ubiquitin-dependent signaling processes. Whereas, expression of AmFaPS1 was markedly increased, even in the absence of methyl jasmonate in A.
microcarpa cells over-expressing Am- rac2. These findings suggested that Rac/
Rop GTPase proteins played important roles in jasmonate-induced enhancement
of terpenoid metabolism in A. microcarpa.
Keywords: Aquilaria microcarpa, Farnesyl diphosphate synthase, Methyl
jasmonate, Signal transduction
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Xu Y, Zheng Z, Mengxi W, Wei J, Hongjiang C, Zhihui G, Chun S, Hongmei L,
Xingli Z, Yun Y, Hui M, Li W. 2013. Identification of Genes Related to Agarwood
Formation: Transcriptome Analysis of Healthy and Wounded Tissues of
Aquilariasinensis. BMC Genomics 14(1): 1-16
Agarwood is an expensive resinous heartwood derived from Aquilaria plants that
is widely used in traditional medicines, incense and perfume. Only wounded trees
can produce agarwood, and the huge demand for the agarwood products has led
all Aquilaria spp. being endangered and listed in the Appendix II of the CITES
(http://www.cites.org). The major components of agarwood are sesquiterpenes
and phenylethyl chromones. Owing to a lack of genomic information, the molecular
basis of wound-induced sesquiterpenes biosynthesis and agarwood formation
remains unknown. Results: To identify the primary genes that maybe related to
agarwood formation, we sequenced 2 cDNA libraries generated from healthy and
wounded A.sinensis (Lour.) Gilg. A total of 89,137 unigenes with an average length
of 678.65 bp were obtained, and they were annotated in detail at bioinformatics
levels. Of those associated with agarwood formation, 30 putatively encoded
enzymes in the sesquiterpene biosynthesis pathway, and a handful of transcription
factors and protein kinases were related to wound signal transduction. Three fulllength cDNAs of sesquiterpene synthases (ASS1-3) were cloned and expressed in
Escherichiacoli, and enzyme assays revealed that they are active enzymes, with
the major products being δ-guaiene. A methyl jasmonate (MJ) induction experiment
revealed that the expression of ASS was significantly induced by MJ, and the
production of sesquiterpenes was elevated accordingly. The expression of some
transcription factors and protein kinases, especially MYB4, WRKY4, MPKK2 and
MAPK2, was also induced by MJ and coordinated with ASS expression, suggesting
they maybe positive regulators of ASS. Conclusions: This study provides extensive
transcriptome information for Aquilaria spp. and valuable clues for elucidating the
mechanism of wound-induced agarwood sesquiterpenes biosynthesis and their
regulation.
Keywords: Agarwood; GC-MS; Sesquiterpenes; Transcriptome; Wound signal
transduction
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Chen C, Kuo TC, Yang M, Chien T, Chu M, Huang L, Chen C, Lo H, Jeng S, Chen
L. 2014. Identification of cucurbitacins and assembly of a draft genome for
Aquilaria agallocha. Genomics 15:578
Agarwood is derived from Aquilaria trees, the trade of which has come under strict
control with a listing in Appendix II of the Convention on International Trade in
Endangered Species of Wild Fauna and Flora. Many secondary metabolites of
agarwood are known to have medicinal value to humans, including compounds
that have been shown to elicit sedative effects and exhibit anti-cancer properties.
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However, little is known about the genome, transcriptome, and the biosynthetic
pathways responsible for producing such secondary metabolites in agarwood. In
this study, we present a draft genome and a putative pathway for cucurbitacin E
and I, compounds with known medicinal value, from in vitro Aquilaria agallocha
agarwood. DNA and RNA data are utilized to annotate many genes and protein
functions in the draft genome. The expression changes for cucurbitacin E and I
are shown to be consistent with known responses of A. agallocha to biotic stress
and a set of homologous genes in Arabidopsis thaliana related to cucurbitacin biosynthesis is presented and validated through qRT-PCR. This study is the first
attempt to identify cucurbitacin E and I from in vitro agarwood and the f