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The 0.6% contribution of the forestry sector to GDP is considered very low despite 64.1% of Indonesia's land area being allocated as forests. Most of the 64.8% production forest allocated is not yet optimized for strengthening national food security, in which Indonesia is ranked 65th in the world. Therefore, an innovative forest management system is needed to synergize timber and non-timber production. This paper presents a multi-business forestry (Mb-F) implementation strategy analyzed through a dynamic system-based multi-criterion decision-making tool named Super Model Mb-F (SM Mb-F). SM Mb-F is built based on a causal loop diagram (CLD), which describes the dynamic relationship between land typology suitability and decisions related to the type of business, commodities, land use area, workload, and financing for many variables relating to 5M business principles and sustainability. Results showed that CLD formulated in 280 sub-models in a total of 4,764 decision variables with an error deviation of 6.4%. The SM Mb-F simulation on two sample concession units produces a projected increase in wood supply, employment, and state revenue, plus the provision of new functions such as food, NTFP, and environmental services. These benefits are obtained by business feasibility. Assuming that gradually until 2030, the Mb-F can be implemented in 32% of Indonesia's production forests, then by 2045, it is projected that there will be an increase in wood production by 296.8%, state revenue by 654.3%, and labor absorption by 985.7%, as well as adding food production up to 19.36 M tons. This is because the land use efficiency of the current operation of forest concessions following the Annual Allowable Cut (AAC) under the selective cutting and replanting system in Indonesia (TPTI) is only about 3% of the total area of forest concession. Assuming the cutting cycle is 35 years, timber could be extracted in 1/35 of the total forest concession area. Implementing Mb-F will significantly improve the land use efficiency from about 3% to 90%. The Mb-F will also restrain the rate of decline in carbon stocks, which is deeper if governance is still under the BAU scenario. This research suggests further global research, emphasizing the importance of innovative models for sustainable forestry governance and food security worldwide.

Gyrinops versteegii and Aquilaria malaccensis are two important species of the Aquilarieae tribe. The main problem of this tribe is the challenge of species identification that is strongly dependent on the presence of flowers and fruit, which are not always available. The availability of whole genome information is expected to address the problems of species identification. This research aims to construct and compare the chloroplast and mitochondrial genomes of G. versteegii and A. malaccensis from short-read data using the NOVOplasty and GetOrganelle assembler. The chloroplast genome assembly revealed a full-length quadripartite circular structure with sizes of 174.814 bp (G. versteegii) and 174.821–174.822 bp (A. malaccensis), with highly conserved gene and organization. Meanwhile, the mitochondrial genome is multipartite with a size of 400.012 bp (G. versteegii) and 400.000 bp (A. malaccensis), with highly variable genes and organization due to the presence of gene cluster repeats. The LSC/IR/SCC region borders and phylogenetic analysis in chloroplasts indicate variations between the genomes of these two species. The investigation of nucleotide diversity in the chloroplast genome revealed that the trnL-rpl32 region had the highest nucleotide diversity (Pi = 0.03). This information will be useful in the future for a variety of downstream analyses.

The selection of tree species suitable for restoration in diverse site conditions is still a challenge. Therefore, this study aimed to analyze the phenotypic and genetic characteristics of Dryobalanops aromatica seedlings growing in mineral soil media and peat media. Phenotypic characteristics were evaluated by analyzing the growth performance, leaf morphological characteristics, leaf color, and chlorophyll content, while genetic characteristics were evaluated by using microsatellite markers. The study revealed that seedlings planted in peat media exhibited greater height and shoot length growth, although the difference was not statistically significant compared to those in mineral soil media. However, seedlings in mineral soil media displayed a significantly higher survival rate than those in peat media. Peat-grown seedlings had higher chlorophyll content in their leaves, while mineral soil-grown seedlings displayed a lighter green leaf color based on digital analysis. Genetic analysis indicated a high genetic diversity of overall D. aromatica seedlings (He = 0.635) and unclear genetic structure between the two media. Overall, these findings demonstrate the successful adaptation of D. aromatica seedlings to peat media, positioning them as a promising choice for peatland restoration.

The amount of data in this world is getting higher, and overwriting technology also has severe challenges. Data growth is expected to grow to 175 ZB by 2025. Data storage technology in DNA is an alternative technology with potential in information storage, mainly digital data. One of the stages of storing information on DNA is synthesis. This synthesis process costs very high, so it is necessary to integrate compression techniques for digital data to minimize the costs incurred. One of the models used in compression techniques is the generative model. This paper aims to see if compression using this generative model allows it to be integrated into data storage methods on DNA. To this end, we have conducted a Systematic Literature Review using the PRISMA method in selecting papers. We took the source of the papers from four leading databases and other additional databases. Out of 2440 papers, we finally decided on 34 primary papers for detailed analysis. This systematic literature review (SLR) presents and categorizes based on research questions, namely discussing machine learning methods applied in DNA storage, identifying compression techniques for DNA storage, knowing the role of deep learning in the compression process for DNA storage, knowing how generative models are associated with deep learning, knowing how generative models are applied in the compression process, and knowing latent space can be formed. The study highlights open problems that need to be solved and provides an identified research direction.

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.

Abstract Forest Health Monitoring (FHM) and International Society of Arboriculture (ISA) methods are used for individual tree health assessment. However, comparing the reliability of both methods in assessing large and old tree health has yet to be evaluated. This study aims to determine reliability of two methods in evaluating the health condition of old (>100 years old) and large Dipterocarp trees in Bogor Botanic Garden (BBG), Indonesia. The parameters observed were growth, morphometry, and tree health of 44 trees. The results showed that, overall, the two methods demonstrated quite similar in assessing the health condition of targeted trees. Visual tree damage domination by conks, fruiting bodies, and other indicators of advanced decay, open wounds, and termite gallery. The average risk rating of three parts of the tree (branches/crown, trunk, roots) is low to moderate. The two approaches could be used simultaneously or separately according to the purpose of the assessment.

Sengon (Falcataria falcata) is an economically important legume tree widely cultivated in community forests, especially in Java Island. However, attacks of gall rust disease by Uromycladium falcatariae is difficult to manage. Understanding sengon genes expressions when artificially infected with gall rust fungi can help unravel its resistance mechanisms. Total RNA was extracted from sengon seedlings samples inoculated with U. falcatariae fungi at 7, 21, and 35 days after inoculation (DAI) and from the control group. Total RNA sequencing was performed using the PCR-cDNA Sequencing protocol (SQK-PCB109) from Oxford Nanopore Technologies. The RNA-Seq obtained varies from 1.3 million to 1.9 million total reads. The assembled full-length transcript was constructed using the RATTLE program, resulting in 21,819 transcripts. The TransDecoder program used to define open reading frames (ORFs) generated 2,342 transcripts, of which 34.15% were 5′prime_partial, 8.15% were 3′prime_partial, 8.5% were internal, and 49.14% were complete. Analysis of differentially expressed genes (DEGs) between resistant and susceptible seedlings, found that 1,013 genes that were up-regulated and 1,130 genes that were down-regulated in the resistant lines. The transcriptome data discussed in this article have been deposited in the DDBJ with accession number DRA015681.

Sengon (Falcataria falcata (L.) Greuter & R. Rankin) plantations in Indonesia are threatened by attacks from Boktor stem borers and gall rust disease. Controlling pests and diseases is difficult; therefore, planting resistant trees obtained from tree selection programs is necessary. Currently, genomic breeding often incorporates GWAS, which uses thousands of SNP markers to identify markers with significant associations with the traits studied. This study aimed to bypass such expensive studies by identifying and developing SNP markers from sequences of putative resistance genes to Boktor stem borer and gall rust disease, identified from sengon transcriptomic data analysis. A total of 496,194 putative SNP sites were identified from transcriptomic sequences using the SAMtools and BFCtools programs, of which 119 SNP sites were associated with resistance genes. Of the 101 non-synonymous SNPs selected, only 12 were located in the conserved domain of each gene and were used for primer design. Of the 13 primers designed, only 10 were successfully amplified. Validation of 10 developed SNP markers on 100 sengon accessions using the HRM method confirmed a significant association between SNP markers and resistance traits, with a -log 10 (P-value) between 10.49 and 16.63. A few SNPs markers developed from putative resistance gene sequences are associated with resistance traits in sengon. Therefore, the SNP markers could be applied in selection programs for sengon trees resistant to Boktor stem borers and gall rust disease.

Cacao (Theobroma cacao) is a commodity that plays an important role in supporting economic and social development. However, cacao production can also be a major contributor to carbon emissions, which has stimulated various efforts toward sustainable cacao farm management. There remains a gap in knowledge regarding the links between carbon stocks and carbon footprints, which can serve as indicators of environment “friendliness.” In this study, we investigated carbon stocks and carbon footprints in two cacao cultivation systems, agroforests and monocultural systems, and the biophysical aspects (biotic and abiotic factors) that might contribute to the variability of carbon levels. System inventories, soil samples, and farmer interviews identified the characteristics and management practices of two cacao production systems. Results show that cacao agroforests accumulated more carbon stocks than cacao monocultures, 134.4 Mg C ha−1 and 104.7 Mg C ha−1, respectively, while cacao monocultural systems had higher carbon footprints than cacao agroforests, 1914.4 kg CO2e ha−1 and 932.1 ± 251.6 kg CO2e ha−1, respectively. Canopy cover, tree density, and soil organic carbon were the biophysical aspects that showed a significantly positive correlation with carbon stock levels, while canopy cover had a significantly negative correlation with carbon footprint levels. These results suggest that cacao agroforests are more climate-friendly management systems due to their ability to maintain high carbon stock levels while producing low carbon footprints.

Ebony (Diospyros celebica Bakh) is an endemic forest tree species found in Sulawesi whose basic information on its metabolite profile is still lacking. The objective of this research was to separate and identify putatively metabolite present in the leaves and wood of ebony across Sulawesi. Separation and identification of ebony metabolites were carried out using UHPLC-Q-Orbitrap HRMS analysis. Using ultrasonication with ethanol as the extracting solvent, we used powdered ebony leaves and wood. The results showed that the metabolites contained in the leaves and wood of ebony were 59 metabolites. About 14 compounds were found in the leaves and wood, 21 compounds in the wood, and 24 compounds in the leaves. The identified metabolites are flavonoids, terpenoids, amino aldehydes, alkaloids, quinones, steroids, amino acids, fatty acids, and saccharides. Clustering of ebony using principal component analysis obtained leaves and wood groups using peak area of known compounds as the variable.

Initial evaluation of phenotypic variability and genetic diversity was conducted on the progeny test of 2 years-old sengon from Solomon provenance, which derived from nine families of mother tree and were then planted in 4 blocks in the Cirangsad Experimental Forest. Phenotypic assessment on eight traits was conducted on 36 trees using a scoring system, while genetic diversity of 15 selected individuals which represented high and low-score phenotypic traits was analyzed using 5 selected RAPD primers. The result on phenotypic assessment showed that family 3 (57.25 points) has the highest average score of phenotypic quality and family 4 has the lowest average score (7.50 points). Furthermore, genetic analysis showed that the low-scoring sengon population had a greater mean genetic diversity (He = 0.2535) than the high-score population (He = 0.2345). The analysis of molecular variance (AMOVA) revealed a significant genetic differences (p-value < 0.001) among high and low-score populations and the dendrogram of genetic distance revealed clustering of individuals having similar superior phenotypic against those having non-superior, indicating the selection based on phenotypes in this study had succeeded in pooling the good quantitative alleles in the selected population. This evaluation results can be used as a reference in determining the best families to produce superior sengon (from Solomon provenance) offspring in the future that have desired adaptability, productivity, and diversity.

Abstract Mangifera casturi Kosterm., a mango plant from Kalimantan Selatan, Indonesia, has limited genetic information, severely limiting the research on its genetic variation and phylogeny. We collected M. casturi’s genomic information using next-generation sequencing, developed microsatellite markers and performed Sanger sequencing for DNA barcoding analysis. These markers were used to confirm parental origin and genetic diversity of M. casturi hybrids. The clean reads of the Kasturi accession were assembled de novo, producing 259 872 scaffolds (N50 = 1 445 bp). Fourteen polymorphic microsatellite markers were developed from 11 040 microsatellite motif-containing sequences. In total, 58 alleles were produced with a mean of 4.14 alleles per locus. Microsatellite marker analysis revealed broad genetic variation in M. casturi. Phylogenetic analysis was performed using internal transcribed spacers (ITS), matK, rbcL, and trnH-psbA. The phylogenetic tree of chloroplast markers placed Kasturi, Cuban, Pelipisan, Pinari, and Hambawang in one group, with M. indica as the female ancestor. Meanwhile, the phylogenetic tree of ITS markers indicated several Mangifera species as ancestors of M. casturi. Thus, M. casturi very likely originated from the cross-hybridization of multiple ancestors. Furthermore, crossing the F1 hybrids of M. indica and M. quadrifida with other Mangifera spp. may have generated much genetic variation. The genetic information for M. casturi will be a resource for breeding improvement, and conservation studies.

Abstract Objectives Development of sequencing technology has opened up vast opportunities for tree genomic research in the tropics. One of the aforesaid technologies named ONT (Oxford Nanopore Technology) has attracted researchers in undertaking testings and experiments due to its affordability and accessibility. To the best of our knowledge, there has been no published reports on the use of ONT for genomic analysis of Indonesian tree species. This progress is promising for further improvement in order to acquire more genomic data for research purposes. Therefore, the present study was carried out to determine the effectiveness of ONT in generating long-read DNA sequences using DNA isolated from leaves and wood cores of Macassar ebony (Diospyros celebica Bakh.). Data description Long-read sequences data of leaves and wood cores of Macassar ebony were generated by using the MinION device and MinKnow v3.6.5 (ONT). The obtained data, as the first long-read sequence dataset for Macassar ebony, is of great importance to conserve the genetic diversity, understanding the molecular mechanism, and sustainable use of plant genetic resources for downstream applications.

Abstract Objectives Efforts to restore tropical peat swamp forests in Indonesia face huge challenges of potential failures due to socio-economic factors and ecological dynamics attributed to lack of knowledge on the adaptive mechanisms of potential tree species such as Kapur (Dryobalanops aromatica C.F.Gaertn Syn. Dryobalanops sumatrensis J.F. Gmelin A.J.G.H Kostermans). This species is a multi-purpose tree that, commonly grows in mineral soils, but also in peat swamp as previously reported, which raised a fundamental question regarding the molecular mechanism of this adaptation. Therefore, a dataset was created aiming to detect candidates of adaptive genes in D. aromatica seedlings, cultivated in two contrasting potting media, namely mineral soil and peat media, based on RNA Sequencing Transcriptome Analysis. Data description The RNA transcriptome data of D. aromatica’s seedlings derived from young leaves of three one-year-old seedlings, raised in each dry mineral soil media and peat media, were generated by using Illumina HiSeq 4000 platform in NovogenAIT, Singapore. The acquired data, as the first transcriptome dataset for D. aromatica, is of a great importance in understanding molecular mechanism and responses of the involved genes of D. aromatica to the contrasting, growing potting media conditions that could also be useful to generate molecular markers.

Sample collection activities for a study of population genetics across the natural distribution of targeted tree species require a lot of resources, mainly if repeated field visits are necessary. Conventionally, population genetic studies use good sample material like leaves. In addition, cambium or small pieces of fresh wood can be used to replace leaf samples. Currently, restrictions from the permit regulation have caused only a limited number of samples that can be collected. Therefore, efficient use of samples must be designed to maximize their uses for research. Due to the small amount of successfully sampled materials, hence there are limitations to extend their uses for other analyses and are often sufficient only for genetic analysis. Therefore, innovation in sampling methods using pickering punch (https://www.agroisolab.com/pickering-punch) to collect ebony wood cores in this study is required to cover multi-analyses not only limited to genetics but also for other analyses such as isotopes, near-infrared spectroscopy (NIRs), anatomy, and chemical compounds. • Pickering punch is recommended for efficient wood core sample collection from ebony standing trees. • 323 wood core samples were successfully collected from 16 natural populations across Celebes (Sulawesi). • Multi-analyses studies on sampled wood cores are possible for ebony wood identification (e.g., species and origin/provenance).

Mistletoes are hemiparasitic macroparasite plants which interfere with trees and other wild plants in nutrient acquisition. As the plant has low leaf water potential, it draws water from teak wood tissues during the deciduous stage of the teak host, thereby killing the twigs and eventually, the teak tree. Mistletoes are also a key player in plant diversity. Therefore, the mistletoe population needs to be regulated not only as a parasite but also as a keystone species affecting biodiversity. Knowledge scarcity on the status of mistletoes includes its genetic variation. Hence, the purpose of this study is to analyze the level of genetic variation of teak mistletoe (Dendrophthoe pentandra) using RAPD marker. At Padangan teak Clonal Seed Orchard (CSO), it was randomly collected leaf samples from three layers of the mistletoe’s crown (upper, middle, and below) were taken from five host teak trees randomly selected from each of the sub-observation measure plots (OMP). Four OMP units inside the observation sample plots (OSP) (n = 3, 50 x 50 m) at different levels of infestation (light, moderate and heavy) were established. Analysis of the genetic variation and genetic distance of mistletoes hanging on the different crown layers were conducted using RAPD markers. The leaf samples from the crown layers, UU (upper crown and sub-section upper), UM (upper crown and sub-section middle), and UB (upper crown and sub-section below), which include U (upper crown) had significantly greater genetic variation (He = 0.181 – 0.255) than those from M layer (middle crown, He = 0.227) and the B layer (below crown, He = 0.114). Furthermore, the widest genetic distance significantly occurred between the mistletoes of the UB and B crown layers (0.310), whereas the nearest genetic distance significantly occurred between mistletoes of UU and UM layers in the upper crown (0.038). Practical implications of the low genetic variation in this study include the control of mistletoe D. pentandra infestation by means of restricting its population so that Perhutani State Owned Forestry Enterprise can maintain the level of damage below the economic threshold.

Malapari (Pongamia pinnata (L.) Pierre) adalah salah satu bahan baku biodiesel yang paling potensial untuk dikembangkan di Indonesia. Tanaman ini secara alami tersebar mulai dari Sumatera sampai Papua, namun belum diketahui informasi mengenai kandungan minyak dan sifat fisiko-kimia minyak malapari khususnya yang ada di Pulau Jawa. Penelitian ini bertujuan untuk mempelajari komposisi kimia biji malapari, mengidentifikasi komposisi asam lemak dari minyak biji yang dihasilkan dan mengkarakterisasi sifat fisiko-kimia minyaknya. Penentuan komposisi kandungan kimia biji malapari dilakukan dengan analisis proksimat. Analisis sifat fisiko-kimia minyak biji malapari dilakukan dengan metode pengujian ASTM. Hasil penelitian menunjukkan bahwa populasi Batukaras merupakan populasi yang paling baik sebagai sumber bahan baku biodiesel karena mempunyai nilai kadar minyak tertinggi. Keunggulan lain dari populasi Batukaras memiliki nilai berat jenis, viskositas, dan bilangan asam yang terendah. Minyak malapari didominasi oleh asam lemak oleat dan linoleat yang merupakan asam lemak tidak jenuh yang berpotensi untuk biodiesel. Berdasarkan nilai asam lemak (oleat dan linoleat) dan sifat fisiko kimia (berat jenis dan nilai kalor) minyak mentah malapari dari kelima populasi telah memenuhi syarat untuk dijadikan bahan baku biodiesel.

Upaya untuk meningkatkan produktifitas suatu sumber benih memerlukan suatu pemahaman yang mendalam tentang ciri reproduksi dan faktor-faktor lingkungan yang berpengaruh terhadap hasil benih. Penelitian ini bertujuan untuk (1) mengetahui ciri morfologi bunga dan fenologinya, dan 2) mengenali serangga pengunjung bunga surian. Kajian dilakukan di hutan rakyat di Kabupaten Sumedang Provinsi Jawa Barat. Bunga surian merupakan bunga majemuk yang tersusun dalam malai berbentuk panikel. Ketika bunga mekar mahkota bunga tidak terbuka sepenuhnya, membentuk mirip tabung. Bunga jantan berukuran lebih kecil dari bunga betina dan tidak pernah mekar, dan bunga jantan rontok lebih dahulu. Malai bunga surian memiliki pola percabangan thyrses, dan bunga mekar tidak serentak. Perkembangan bunga dari tunas yang berwarna hijau hingga bunga mekar memerlukan waktu sekitar 12 hari, bunga mekar bertahan 2 atau 3 hari, Perkembangan buah hingga buah masak dan terbuka memerlukan waktu 5 - 5.5 bulan. Terdapat 12 jenis serangga yang mengunjungi bunga surian, 11 jenis berukuran sangat kecil. Serangga yang ditemukan dalam jumlah banyak adalah thrips dan 3 jenis serangga Famili Nitidulidae.

Perkecambahan benih mindi (Melia azedarach) masih mengalami kendala, yang terekspresikan dari masih rendahnya daya berkecambah benih, sehingga akan mempengaruhi penyediaan bibit mindi yang berkualitas. Tujuan penelitian ini adalah mengetahui struktur morfologi, anatomi serta kandungan kimia pada benih mindi. Struktur morfologi dan anatomi benih didasarkan pada struktur makroskopis dan mikroskopis, sedangkan kandungan kimia benih adalah lignin, lemak dan Abscisic acid (ABA). Berdasarkan hasil pengujian terhadap struktur anatomi benih mindi, ketebalan endocarp berkisar antara 331,4 –1448,2 µm dan tebal testa berkisar 41,9–148,6 µm, dengan kerapatan sel berkisar 2031-4635 sel per mm2. Benih mindi mengandung ABA cukup tinggi (0,0386- 0,0955 mg/g ) dengan kadar lignin pada kulit benih termasuk kategori sedang yaitu berkisar antara 22,26-26,57%. Keberadaan ABA pada benih dapat menjadi faktor penghambat dalam perkecambahan, demikian pula dengan ketebalan dan kekerasan endocarp yang disebabkan oleh adanya lignin. Oleh karena itu perlu dilakukan delignifikasi untuk dapat meningkatkan daya berkecambah benih mindi.

Large-scale genetic structure revealed in tree populations in SE Asia, as well as in many temperate forests, has been shaped by climatic fluctuation in the late Pleistocene, most importantly by that in the last glacial period. In a comparative study of the phylogeographic patterns of two closely related dipterocarp species, Dryobalanops aromatica C.F.Gaertn. and D. beccarii Dyer, we investigated how changes in land area associated with changes in climate affected large-scale genetic structure. We examined the genetic variation of D. aromatica, collected from nine populations throughout the Sundaic region, and of D. beccarii, collected from 16 populations mainly in Borneo, using seven polymorphic microsatellite markers. The two species were clearly distinguishable in the STRUCTURE analysis, although hybridisation probably occurred in sympatric populations and also in several other populations. The D. aromatica populations were divided into two main groups by the STRUCTURE analysis: Malay–Sumatra and Borneo. Mixing of the Sumatra and Borneo clusters occurred on the Malay Peninsula, supporting the hypothesis that tropical rainforests expanded over a dried Sunda Shelf during the last glacial period. The two main genetic clusters might have been formed by repeated cycles of fluctuation in land area. The D. beccarii populations in Borneo were divided into four geographically distinct groups: western Sarawak, central inland Sarawak, central coastal Sarawak and Sabah. The population on the Malay Peninsula (Gunung Panti) was an admixture of the four Bornean clusters. This suggests that this population is a relic of the recent range expansion of D. beccarii during the last glacial period.

For effective teak plantation management, early detection system in controlling teak mistletoe requires various basic information, including degree of infestation and accuracy of the species names. Mistletoe infestations in teak and mistletoe species name have been reported, but there are still problems in identifying the correct species or subspecies due to morphological similarity. The objective of this study was to clarify the species identity of hemi-parasitic mistletoe plants, which were found in teak Clonal Seed Orchard (CSO) in Padangan, East Java Province, Indonesia using DNA barcodes. Species identification of teak mistletoe based on leaf morphological characteristics and universal DNA barcode regions (i.e. matK and rbcL) were carried out. The results showed that the Canonical Discriminant Analysis (CDA) could differentiate Dendrophthoe pentandra and Macrosolen tetragonus based on leaf morphological characteristics. Variables having high correlation to distinguish both species were length of petiole,  width of the widest leaf, number of secondary leaf veins, leaf base shape, aspect ratio, form factor and perimeter ratio of diameter. The results of DNA barcoding showed that the two DNA barcode regions presented good  amplification and sequence results. Both DNA barcode regions successfully differentiated two species i.e. D. pentandra and M. tetragonus which belong to Loranthaceae family and have similar leaf morphological characteristics. Those regions were also able to identify Viscum articulatum and other species belonging to Santalaceae family. These results suggested that the two DNA regions could become recommended universal DNA barcode for identifying teak mistletoe.

Methods of analysis to infer the possible causes of segregation distortion were carried out using single tree progenies of Pinus merkusii. Tests on the progenies of the seed trees showing significant segregation distortion were performed at six gene loci, i.e. GOT-C, GOT-D, PGM-B, SKDH-A, NDH-A, and FDH-A. Results indicated that most fertilisation combination between female and male gametes occurred randomly. This study revealed that 11 out of 17 cases of distortion were detected in both gametes, while the other six were detected only in female gamet. The primary sources of such segregation distortions are discussed regarding to linkage relationships system of mating and post-zygotic viability selection.

Background Dipterocarpus littoralis Blume is a critically endangered dipterocarp species found only on Nusakambangan Island, Central Java, Indonesia. Patterns of genetic diversity and population genetic structure of adults and saplings in two extant populations (Kali Jati and Solok Besek) were estimated using ten microsatellite markers. Results A total of 39 alleles was found, with two and four alleles being unique in adult and sapling populations, respectively. Allelic richness and heterozygosity was similar between adult (Ar = 3.00; He = 0.423) and sapling (Ar = 3.25; He = 0.441) populations.Inbreeding coefficientsin saplingswere positive in both populations and statistically significant in Kali Jati, while those in adult populations were not significantly different from zero, indicating excessive inbreeding and selfing in the sapling populations. Genetic differentiation of the sapling populations (FST = 0.036) was slightly lower than in the adult populations (0.050), but only significantly so for saplings. Conclusions This study revealed that D. littoralis has low genetic diversity in both adults and saplings. Similarly low values in allele richness and heterozygosity suggest that reductions of population size have been ongoing for long periods in this species. Significant genetic differentiation between sapling populations but not adult populations indicates that recent fragmentation is further accelerating the isolation process.

Analysis of genetic parameters in seedling seed orchard progeny trial of Paraserianthes falcataria at Taman Hutan Blok Cikabayan are very important to decide to continue the breeding program. The analysis was coducted on estimation of individual heritability and genetic correlation between traits. Result of analysis shows that individual heritability for height, diameter and form traits.

Analysis of genetic parameters in seedling seed orchard progeny trial of Paraserianthes falcataria at Taman Hutan Blok Cikabayan are very important to decide to continue the breeding program. The analysis was coducted on estimation of individual heritability and genetic correlation between traits. Result of analysis shows that individual heritability for height, diameter and form traits.

Forest exploitation and conversion to other landuse may cause lost of biodiversity, including most important dipterocarp trees species, i.e. Shorea leprosula and Shorea laevis. The objective of this study was to determine the rarity status of the two important shorea species, i.e. S. laevis and S. leprosula, based on IUCN criteria, their habitat characteristics, and their association with other species, as one of the basis for determining their conservation strategy as a part of forest management. This study was conducted in three types of ecosystem (virgin forest, secondary forest, and fragmented forest) in Muara Teweh, Central Kalimantan. Methodology used in this research includes vegetation and tree diversity analysis. Study results showed that both S. laevis and S. leprosula were included within category of “low risk” in the 3 types of ecosystem in the forest area being studied. Habitat characteristics which determined the absence of S. laevis in the virgin forest habitat was the soil permeability which was too low, whereas other soil chemical and physical properties in the three types of ecosystems were relatively similar. Presence of S. laevis were positively associated with species of S. uliginosa, Dialium platysepalum, Dipterocarpus ibmalatus, Palaquium rostatum, Vatica rasak, Adinandra sp., and Memecyclon steenis. On the other hand, S. leprosula were positively correlated with S. kunstleri, Castanopsis sp., Shorea sp., Quercus bennettii, Castanopsis argentea, and D. hasseltii.Keywords: threatened species, Shorea spp., habitat characteristic, ecosystems type, associated species

The study was aimed to determine flower initiation, floral morphology and to observe the stages of flowering and fruit development of mindi (Melia azedarch L) within a population for one period of time 2008–2009. The methods used were observing directly over the trees and some vegetatives and generatives buds were sampled for dissecting. The observation revealed that the inflorescence type of mindi was panicle, located at the end of a branch. The number of flower varied among inflorescences, ranged between 30–80 that bloomed simultaneously. The flower was hermaphroditic with position of anther was closed to stigma that selfing might be happened. Usually, the ovary contained 5 ovules that developed into seeds. Reproductive cycle was proceeded for 6–7 months within the year, first observation commenced from flower initiation that occur in August, generative buds to flower burst in September–October. Early fruits were formed in October–November and fruits reached physiological-maturity in January–February. Reproductive success was 34%, indicated that the rate of fertilized ovules proportion to be potencially viable seeds were relatively low.Keywords: indian lily, phenology, reproductive biology, reproductive cycle, seed production

Dipterocarpus hasseltii (palahlar) and Dipterocarpus retusus (mountain palahlar) are plant species of Dipterocarpaceae family that originate from West Java which population is getting rare. Information about growth development and genetic variation of palahlar is important to support culturing program and its genetic conservation. One of the techniques to study palahlar growth is through observation of the plant height and stem diameter increment. DNA analysis is use to gain information of palahlar genetic diversity. One of the DNA based molecular marker widely used as plant genetic marker is RAPD. There were 2 primary that resulting the best amplifying quality in genetic diversity analysis that was OPO-13 dan OPY 20. Analysis result with POPGENE 32 was resulting average genetic diversity between classes as much as 0.1869. The biggest genetic diversity for palahlar was on the medium growth class as much as 0.2498 dan for mountain palahlar was in small growth class as much as 0.2240. Cluster analysis shows that there were 2 big groups that were medium-high growth class group and small growth class group. Dendrogram shows that there were 2 species in one group, that was palahlar and mountain palahlar that was in one group of small growth class. The closed genetic distance existed between medium growth class group of palahlar and high growth class group (0.0383), while the far distance is between palahlar of small growth class group with mountain palahlar of mediaum growth class group as much as 0.1826.

* Azadirachta excelsa (Jack) Jacobs, Kayu bawang (Meliaceae) is economically valuable and widely used by the local community in Bengkulu (Sumatra) as carpentry and construction wood because of its good durability class. However, it still has ambiguous scientific multiple names, such as Azadirachta excelsa, Protium javanicum, and Dysoxylum mollissimum. Additional tools such as molecular approaches can be used to verify whether it is true or not that Kayu bawang is scientifically named as Azadirachta excelsa based on previous morphological identification. This study aimed to construct draft chloroplast genome and verify the scientific name based on molecular identification using a single rbcL gene marker. Genomic DNA was extracted from bark cambium originated from three different provenances in Bengkulu, Indonesia, namely TBT-A, TBT-K, and TBT-S. MinION from Oxford Nanopore Technologies was used to sequence the samples following manufacture protocols SQK-LSK109 yielding 481.6 Mb for TBT-A, 597.4 Mb for TBT-K, and 853.1 Mb for TBT-S, respectively. Generated data were assembled and constructed, namely 58,780 bp (14 tRNAs and 47 encoding genes) for TBT-A, 142,139 bp (4 rRNAs, 24 tRNAs, and 78 encoding genes) for TBT-K, and 84,906 bp (24 tRNAs and 53 encoding genes) for TBT-S. Based on the phylogenetic tree, Azadirachta excelsa from three identified tree stands were placed in the same group with other Azadirachta excelsa accessions.