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Hartoyo APP, Khairunnisa S, Pamoengkas P, Solikhin A, Supriyanto, Siregar IZ, Prasetyo LB, Istomo. 2022. Estimating carbon stocks of three traditional agroforestry systems and their relationships with tree diversity and stand density. Biodiversitas 23: 6137-6146. One of the important sectors as a strategy for climate resilience and low carbon development in Indonesia is Forestry and Other Land Uses (FOLU) including the agroforestry sector. Carbon stock and tree diversity in an ecosystem are dynamic over time and still need to be investigated. This study was aimed: i) to estimate aboveground carbon stocks in the traditional agroforestry of Mount Halimun Salak National Park (MHSNP), in Kampung Birang and Kampung Merabu, East Kalimantan, as well as ii) to analyze the correlation between carbon stock with tree diversity and stand density in traditional agroforestry of Mount Halimun Salak National Park (MHSNP), in Kampung Birang and Kampung Merabu, East Kalimantan. The total plots were 75 plots (a plot size of 50x50 m), and carbon stock estimation was focused on pole and tree levels. The average carbon stock in the traditional zone of MHSNP, Kampung Birang, and Kampung Merabu respectively was 51.02 Mg C/ha, 96.25 Mg C/ha, and 82.17 Mg C/ha. The carbon stock in traditional agroforestry of all study sites was very significantly affected by the basal area (m2/ha) (p-val

Arobaya AYS, Zuhud EAM, Siregar IZ, Irawati. 2022. Short Communication: Diversity and distribution of epiphytic orchid Dendrobium section Spatulata on the host plants in the Cycloop Mountain Nature Reserve of Papua, Indonesia. Biodiversitas 23: 2025-2034. Knowledge of species diversity and distribution is indispensable to assist in formulating a sound conservation strategy. This is truly significant for epiphytic orchids that grow on tree surfaces or phorophyte. The data and information are still limited despite their important role as biological indicators in forest ecosystems. The aim of the study was to carry out an inventory of epiphytic orchids and the phorophytes (host tress) in the Tropical Rain Forest of Cycloop Mountain Nature Reserve. The study took place in four sites located in the regency and city of Jayapura. Exploratory and sampling strip methods of 20x100 square meters were employed during the fieldwork. Orchids were observed and samples were collected based on their distribution in the host plants divided into five zones (Stem zone I and II; Crown zone III to V). The habitat's vegetation profiles were described using computer-aided design (CAD) verse 2018. Plant samples were identified in herbarium Manokwariense and the identified species were incorporated into CAD. Nineteen species of Dendrobium section Spatulata were identified as living as an epiphyte on the 12 phorophytes. These orchids and the host plants were described, determined and analyzed using PATN software. Most orchids are growing abundant in zone II and III. The phorophytes hosting the orchids in the lowland are mainly Syzygium and Intsia, while in the highland are Agathis and Podocarpus. Two types of vegetation profiles were described as savannah woodland in the low land area and coniferous trees vegetation in the highland above 650 m above sea level.

Nugroho A, Matra DD, Siregar IZ, Haneda NF, Istikorini Y, Rahmawati R, Amin Y, Siregar UJ. 2021. Early growth evaluation and estimation of heritability in a sengon (Falcataria moluccana) progeny testing at Kediri, East Java, Indonesia. Biodiversitas 22: 2728-2736. Sengon (Falcataria moluccana) is widely cultivated as a monoculture plantation in community forests that still poses a high risk of pest and disease attacks. Although plants naturally show signs of resistance, there is still however a lack of understanding on the influence of relative plant resistance on growth due to environmental and genetic factors. This study was aimed to evaluate the early growth of a sengon progeny testing in Kediri, East Java and to estimate the genetic parameters with respect to its resistance and susceptibility to stem borer and rust disease. Progeny test was designed using randomized complete block design (RCBD) with four blocks as replications. Each block consists of 100 families which was grouped into two categories, 50 families for resistant group and 50 families for susceptible group. Observations were made at the age of 0 and 9 months after planting on 9 individuals per plot in each family. Growth characteristics were measured as germination (%), height (m), and diameter (cm). Results indicated that the sengon growth rate from resistant and susceptible plant groups showed a significant difference. Heritability values are classified as moderate, ranging between 0.107 to 0.133 and 0.102 to 0.150 for height and diameter variables, respectively. These information may be used for gradual selection by considering the appropriate intensity.

Siregar IZ, Muharam KF, Purwanto YA, Sudrajat DJ. 2020. Seed germination characteristics in different storage time of Gmelina arborea treated with ultrafine bubbles priming. Biodiversitas 21: 4558-4564. Gmelina (Gmelina arborea) seed collected from tropical Indonesian forest experience seed deterioration during storage which is relatively faster than the gmelina seeds originating from temperate regions, such as India and Myanmar. Various treatments have been made to improve the seed viability and vigor after storage through various invigoration techniques. However, the utilization of promising novel technology such as ultrafine bubbles (UFB) has not been evaluated yet. The objective of this study was to determine the effect of seed priming using UFB, polyethylene glycol (PEG), and gibberellic acid (GA3) on the viability and vigor of gmelina seeds that have been stored for one and two years. This study was conducted by employing Completely Randomized Design (CRD) using three replicates. The study showed priming treatment had significant effect and formed average germination capacity of 80% for the seed stored for 1 year. On the other hand, the priming treatment using PEG-0.8 MPa was the best treatment for germination capacity of 74.67% on 2 years stored seeds. UFB had significant effect on germination capacity, germination rate, growth uniformity, and germination value. This result was expected due to reactive oxygen species (ROS) produced by micro-nano bubbles that could increase physiological activity of the seed cells.

Ariawan I, Herdiyeni Y, Siregar IZ. 2020. Short Communication: Geometric morphometric analysis of leaves venation in Shorea spp. for identification using Digital Image Processing. Biodiversitas 21: 3303-3309. Shorea is one of the genera of the Dipterocarpaceae family which consists of more than 190 species. Massive exploitation of forests has threatened the sustainability of Shorea in nature. A total of 156 species has been listed on the IUCN (International Union for Conservation of Nature) red list. From the 156 species, 59.6% are in the critically endangered category, so urgent conservation is needed. However, during collection of Shorea at the seedling phase for conservation purposes, it is often difficult to distinguish among them that can cause errors in their collection process. To avoid these errors, identification needs to be done, usually based on plant leaf and flower morphology. Leaves are easier because they have the main features that distinguish each plant species, one of which is the venation structure. Geometric morphometric techniques are a modern approach recognized as useful for the identification of species in many plants. Geometric morphometrics analyzes the position of the venation point using coordinate geometry values. This research was aimed to extract venation features of Shorea leaves using a geometric morphometric approach. The extraction process result in some features, such as straightness, different angle, length ratio, scale projection, and secondary nerves. On extracted features, an analysis was then performed to find out the best features in classifying species of Shorea spp. The results of this study indicated that the geometric morphometric approach could extract the value of the features of straightness, different angle, length ratio, scale projection, and secondary nerves. The secondary nerve feature is the best feature because it can distinguish between fourcommonly planted species of Shorea spp. (S. acuminata, S. leprosula, S. ovalis, and S. selanica). By using the support vector machine classification technique to identify species of Shorea spp., the classification results obtained an average accuracy of 84.46%.

Indriani F, Siregar U, Matra DD, Siregar IZ. 2019. Ecological aspects and genetic diversity of Shorea balangeran in two forest types of Muara Kendawang Nature Reserve, West Kalimantan, Indonesia. Biodiversitas 20: 482-488. Shorea balangeran (balangeran) belongs to the Dipterocarpaceae family that is distributed naturally in Indonesia with a wide range of ecological conditions including peat swamp and heath forests. Good adaptability of S. balangeran remains unknown concerning molecular (genetic) responses that are important to provide scientific knowledge for supporting forest restoration, especially for peatland restoration efforts. The main objective of this research was to analyze the ecological aspects and genetic diversity of S. balangeran in two types of forests, namely: peat forests (wetland) and heath forests (dry land). Field research was conducted in Muara Kendawangan Nature Reserve, West Kalimantan following standard vegetation analysis by establishing purposively sample plots (50 m x 50 m). Genetic diversity was assessed by RAPD analysis using ten random polymorphic primers. Results showed that both in heath and peat forests, S. balangeran was dominant, but only at pole and tree stages indicating that poor regeneration capacity of S. balangeran. This finding also confirmed the critically endangered status of S. balangeran as listed in the IUCN Red List of Threatened Species. Genetic analysis using RAPD did not show a clustering of S. balangeran between peat forest and heath forest populations, indicating that S. balangeran has good adaptability to grow in both forest types.

Arianto W, Zuhud EAM, Hikmat A, Sunarminto T, Siregar IZ. 2018. Genetic diversity of Amorphophallus titanum in Bengkulu, Indonesia based on RAPD markers. Biodiversitas 19: 1783-1790. Titan Arum [Amorphophallus titanum (Becc.) Becc. Ex Arcang], a plant species belonging to the family of Araceae is known for its gigantic floral size and elicited rotten fragrance when the flower bloom. Since it remains only found in Sumatran island, many authors categorized the plant as endemic species. The population of the species in the natural habitat has significantly declined because of the conversion of forest land mainly into plantations or other land uses. Considering the importance of conservation attempts to A. titanum, a sufficient data on genetic diversity of the species is necessary. The research was aimed to determine the genetic diversity within and among populations of A. titanum in some area of protected forests in Bengkulu Province, comprising the population of Palak Siring, Tebat Monok, and Air Selimang. RAPD genetic DNA fingerprinting approach was used to assess the genetic diversity of A. titanum using 13 preselected DNA primer: OPA 11, OPA 19, OPC 04, OPN 14, OPN 19, OPU 03, OPU 06, OPU 07, OPB 17, OPC 07, OPO 04, OPU03-1, OPNI 18E. The result revealed that the method has successfully produced several DNA fragments with varied length ranging from 250 bp to 2000 bp with 4-16 variation in polymorphic bands. Based on RAPD marker analysis, the population of Air Selimang was considered as a potential center of diversity of A. titanum because of the others two populations had a lower genetic diversity. In general, the genetic diversity among populations was lower than within population. The cluster analysis of the genetic similarity of 22 individuals of the three populations resulted in the separation into two main groups with the first group consisting of 17 individuals (Population Air Selimang and Tebat Monok) and the second group of 5 individuals (Palak Siring population).

Sudrajat DJ, Suwandhi I, Siregar IZ, Siregar UJ. 2018. Variation in seed morpho-physiological and biochemical traits of Java olive populations originated from Java, Bali, Lombok, and Timor Islands, Indonesia. Biodiversitas 19: 1004-1012. Java olive (Sterculia foetida L.) is one of the promising non-edible feedstocks for biodiesel production. Utilization of this tree species for plantation is limited due to knowledge gaps in many fundamental aspects of seed properties. The aim of the study was to determine the variation that may exist among java olive seed collected from Bogor, Palimanan, Tuban, Gilimanuk, Pemenang and Naioni populations, and to analyze correlations between one or many seed morpho-physiological and biochemical traits. Analysis of variance showed significant differences of seed morphological and biochemical traits, except for the germination capacity. Seed morphological traits were not significantly correlated with agro-climate factors, while some of biochemical traits revealed significant correlation with some agro-climate factors. Genotypic variance and genotypic coefficient of variation were higher for fruit length, fruit width, carbohydrate, fat, protein and oil contents, indicating higher genetic contribution on the variance of these traits. High heritability values combined with high genetic gain was found for protein content, fruit width and oil content, that revealed the characters having highly genetic origin with a good number of heritable components. Population clustering exhibited that most of the geographically distant population are genetically related. Pemenang population was found highly associated with oil content, indicating that the population have high potency to develop as the feedstocks for for biodiesel production.

REDD+ aims to reduce emissions from deforestation and forest degradation, conservation, enhancement of forest carbon stocks, and sustainable forest management (SFM). An assessment of agroforest is important for REDD+ implementation in Indonesia. In this context, evaluation of the existing agroforests and their uses is an important issue. The objectives of this research were to characterize agroforest diversity with respect to habitat, regulation, production and information functions in Kampung Birang and Kampung Merabu, Berau, East Kalimantan. This research focused on two size classes of trees, namely medium trees (10≤dbh≤20 cm) and large trees (dbh>20 cm). Local community members were trained in plot establishment (60 plots, 50x50 m), tree diameter measurement, trees tagging, and herbarium collection. Local community members identified tree species by local names and listed the species uses. Results showed that agroforests as habitat obtained diversity indices (H’) of moderate category for Kampung Birang and high category for Kampung Merabu. Otherwise, Margalef’s index (Dmg) for the medium and large tree classes in Kampung Birang and Kampung Merabu were classified as high species richness category. This finding implies that enrichment planting using high economic value species is still necessary in Kampung Birang. Kampung Merabu was found to be more diverse than Kampung Birang, although soil quality in Kampung Birang was better than that in Kampung Merabu. Disturbances due to human activities that potentially impact agroforest stability were also pre-identified. The top ten tree species were classified based on importance value index (IVI) across both villages consisting of 80% shade intolerant and 20% semi-tolerant species. Agroforest showing production and information function as produces various edible fruits that are considered as key component for maintaining biodiversity sustainability and ecosystem functioning. REDD+ aims to reduce emissions from deforestation and forest degradation, conservation, enhancement of forest carbon stocks, and sustainable forest management (SFM). An assessment of agroforest is important for REDD+ implementation in Indonesia. In this context, evaluation of the existing agroforests and their uses is an important issue. The objectives of this research were to characterize agroforest diversity with respect to habitat, regulation, production and information functions in Kampung Birang and Kampung Merabu, Berau, East Kalimantan. This research focused on two size classes of trees, namely medium trees (10≤dbh≤20 cm) and large trees (dbh>20 cm). Local community members were trained in plot establishment (60 plots, 50x50 m), tree diameter measurement, trees tagging, and herbarium collection. Local community members identified tree species by local names and listed the species uses. Results showed that agroforests as habitat obtained diversity indices (H’) of moderate category for Kampung Birang and high category for Kampung Merabu. Otherwise, Margalef’s index (Dmg) for the medium and large tree classes in Kampung Birang and Kampung Merabu were classified as high species richness category. This finding implies that enrichment planting using high economic value species is still necessary in Kampung Birang. Kampung Merabu was found to be more diverse than Kampung Birang, although soil quality in Kampung Birang was better than that in Kampung Merabu. Disturbances due to human activities that potentially impact agroforest stability were also pre-identified. The top ten tree species were classified based on importance value index (IVI) across both villages consisting of 80% shade intolerant and 20% semi-tolerant species. Agroforest showing production and information function as produces various edible fruits that are considered as key component for maintaining biodiversity sustainability and ecosystem functioning.

Pamoengkas P, Siregar IZ, Dwisutono AN. 2018. Stand structure and species composition of merbau in logged-over forest in Papua, Indonesia. Biodiversitas 19: 163-171. Single selective cutting is the most common form of timber extraction in natural forest in the tropics. Although, vast tracts natural forests are already logged-over, the effect of logging on the structure and species composition has been sparsely documented, especially for merbau (Intsia bijuga). Merbau is an excellent timber species and intensively harvested in Papua. The objective of this study was to analyze the structure and species composition of merbau in the several logged-over forests at different ages, i.e., 1, 5, 11, 16, 21 years old after selective logging and primary forest as the reference plot. The study was conducted in February 2016 at Sarmi District, Papua. The distributions of merbau in each plot varies but when they were compared with that in the primary forest that had reached 9.81%. Thus, the decrease of merbau trees in the plots of logged forest areas was not significant. Index of Diversity of all growth stages was high. In general, the number of merbau seedling regeneration in the study plots are above the average value standardized in Selective Cutting and Replanting System (TPTI) regulation. With regard to the condition of sapling regeneration, we concluded that selective logging might not provide enough growing space for regeneration of merbau. Providing appropriate growing space is one of the key factors to achieve adequate merbau natural regeneration.

Manurung J, Siregar IZ, Kusmana C, Dwiyanti FG. 2017. Genetic variation of the mangrove species Avicennia marina in heavy metal polluted estuaries of Cilegon Industrial Area, Indonesia. Biodiversitas 18: 1109-1115. Mangrove forests are often facing various anthropogenic disturbances, particularly in the industrial area. However, information on the status of industrial heavy metal pollution and its impact on the genetic variation of mangrove species, such as Avicennia marina, particularly in Indonesian industrial area has not been assessed. In this study, the classification of heavy metals in two estuaries of Cilegon Industrial Area (Pelabuhan Warna Sari and Krakatau) and one estuary outside Cilegon Industrial Area (Pulau Sangiang) were determined by Sediment Quality Guidelines- States Environment Protection Agency (SQGs-USEPA). Furthermore, the genetic diversity of 72 individuals of A. marina in the three estuaries were examined using four microsatellite loci (M3, M64, M81 and M98). The results showed that Krakatau area was the heavily polluted estuary based on SQGs-USEPA and have a lower genetic variation (He= 0.54) than Pelabuhan Warna Sari (moderately polluted, He= 0.56) and Pulau Sangiang (non-polluted, He= 0.60) suggesting a notable of deficiencies of genetic variation of A. marina in heavy polluted estuary compared to moderately and non-polluted estuary. Considering the low level of genetic variation in heavily polluted area, transplantation among estuaries and introduction of propagules from non-polluted estuary or other regions are needed as one of the conservation efforts.

Aminah A, Supriyanto, Suryani A, Siregar IZ. 2017. Genetic diversity of Pongamia pinnata (Millettia pinnata, aka. malapari) populations in Java Island, Indonesia. Biodiversitas 18: 677-681. One of the promising tree species to be utilized as biodiesel legume in Indonesia is malapari (Pongamia pinnata (L.) Pierre). The tree grows naturally along the North and South Coasts of Java Island. Malapari is now subjected to an initial breeding program, but its population diversity in Indonesia is not known yet. The objective of this study was to estimate genetic diversity in Java Island, namely populations of Carita, Batukaras, Kebumen, Alas Purwo National Park and Baluran National Park. RAPD markers were used to study the genetic diversity using the following DNA primers: OPL-11, OPAH-15, OPAO-01, OPAB-14 and OPAH-13. Results showed that DNA fragment lengths ranged from 250 to 1000 bp with a variable number of polymorphic bands, ranging between 13-24. Based on these RAPD markers, the population in Baluran was considered as a potential diversity center of malapari in Java, whereas the population in Kebumen was found to have the lowest genetic diversity. In general, the average genetic diversity within an population was lower than that among the populations. Cluster analysis of genetic similarity in five malapari population resulted in separation into two main clusters, the first group consisted of four populations (i.e., Carita, Batukaras, Kebumen and Alas Purwo). The other cluster was only one population only, namely Baluran.

Adzkia U, Nugroho N, Siregar IZ, Karlinasari L. 2020. Ultrastructure of royal palm (Roystonea regia) leaf sheath. Biodiversitas 21: 967-974. The royal palm (Roystonea regia (Kunth) F.Cook is one of the palm species that are many planted along the streets as part of urban landscapes. As biologically products, in nature they can self-cleaning with drop off their big leaves. The study aims to examine the morphological characteristics of ultrastructure and elemental content, crystallinity, as well as fibers derivation characteristics from the royal palm. The samples were taken out from leaf sheaths that divided into three sections along the width of i.e. outside, middle, and inside; in two conditions of leaf sheaths namely green and brownish-dry. The morphology structure and elemental content were observed by the Scanning Electron Microscopy (SEM) and the Energy Dispersive X-ray analysis (EDX), while the crystallinity was analyzed using X-ray diffraction (XRD), and fiber characteristics were measured to determine cell dimensions as well as to calculate Runkle ratio (RR), muhlsteph ratio (MR), coefficient of rigidity (CR), felting powder (FP), and flexibility ratio (FR). The diameter of palm fiber bundles was decreased from outside towards inside. The model of vascular tissue was rounded which located in the central region of the fiber bundles. The silicon content in the inside section was lower than those in the middle and outside sections. It was in line with the degree of crystallinity in the inside section which that higher than other sections. The highest degree of crystallinity was about 18 %. The fiber length of royal palm leaf sheath was in values around 6000 μm. However, the royal palm leaf sheath had thick fiber walls and thin lumen, as well as other fiber derivation characteristics of muhlsteph ratio, the coefficient of rigidity and the flexibility ratio, were in low-quality values. For that reason, the study provides information that the royal palm sheath was recommended as a composite reinforcing material.

Anna N, Supriyanto, Karlinasari L, Sudrajat DJ, Siregar IZ. 2020. The growth, pilodyn penetration, and wood properties of 12 Neolamarckia cadamba provenances at 42 months old. Biodiversitas 21: 1091-1100. Jabon (Neolamarckia cadamba (Roxb) Bosser) is a potential tree species for the development of plantation forests and community forests to supply timber demands. Information on the growth characteristics and wood properties of N. cadamba is important for the present and future development, yet. Those data is not available. This study aimed to assess the variations on growth (height, diameter), pilodyn (Pilodyn®) penetration, and physical properties of wood from core sample; and characterize the wood properties of 12 N. cadamba provenances at Parung Panjang, Bogor. The assessment of growth characteristics, pilodyn penetration, and physical properties of wood from core sample was carried out through census (1030 trees) on all provenance (using non-destructive method). The wood properties analysis was carried out using destructive method to one sample for each of the 12 N. cadamba provenances. Growth characteristics observed were the height (numerical scale pole), diameter (calipers), and pilodyn penetration. Meanwhile, the wood properties consisted of wood density, specific gravity, moisture content, fiber length (light microscope), MFA (x-ray diffraction), MOE, and MOR. The results showed that the correlation between the height and moisture content with pilodyn penetration was weak and positive, while the correlation between diameter, wood density, and specific gravity was weak and negative. The result of non-destructive test showed that Gowa provenance is superior. The results of destructive tests to investigate the wood properties of the twelve provenances showed that Batu Licin provenance is superior in terms of specific gravity and MOE, while Gowa provenance is superior in terms of MOR and fiber length. The results of the wood properties (i.e. density, specific gravity, moisture content, MOE, MOR, MFA, and fiber length) of the 12 N. cadamba provenances showed that the woods can be potentially used as non-structural materials only.

Hartoyo APP, Prasetyo LB, Siregar IZ, Supriyanto, Theilade I, Siregar UJ. 2019. Carbon stock assessment using forest canopy density mapper in agroforestry land in Berau, East Kalimantan, Indonesia. Biodiversitas 20: 2661-2676. In the Reducing Emissions from Deforestation and forest Degradation (REDD+) program, remote sensing is the most important tool for measuring forest cover and carbon dynamic, including the utilization of software Forest Canopy Density (FCD) mapper. However, there have been rarely untested the accuracy of FCD applied in agroforestry landscapes to support carbon stock assessment compared to conventional field measurement data. This research was aimed to investigate the correlation between: (i) the value of FCD (%) and tree stand density (N/ha), (ii) the value of FCD (%) and basal area (m2/ha), (iii) the value of FCD (%) and total carbon stock (Mg C/ha), and iv) total carbon stock and percentage of canopy closure (%). Tree stand density, basal area, carbon stock and canopy profile were conventionally measured by trained members of local communities. The results of this study showed that the R2 between FCD and tree density was 37.7% (r = 61.4%), while the R2 between FCD and the basal area was 3.33% (r = 18.3%). The result of normality and heteroscedasticity tests showed that FCD was more accurate and precise in estimating the tree stand density model than the basal area model. Total carbon stock differed significantly (p

Chaerani N, Sudrajat DJ, Siregar IZ, Siregar UJ. 2019. Growth performance and wood quality of white jabon (Neolamarckia cadamba) progeny testing at Parung Panjang, Bogor, Indonesia. Biodiversitas 20: 2295-2301. The aim of this study was to evaluate the genetic parameters of growth and wood quality in white jabon progeny test at 54 months old in Parung Panjang, Bogor. The 105 half-sib families obtained from 12 provenances were evaluated in a randomized complete block design with five replications. Wood quality was assessed both in a non-destructive way using a pilodyn and by destructive method using wood sample taker. Results indicated that the mean value ranged from 5.10 to 10.15 m for height, 6.67 to 15.30 cm for diameter, 2.30 to 3.62 cm for pilodyn penetration, 0.66 to 0.82 g/cm3 for wood density, 0.33 to 0.50 for specific gravity, and 66 to 111 % for moisture content, respectively. There were significant differences among 105 families for all traits except moisture content. The high heritability estimate was found for height (0.4-0.69) and basic density (0.27-0.59). Applying 80% selection intensity on diameter and leaving 84 best families in each block will produce a high total genetic gain. Pilodyn penetration had negative correlation with diameter, wood density, and specific gravity.

Shabrina H, Siregar UJ, Matra DD, Kamiya D, Siregar IZ. 2019. Short Communication: DNA extraction from stored wood of Falcataria moluccana suitable for barcoding analysis. Biodiversitas 20: 1748-1752. Sengon or Falcataria moluccana (Miq.) Barneby & J.W.Grimes is the main crop in community tree plantations in Java, Indonesia, favored because of its fast-growing property and the promising economic return. The wood itself is mostly used for light construction, furniture, plywood, packing materials, and recently as feedstock for bioenergy. Sometimes the wood is used as DNA source for example in the wood identification analysis. However, extracting DNA from woods is considered difficult due particularly to very small quantities of DNA. The objective of this research was to optimize and modify the common CTAB protocols to extract DNA from Sengon wood without liquid nitrogen which sometimes unavailable in some laboratories. The extracted DNA was quantified with nanophotometer and gel visualization and amplified with primer coding psbA-trnH intergenic spacer for testing. The highest concentration of DNA extracted was from 100 mg of wood stored for 24 hours in -30 °C (257.80 ng/µL or 14.18 µg in total) and even the lowest concentration produced by this method able to produce sufficient amount of PCR product for sequencing. Compared with results from 200 mg samples and longer freezing time (72 hours) and extraction using liquid nitrogen, this method considered gave the best results.

Mindi ( Melia azedarach L.) is mostly found in community forests of West Java. One of the important factors affecting productivity of community forests is the use of quality seed. Due to scarcity of seed sources, however, seed quality is not easily available. Currently, community forests serve also as ad hoc seed sources that are usually without appropriate quality assessment. This research was aimed to determine baseline information on spatial variability of mindi fruits collected from five seed sources, and seedling growths treated in seven different growing media consisting mixtures of soil, rice husk, sand and cattle manure. Five mindi populations were selected in the following villages: Nagrak (Bogor), Babakan Rema (Kuningan), Padasari (Sumedang), Sukakarya (Bogor) and Gambung (Bandung). The results showed that variability of seed dimension (CV=4.82-14.37%) and seedling growth (11.79-21.77%) were moderate. The mindi fruits from Nagrak were found to be the biggest in terms of size (1.22 ± 0.17 cm), weight (0.40 ± 0.04 g), and seed set (85.47 ± 15.09%). In addition, the seedling growth from Nagrak was also better than those of other villages showing its potential for future seed sources. Growing media containing cattle manure were observed consistently to be the best for seedling growth. The findings are useful in supporting scientifically the selection of seed sources from community forests.

Zulfahmi, Siregar IZ, Siregar UJ (2010) Chloroplast DNA variation of Shorea acuminata Dyer in Sumatra assessed by microsatellite markers. Biodiversitas 11: 107-111. Shorea acuminata Dyer is member of the Dipterocarpaceae family. It is ecologically and commercially important in the Indonesian region. In the present study, chloroplast microsatellites (cpSSRs) were used to study the distribution of chloroplast DNA haplotypes and to assess the variation within and among populations of S. acuminata from Riau and Jambi provinces eastern part of Sumatra. Based on chloroplast microsatellite analysis, six haplotypes were observed for S. acuminata,namely haplotype P, Q, R, S, T, and U, respectively. The high haplotype variation was detected in Bukit Barisan National Park (TNBT) population (five haplotypes); it may be due to TNBT population status as national parks (conservation area) under government protection. The value of genetic differentiation measured for S. acuminata was Gst = 0.150. The Gst values in this study is lower than the mean Gst value estimated in angiosperms plant for maternally inherited. Information on the status of genetic variation of the species in this study could be used as scientific consideration in formulating appropriate strategies for conservation and sustainable utilization ofgenetic resources.Key words: Dipterocarpaceae, Shorea acuminata, chloroplast microsatellites, genetic variation

Attempt to rehabilitate degraded natural forests in Indonesia is recently carried out by applying selective cutting and line planting (TPTJ) silvicultural system. One of the most important aspects of TPTJ silvicultural system is the procurement methods of large number of planting stocks. Shorea johorensis Foxw was investigated in this regards as one of promising Shorea species for rehabilitating degraded forests due to its fast growing character. The species is usually propagated by three different propagation techniques, namely up-rooted seedlings, seeds and cuttings. Genetic consequences due to different propagation methods in this species are poorly known and need to be studied in order to determine genetic variation and differentiation. Material from five origins (populations), namely: (i) up-rooted seedlings, (ii) seeds, (iii) cuttings, (iv) young plantation and (v) natural forest were randomly taken in the field and subsequently assessed by RAPD using threepreviously tested random primers of OPO-11, OPO-13 and OPO-16. Results showed that natural tree populations showed the highest levels of genetic variation with mean values na = 1.2593, ne = 1.2070, PLP = 25.93% and He = 0.1109. Cutting populations showed the lowest levels of genetic variation with mean values na = 1.1111, ne = 1.0773, PLP = 11.11% and He = 0.0445. Meanwhile, according to the propagation techniques, up-rooted seedling population revealed the highest levels of genetic variation with mean values na = 1.2222, ne =1.1613, PLP = 22.22% and He = 0.0886. Particular methods of plant propagation in this company, especially cutting method, reduced significant genetic variation of S. johorensis.Key words: Shorea johorensis Foxw, RAPD, genetic variation, silvicultural system

Genetic differentiation was investigated among 54 Indonesian species of Dipterocarpaceae, a dominant tree family in Asian tropical rainforests, using amplified fragment length polymorphism markers. The tree developed from the resultant unweighted pair group method using arithmetic averages clearly separated all investigated dipterocarps into two major groups that corresponded to tribe Dipterocarpeae and tribe Shoreae, respectively. These results are in accordance with the topology of molecular phylogenetic trees derived from PCR-restriction fragment length polymorphism analysis of chloroplast DNA and generally support the traditional taxonomic assessments. The possibility of interspecific hybridization is also discussed.

Yulianti, Siregar IZ, Wijayanto N, Tapa Darma IGK, Syamsuwida D (2011) Genetic variation of Melia azedarach in community forests of West Java assessed by RAPD. Biodiversitas 12: 64-69. Melia azedarach L. or mindi (local name) is one of the widely planted exotic species in Indonesia, mostly found in community forests in West Java. However, improving and increasing the productivity of mindi commmunity plantation in West Java requires information on patterns of existing genetic diversity. The present work was aimed at estimating the genetic variation of mindi by using RAPD markers. Outcome of the activities was to propose appropriate conservationand management strategies of genetic resources in order to support the establishment of seed sources. Six populations of mindi plantation in the community forests were chosen for this research, i.e Sukaraja (Bogor-1), Megamendung (Bogor-2), Bandung, Purwakarta, Sumedang and Kuningan. Five primers (OPA-07, OPY-13, OPY-16, OPA-09 and OPO-05) producing reproducible bands were analysed for 120 selected mother trees in total, in which 20 trees per locality were sampled. Data were analysed using Popgene ver 1.31, NTSYS 2.02 and GenAlEx 6.3. Based on the analysis, the observed number of alleles per locus ranging from 1.43 to 1.60, and percentage of polymorphic loci (PPL) ranging from 43.33 to 60.00.%. The levels of genetic variation were considered as moderate for all populations (He range from 0.1603 to 0.1956) and the the mean level of genetic diversity between population (Gst) was 0.3005. Cluster analysis and Principal Coordinates showed three main groups, the first group consists of 4 populations i.e Bandung, Kuningan,Purwakarta and Megamendung, the second was Sukaraja and the third was Sumedang. Based on Analysis of Molecular Variance (AMOVA), the Percentages of Molecular Variance within population (69%) is higher than that of between populations (31%). The moderate level of genetic variation in the community plantation forests, might be due to small population size, leading to reduce genetic variability. Further analysis is required to confirm this findings using other genetic marker.