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

Callus induction of F. moluccana (sengon) was still an obstacle to indirect organogenesis regeneration. The purpose of the study was to determine the callus induction formation from root fragments of F. moluccana plantlets. Primary explants (fragments of roots) were cultivated on MS induction basal media and three concentration combination of PGRs (BAP and NAA): 0.5 ml/l BAP; 0,1 ml/l NAA (single PGR); and combination of 0.5 ml/l BAP + 0.1 ml/l NAA (double PGR). When roots were used as explants, high formation rates of callus (more than 70%) were obtained. Highest formation rates of callus were in NAA added at all clones (12 clones), then BAP added (7 clones) and BAP + NAA added (5 clones). The results indicated that BAP and NAA concentrations used in the media were influence the producing callus and affect the amount of callus produced from roots of sengon. The addition of NAA also gives higher callus proliferation results than the addition of BAP or the addition of a combination of the two hormones. The results indicated that BAP and NAA concentrations used in the media were influence the producing callus and affect the amount of callus produced from roots of sengon.

This study aimed to assess genetic structure of Calophyllum inophyllum using simple sequences repeats (SSR) markers to control genetic diversity at a provenance seed stand. Leaf samples were collected for DNA templates and 6 SSR primers were used. Genetic data of 280 trees were analyzed by FSTAT software , while PCoA was analyzed by GeneAlex. Results showed that number of allele (N A ) per SSR primer between 3 and 4, the allelic richness (A R ) ranged 2.805 to 4.000, the gene diversity (H E ) ranged 0.018 to 0.631 , coefficient inbreeding (F IS ) of overall SSR primers were insignificant deviate from Hardy-Weinberg Equilibrium, excepted NY3. The mean H E values in the TBP was in low (mean H E = 0.272). However, the mean coefficient inbreeding value s was not significant. PCoA analysis showed that the seed stand consisted genetically related trees; the 280 trees originated from only 5-6 mother trees. This is because the stand was originated from a conservation stand with narrow genetic di fferentiation . Management of the seed stand was discussed.

Vulnerable status of kayu kuku (Pericopsis mooniana) is due to heavily wood harvesting. Aim in this study is to asses genetic diversity and structure of kayu kuku at Lamedai forest, Southeast Sulawesi using RAPD markers. Leaves samples were collected from 4 natural populations at Lamedai forest i.e. Lamedai natural reserve, Lamedai village, Balijaya and Tangketada. The 22 polymorphic loci of 5 RAPD markers were subjected to the genetic analysis, binary data were calculated by GenAlex software to obtain parameters in genetic diversity within population and analysis molecular variant (AMOVA), while PopTree software was used to construct a dendrogram. Results showed that genetic diversity of the 4 populations was in moderate level (mean He: 0.361 ± 0.017) and the values was similar each other. There was no private allele at any populations, indicating that there was no genetic specification. A dendrogram analysis showed that Lamedai natural reserve genetically closed to Tangketada population and Balijaya, while Lamedai was separated into another cluster. AMOVA analysis showed 13% genetic diversity were observed among populations. In conclution, kayu kuku at Lamedai forest might be a large and continuous population in ancient period.

Qiptiyah M, Pudyatmoko S, Widyatmoko AYPBC, Nurtjahjaningsih ILG, Imron MA. 2019. Cytochrome-b mitochondrial DNA characteristic from non-invasive samples of wild population Javan Banteng (Bos javanicus d’Alton, 1823). Biodiversitas 20: 350-355. Javan banteng (Bos javanicus javanicus) is one of the protected big mammals in Indonesia, due to its population decline. The main populations of Javan banteng are currently in Ujung Kulon National Park (UKNP), Alas Purwo National Park (APNP), Meru Betiri National Park (MBNP) and Baluran National Park (BNP). These four remaining populations are fragmented with wide geographical distances. Population reduction and fragmentation between populations can promote depletion of genetic characters. This study aim to examine the genetic characteristics of Javan banteng based on cytochrome b region of mitochondrial DNA. Genetic materials were obtained by a non-invasive method (feces) from four national parks in Java.The sequencing results were aligned with cytochrome b mitochondrial DNA sequences from the other banteng (B. j. lowi and B. j. birmanicus) from the GeneBank sequence database. The results from this study revealed that the genetic distance of Javan banteng between UKNP, APNP, and BNP were 0, while the genetic distance between these populations with MBNP was 0.005. Moreover, the population of MBNP has only one haplotype that does not exist in the other populations. Based on these results, there should be caution in conducting genetic infusion of Javan banteng in their natural populations, especially in Meru Betiri National Park.

Novel single nucleotide polymorphism loci were identified for teak (Tectona grandis Linn. f.) using a combined Next Generation Sequencing approach on the Illumina MiSeq system with genotyping on the Agena MassARRAY iPLEX™ platform. Three hundred and forty four putative loci were identified through sequencing of DNA fragments following a modified double digest Restriction Associated DNA Sequencing method. One hundred and eighty nine loci successfully amplified in 172 individuals from 20 populations in Myanmar. A total of 33 loci were removed from the final panel as two showed evidence of deviation from Hardy–Weinberg equilibrium, 17 were significantly linked and 23 were non-polymorphic. For the remaining 156 loci, expected heterozygosity ranged from 0.041 to 0.456 and FST from 0.062 to 0.632. These genetic resources will prove useful for future studies into the population genetics and phylogeography of this important and iconic timber species.

Aquilaria microcarpa is one of the agarwood producers species included in the endangered category based on the IUCN red list. Kalimantan is one of the natural distributions of this species. The high demand for agarwood causes this species to be commonly cultivated in community plantations. This study aimed to assess the genetic diversity of A. microcarpa using the RAPD markers. Forty-four leaf samples of A.microcarpa were collected from the local community in Gumbil (South Kalimantan) and Sanggau (West Kalimantan). The results showed that 9 out of 24 RAPD primers were stable in amplification, and polymorphic totally consisted of 49 polymorphic loci. The values of unbiased expected heterozygosity (uHE) were at a low level; they ranged between 0.152 (Gumbil II) to 0.249 (Gumbil I). The average genetic distance between Gumbil and Sanggau is 0.1733, related to their geographic distance. A private allele was only found at Gumbil at locus G18/540 and Sanggau at locus G18/550, respectively. A great DA value between Gumbil I and II showed that the plantations originated from different seed sources. AMOVA also verified the differences between the two populations. This finding has important implications in managing plantations and seeds transfer.

The study aimed to assess genetic diversity and genetic relationship of ulin wildlings randomly collected from a nursery and originated from Bukit Soeharto natural forest, East Kalimantan. DNA templates were extracted from leaf samples of 1.5 years old wildings. Five RAPD primers consisted 55 polymorphic loci were used for genetic studies. Genetic diversity and relationship were analyzed using GenAlex software. The results showed moderate mean value of genetic diversity (HE=0,345, SE 0,015) of the wildings. Forty eight wildings were clustered in only 3 groups; almost all wildings (65%) were clustered in one main cluster. Moreover, 4 wildlings were clones (8%). In conclusion, the 48 wildings of ulin consisted high genetic relationship and individual clones that reflects the low genetic diversity of this species.

Qiptiyah M, Pudyatmoko S, Widyatmoko AYPBC, Nurtjahjaningsih ILG, Imron MA. 2019. Phylogenetic position of Javan banteng (Bos javanicus javanicus) from conservation area in Java base on mtDNA analysis. Biodiversitas 20: 3352-3357. Two of three subspecies of banteng (B. javanicus) can be found in Indonesia, namely B. j. lowi and B. j. javanicus. The taxonomic assignment of the two subspecies is still in the discussion researchers currently. One of the reproductive characters of members the Bovidae family, including the banteng, is known to have interbreeding ability between species and can produce fertile offspring. In some places, there exist grazing cattle near or in the banteng’s natural habitat. This phenomenon aimed to provide banteng mates with cows, which later they will breed high-quality offsprings. Regarding interbreeding capability, this condition can be a threat to the genetic purity of wild banteng. The main objectives of this study were to identify the phylogenetic position of Javan banteng from conservation areas in Java in relation to the other taxon and detect their genetic purity. We analyzed 28 cytochrome b and d-loop region sequences of Javan banteng from feces materials of four conservation areas (Ujung Kulon National Park, Alas Purwo National Park, Meru Betiri National Park, and Baluran National Park). We compared our data with reference sequences data of the other Bovidae species and Capra hircus as outgroup. The reference data was taken from NCBI, and they were analyzed using maximum likelihood. The results showed that Javan banteng was in a different group from other taxa. Separation of subspecies B. j. javanicus and B. j. lowi occurred circa 1.25 mya. The results from this study suggested that there is no indication of genetic introgression between Javan banteng and the (domesticated) cattle.

Calliandra calothyrsus was introduced to Indonesia from Guatemala in 1930s and had been planted widely throughout Indonesia for fuel wood. Genetic diversity within and among population is an important factor for initiating breeding program. Aim in this study was to evaluate genetic structure of C. calothyrsus in Indonesia, to obtain a better understanding of the history of the distribution and efficiency of breeding strategy of this species. Leaf samples were collected in a seedling seed orchard plot from 10 populations. Six RAPD markers consisted of 34 loci were used to analyze genetic diversity and genetic structure. The results showed that genetic diversity was in low to moderate level (mean HE= 0.321). The AMOVA analysis showed that genetic differentiation among geographical sources was significant, also among populations within geographical sources and among individual within populations as well. It was revealed that the 10 populations originated from only two ancestors. The limited number of ancestors resulted low to moderate genetic distances among populations (mean Da=0.070). In conclusion, C. calothyrsus has moderate genetic diversity within population and weak genetic structure among populations. Genetic diversity in population/individual level should be considered as a selection unit in the breeding strategies.

Variation of parent gametes' contribution might affect the growth patterns among offspring produced from seed orchards. This paper studies the mating system statuses and to identify parent trees that produce good growth performance of offspring in seedling seed orchard of A. mangium. The study was conducted in two seed orchards, i.e. a first generation seedling seed orchard (F1 SSO) of A. mangium, used as the parent population hereafter and a multi location trial (MLT) as an offspring population. Based on 10 microsatellite markers, mating system in the F1 SSO was under panmictic equilibrium condition. The good growth trees in the MLT originated from various parent genes contribution in the F1 SSO. Several behaviors were observed: a). the best trees in MLT dominantly originated from singlepair trees, between maternal and paternal trees, in F1 SSO; b). a maternal tree was pollinated by two paternal trees; c). a paternal tree pollinated several maternal trees. Flowering synchronization and genetic compatibility among trees might be responsible for these mating system patterns. In order to maximize seeds production, studies on male and female flowers characteristic should be employed to assess flowering synchronization among individual trees in the seed orchard.

A DNA barcoding is a taxonomy method that provide fast and acurate species identification, thus it can be applied to anticipate when a species can not be identified morphologically. This study aimed to assess molecular characteristics ofPericopsis moonianafrom two wild populations in Indonesia using a barcoding marker rDNA ITS (Internal Transcribed Spacer) as additional information for establishing conservation strategy of this species. Leaf samples ofP. moonianawere collected from natural forests at South East Sulawesi and South Kalimantan, and a germplasm orchard at Purwodadi Botanic Garden. Molecular characteristic was evaluated based on a pair of ITS primers that produce between 634-641 bp nucleotide. The sequence data were analyzed by Bioedit version 7.0.5.3 and Mega 7 software. Results showed thatP. moonianafrom South East Sulawesi and South Kalimantan were clustered together, whileP. moonianafrom Purwodadi Botanic Garden were separated with only one base difference from those two population. In conclusion, ITS barcoding in this study shows a diffences betweenP. moonianacollected from South East Sulawesi and South Kalimantan withP. moonianathat originally from Papua. A further study using more barcoding marker and more population could be approached to obtain more information on molecular characters ofP. moonianapopulations that will useful for establishing conservation and tree breeding program of this species.

Calophylluminophyllum is an indigenous species and distributed mostly at shoreline areas in Indonesia. Genetic conservation of this species inits natural habitats is very important. A study aimed to assess genetic diversity and structure of C. inophyllum at Dompu natural forestwas carried out. Leaf samples were collected from three natural populations at Dompuregency (Kilo, Kempo and Pekat). Genetic analysis was carried out using six simple sequence repeats (SSR) markers. Private alleles were only found at Kilo population. Number of detected alleles (NA), values of alleles diversity (AR) and gene diversity (HE) were also higher at Kilo (NA: 17; AR: 2.219; HE: 0.339) than at Kempo (NA: 10; AR: 1.661; HE: 0.219) and Pekat (NA: 12; AR: 1.941; HE: 0.276). The values of the inbreeding coefficients (FIS) were insignificant among the populations. The medium- scale genetic structure showed that genetic relations. Fine-scale genetic structure analysis showed insignificant genetic structure among trees in distance of 2 m at Kilo and 400 m at Pekat, respectively, suggesting that C. inophyllum was dispersed as far as 2 m to 400 m.

The mating system is a process that describes travelling pollen reached an ovul during reproductive stages; thus, this proses effects on genetic diversity and structure of plant species. Ficus variegata Blume (nyawai) and Dodonaea viscosa Jaeq. (tesek) are two priority species for ecosystem restoration program at Mount Merapi. Its conservation status has been threatened by a regularly volcanic eruption. To understand the mating system, this study aimed to assess the genetic diversity of seedlings and outcrosing rate of nyawai and tesek. DNA template for genetic analysis was obtained from 94 seedlings of nyawai that collected from a mother tree and 24 seedlings of tesek from a mother tree in its natural distribution, respectively. Genetic analysis was employed using 24-38 loci of random amplified polymorphism DNA (RAPD) markers. As results, genetic diversity (HE) of seedlings of the two species were maintained at moderate level; it ranged between 0.357 to 0.377 for nyawai and 0.411 for tesek, respectively. PCoA analysis described the seedlings were genetically unrelated. These results might be in consequence of high outcrossing rate (tm=1) and zero inbreeding coefficient among maternal trees (to-ts=0). The results also suggest that seeds translocation and deployment of nyawai and tesek, should be strictly managed; thus, specific alleles that characterize a population could be maintained.

The aims of this study were to assess genetic diversity within populations and genetic relationship among populations of C. inophyllum. Leaf samples as template DNA were collected from 10 natural populations and 1 plantation. Five random amplified polymorphism DNA (RAPD) markers consisted 30 loci were conducted to genetic analysis. Results showed genetic diversity within populations were in low to moderate level (mean H E =0.186). There is no private allele in any populations. The analysis of molecular variance (AMOVA) showed that genetic differentiation among Islands was insignificant; but the differentiation was siginificant among populations and individual trees. Genetic distance among populations was in low to moderate level (mean Da=0.250). Cluster analysis clearly divided the 11 populations into 2 clusters; cluster I consisted Selayar, Lombok, Gunung Kidul and Padang populations; cluster II consisted Way Kambas, Madura, Ketapang, Dompu, and Yapen populations. The genetic relationships did not associate with their geographical locations. In conclusion, genetic diversity and genetic relationship among populations of C. inophyllum was in moderate level.

Borneo ironwood (Eusideroxylon zwageri) is a tall tropical tree that is threatened by illegal logging and exploitation due to its economic value. In the present study, approximately 10,618 bp of E. zwageri chloroplast DNA were sequenced genome-wide and 16 polymorphic markers of chloroplast DNA were developed, using next-generation sequencing technology. In total, 26 nucleotide substitutions, 3 indels, 1 sequence inversion, and 1 mononucleotide repeat variation were detected in samples of 10 trees collected from 5 populations in Kalimantan, Indonesia. These markers are a powerful tool that may be used to describe the phylogeographical genetic structure of E. zwageri and will be essential for the conservation and management of this endangered tree.

Genetic diversity value of offspring might indicate a reproductive success in a forest. Aim in this study was to access genetic diversity values of offspring of Shorea leprosula from different forest types. Leaf samples were collected from six population i.e. a plantation from Carita, and five natural forests from Gunung Bunga A and B, SBK, ITCI and Gunung Lumut. Using four microsatellite markers, the results showed that SBK population maintained high value of genetic diversity. Values of expected heterozygosity (HE) ranged between 0.717 (Carita) and 0.836 (SBK). Values of coefficient inbreeding (F) were insignificant deviated from Hardy-Weinberg Equilibrium, but the value was significant in SBK population. PCA analysis demonstrated a cluster among Gunung Bunga A, SBK, ITCI, and Gunung Lumut. Amova showed that different province significantly contributed 1% to the value of genetic diversity of S. leprosula.

Flowering are influenced by internal factors, such as genetic and phytohormone, and environment factors, such as sunlight and nutrition intake. The flowering characteristics influence fruiting and genetic diversity seedlings through mating systems. This study aims to assess flowering and fruiting characteristics and to determine pattern of mating system of a Calophyllum inophyllum plantation at Watusipat, Gunung Kidul. Flowering and fruiting were observed at 4 locations, 3 parts of crown, and 4 main directions to know the effects of sunlight, nutrition intake and phytohormone in the flowering process. Mating system was assessed by comparing genetic diversity values between parent trees and offsprings. The values of genetic diversity were analyzed using 5 RAPD primers with 17 polymorphic loci. Analysis of variant showed that the locations, crown parts, directions and interaction between a location and direction significantly affected to differences number of flowers and fruits. Values of genetic diversity (h) of parent trees ranged between 0.1471 and 0.3056. The values increased at almost overall offsprings; it ranged between 0.2864 and 0.3750. Values of genetic distance (Da) between parent trees were high and very high (0.197 – 0.364), but the values was decreased between parent trees and their offspring, even between offspring populations. A dendrogram showed two main clusters; first cluster consisted parent trees at up edge with rare trees and second cluster consisted sub cluster parent trees at up edge; sub cluster parent trees at down middle; and sub cluster parent trees at down edge and overall offsprings. Flowering/ fruiting characteristics and pattern of mating systems of C. inophyllum were briefly discussed. Key words : Flowering characteristic, genetic diversity, Calophyllum inophyllum, RAPD analysis

Screening primer is an effective method to develop microsatellite markers from related taxa. Aim of this study was to develop microsatellite markers of four Shorea producing tengkawang oil, i.e. Shorea gysbertiana, Shorea macrophylla, Shorea pinanga and Shorea stenoptera by screening microsatellite primers of Shorea curtisii. Leaf samples of the four Shorea were collected from nursery at Center for Forest Biotechnology and Tree Improvement Research in Yogyakarta. Four microsatellite primers of S. curtisii i.e. Shc-1, Shc-2, Shc-7 and Shc-9 had been used to screen. Results showed that numerous alleles were shared among the Shorea. The expected heterozygosity (HE) for locus Shc-1 ranged between 0.594 and 0.722; locus Shc-2 ranged between 0.219 and 0.611; locus Shc-7 ranged between 0.594 and 0.778; and locus Shc-9 ranged between 0.594 and 0.844. Coefficient of inbreeding (FIS) value was low and it was insignificant deviated from Hardy-Weinberg Equilibrium (HWE) at almost all loci except Shc-1 of S. pinanga. A dendrogram showed two clusters; S. gysbertsiana and S. macrophylla represented in one cluster, while S. pinanga and S. stenoptera represented in another cluster. Therefore the developed microsatellite markers are possible to be applied for studying population genetics and mating system of these species.

When genetic base in a seed orchard is narrow, a startegy of genetic infusion should be applied to broaden and maintain its ganetic variation over several successive generations. For this purpose, genetic-infusion populations were established in tree improvement programs of Pinus merkusii located in jember. To be successful genetic variation of the infusion populations should be assessed. This study was aimed to determine genetic diversity of three infusion populations of P merkusii i.e. Takengon, janto and Blankejeren population using five microsatellite markersi. The results showed that gene diversity of plus trees in the seed orchard was at a moderate level (H E =0.508).Significant inbreeding deviation from the Hardy-Weinberg equilibrium (HWE) was detected (F IS = 0.073). Gene diversity of the infusion populations was comparatively high. It ranged between 0.498 (Janto) and 0.524 (Blankejeren). The FIS was low and insiqnificant deviation from HWE at any genetic infusion populations. The genetic differentiation among the populations (in both seed orchard and genetic infusion) was very low (F ST =0.003) indicating that they were genetically related. It is recommended that the infusion populations have a potential to maintain to genetic diversity in the seed orchard.However, Since they are related, it is necessary to find other potential genetic infusion populations that could broaden genetic diversity more effectively in the seed ochard.

Pollen movement is a critical determinant in population genetic, plays important role in forest tree improvement and conservation genetic. This study was conducted to understand physical pollen movement and to determine seasonal genetic diversity of seed crops in a seedling seed orchard (SSO) of Pinus merkusii , located at Jember, East Java. Physical pollen movements were measured using 25 pollen traps conducted at three flowering seasons i.e. August 2005, November 2005 and March 2006. For offspring populations, seeds were collected at June, September and December that represented mating in each pollen observation season. Then, genetic diversity of the seed crops were analyzed using five microsatellites markers for P. merkusii . Results showed that number of pollen grains was significantly difference among seasons, but insignificant to both trap locations and interaction season-trap locations. The trapped pollen number was low in both August and March, but it was abundant in November. Value of gene diversity of offspring was highest in August (H E = 0.402) compared to other seasons. This study showed that physical pollen movement in the SSO might synchronize, however level of the H E varied among seasons. Seasonal variation in mating status was briefly discussed.

Eusideroxylon zwageri is a large tropical rainforest tree native to Indonesia, Malaysia, the Philippines, and Brunei. Because of its high economic value, illegal logging and overexploitation is threatening this species in several locations in Indonesia. In this study, in order to conserve genetic resources, we investigated the genetic structure of E. zwageri in Indonesia using chloroplast DNA sequencing. Eusideroxylon zwageri samples were collected from the Kalimantan (56 trees from seven populations) and Sumatra (16 trees from two populations) islands of Indonesia. Approximately 3137 bp of chloroplast DNA was sequenced for each tree. Twenty-one haplotypes were identified, of which six haplotypes were detected from two or three populations, whereas the other 15 haplotypes were detected from one population each. For each population, one to six haplotypes were detected, and phylogenetically closer haplotypes were detected within the same population. Although the haplotypes were roughly divided into two groups, geographically-close populations did not always have phylogenetically-close haplotypes. Our results suggest that in Indonesia, E. zwageri showed a high genetic diversity at the chloroplast DNA level, and populations within a population were derived from similar maternal lineages. Therefore, transplantation within a population may be a feasible option for E. zwageri conservation. However, transplantation among different populations should be conducted with careful consideration, because geographic distances are not always related to phylogenetic distances in E. zwageri.