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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.

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.

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.

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.

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.

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.