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Many tree planting programmes have long been initiated to increase forest cover to mitigate the effects of global climate change. Successful planting requires careful planning at the project level, including using suitable species with favourable traits. However, there is a paucity of improvement data for tropical tree species. An experimental common garden of Shorea leprosula was established to study traits related to growth performance which are key factors in planting success. Seedlings of S. leprosula were collected from nine geographical forest reserves. To study the effects of genetic variation, seedlings were planted in a common environment following a randomized complete block design. From performance data collected 2017‒2019, one population showed the highest coefficient for relative height growth, significantly higher than most of the other populations. Interestingly, this population from Beserah also exhibited the lowest coefficient for scale insect infestation. This study provides preliminary results on growth performance and susceptibility to scale insect infestation in S. leprosula and the first common garden experiment site conducted on dipterocarp species. It lays a foundation for future genome-wide studies.

Worldwide, many mangrove species are experiencing significant population declines, including Rhizophora apiculata, which is one of the most widespread and economically important species in tropical Asia. In Malaysia, there has been an alarming decline in R. apiculata populations driven primarily by anthropogenic activities. However, the lack of genetic and demographic information on this species has hampered local efforts to conserve it. To address these gaps, we generated novel genetic information for R. apiculata, based on 1,120 samples collected from 39 natural populations in Peninsular Malaysia. We investigated its genetic diversity and genetic structure with 19 transcriptome and three nuclear microsatellite markers. Our analyses revealed a low genetic diversity (mean He: 0.352) with significant genetic differentiation (FST: 0.315) among populations of R. apiculata. Approximately two-third of the populations showed significant excess of homozygotes, indicating persistent inbreeding which might be due to the decrease in population size or fragmentation. From the cluster analyses, the populations investigated were divided into two distinct clusters, comprising the west and east coasts of Peninsular Malaysia. The western cluster was further divided into two sub-clusters with one of the sub-clusters showing strong admixture pattern that harbours high levels of genetic diversity, thus deserving high priority for conservation.

Southeast Asian rainforests at upper hill elevations are increasingly vulnerable to degradation because most lowland forest areas have been converted to different land uses. As such, understanding the genetics of upper hill species is becoming more crucial for their future management and conservation. Shorea platyclados is an important, widespread upper hill dipterocarp in Malaysia. To elucidate the genetic structure of S. platyclados and ultimately provide guidelines for a conservation strategy for this species, we carried out a comprehensive study of the genetic diversity and demographic history of S. platyclados. Twenty-seven populations of S. platyclados across its range in Malaysia were genotyped at 15 polymorphic microsatellite loci and sequenced at seven noncoding chloroplast DNA (cpDNA) regions. A total of 303 alleles were derived from the microsatellite loci, and 29 haplotypes were identified based on 2892 bp of concatenated cpDNA sequences. The populations showed moderately high genetic diversity (mean HE = 0.680 for microsatellite gene diversity and HT = 0.650 for total haplotype diversity) and low genetic differentiation (FST = 0.060). Bayesian clustering divided the studied populations into two groups corresponding to western and eastern Malaysia. Bottleneck analysis did not detect any recent bottleneck events. Extended Bayesian skyline analyses showed a model of constant size for the past population history of this species. Based on our findings, priority areas for in situ and ex situ conservation and a minimum population size are recommended for the sustainable utilization of S. platyclados.

Our study highlights the utilization of a genetic database for wood-origin identification in Intsia palembanica, a valuable heavy hardwood from the tropical forests. This forensic tool is essential for strengthening the verification of legality in the wood supply chain from the forest to the end-users. An increasing number of rules and regulations are being put in place to promote sustainable practice in the timber trade, one of which involves ensuring that importers declare the correct species name and source of geographic origin of the timber. We aimed to determine the origin of the I. palembanica seed source used in the early establishment on the Forest Research Institute Malaysia (FRIM) campus. DNA samples of I. palembanica individuals from the FRIM campus were obtained and analyzed using four chloroplast (cp) DNA markers to characterize the haplotype variants for population identification. In addition, the DNA samples were also genotyped at 14 short tandem repeat (STR) loci for individual identification. Individual assignment to the possible geographic origin was done through an assignment test. On the basis of our recently developed I. palembanica genetic databases, the I. palembanica seed source for the early establishment was inferred to be originated from a mixture of several sources, with a large portion from the southern region (89%) and a relatively small portion from the northern region (11%) of Peninsular Malaysia. The I. palembanica seed source used for the early establishment on the century old FRIM campus was inferred to be originated from several forest reserves located not far from the planting sites. This study proves the applicability of the DNA method in supply-chain verification, where an unknown I. palembanica tree can be traced to its geographic origin using genetic databases.

Aquilaria malaccensis (Thymelaeaceae) is the main source of high-grade agarwood in Southeast Asia. Aggressive collections and trade activities over the past decades have put great pressure on the natural stands and raised concerns over the long-term survival potential of A. malaccensis. Tracking and authentication of agarwood require method with a high degree of accuracy. Therefore, this study aimed to develop DNA databases of A. malaccensis as the tracking tools at species, population and individual levels for forensic identification and chain of custody certification. Using two cpDNA (rbcL and matK) and an rDNA (ITS2) markers, species identification database of Aquilaria was developed to distinguish A. malaccensis from A. hirta, A. microcarpa, A. beccariana, A. crassna, A. sinensis and A. rostrata. In addition, based on 35 populations of A. malaccensis throughout Peninsular Malaysia, cpDNA haplotype and STR allele frequency databases were developed for population and individual identification. A haplotype distribution map based on 29 haplotypes derived from seven cpDNA showed that the A. malaccensis in Peninsular Malaysia can be associated to Kedah-Perak and Kelantan-Johor regions. Similarly, genetic relatedness and Bayesian clustering analyses based on 10 STR markers also divided the 35 populations into two main genetic clusters, corresponding to Kedah-Perak and Kelantan-Johor regions. The STR allele frequency databases were established and characterized according to these two regions. To determine the performance of the STR allele frequency databases for population identification, independent self-assignment tests showed that the percentage of individuals correctly assigned into the origin population was 93.88% in Kedah-Perak and 90.29% in Kelantan-Johor. For the STR allele frequency databases to be used for individual identification, conservativeness tests showed that the θ should be adjusted to 0.250 and 0.200 in the Kedah-Perak and Kelantan-Johor databases, respectively. To ensure consistency in allele calling for the dinucleotide repeat loci across different electrophoretic platforms or laboratories, allelic ladders have been developed for the 10 STR loci. Two case studies are presented of how these databases were used to track A. malaccensis to the origin population and stump. These databases are ready to be used to provide admissible forensic evidence for legal proceedings against the illegal harvesters of agarwood and for agarwood certification to meet the consumer country regulations.

To inform product users about the origin of timber, the implementation of a traceability system is necessary for the forestry industry. In this study, we developed a comprehensive genetic database for the important tropical timber species Merbau, Intsia palembanica, to trace its geographic origin within peninsular Malaysia. A total of 1373 individual trees representing 39 geographically distinct populations of I. palembanica were sampled throughout peninsular Malaysia. We analyzed the samples using a combination of four chloroplast DNA (cpDNA) markers and 14 short tandem repeat (STR) markers to establish both cpDNA haplotype and STR allele frequency databases. A haplotype map was generated through cpDNA sequencing for population identification, resulting in six unique haplotypes based on 10 informative intraspecifically variable sites. Subsequently, an STR allele frequency database was developed from 14 STRs allowing individual identification. Bayesian cluster analysis divided the individuals into two genetic clusters corresponding to the northern and southern regions of peninsular Malaysia. Tests of conservativeness showed that the databases were conservative after the adjustment of the θ values to 0.2000 and 0.2900 for the northern (f = 0.0163) and southern (f = 0.0285) regions, respectively. Using self-assignment tests, we observed that individuals were correctly assigned to populations at rates of 40.54−94.12% and to the identified regions at rates of 79.80−80.62%. Both the cpDNA and STR markers appear to be useful for tracking Merbau timber originating from peninsular Malaysia. The use of these forensic tools in addition to the existing paper-based timber tracking system will help to verify the legality of the origin of I. palembanica and to combat illegal logging issues associated with the species.

Baeckea frutescens or Cucur Atap, is a medicinal plant that has been traditionally used as herbal medicine and has great potential for pharmaceutical application due to its biological properties. The increasing demand for B. frutescens herbal medicinal products has led to its over-exploitation. Therefore, it is crucial to generate baseline genetic information in order to formulate conservation and breeding programmes for this species. In this study, a total of 26 polymorphic simple sequence repeat (SSR) markers have been developed in B. frutescens based on the leaf transcriptome sequence data obtained via next generation sequencing (NGS) technology. These markers were evaluated using 32 individuals from Forest Research Institute Malaysia Research Station in Setiu, Terengganu. The mean number of alleles was two and the average expected (HE) and observed heterozygosity (HO) were 0.484 and 0.900, respectively. Cluster analysis revealed high genetic similarity among the individuals, whereby many of them were of the same clones. It is essential to assess more individuals from other populations for better understanding on the genetic diversity of this useful medicinal plant.

Background: Dipterocarpaceae is a pantropical tree family that plays an important role in our understanding of the ecology of Asian tropical rain forests. However, genome sizes for members of the Dipterocarpaceae are still poorly known.Aims: To report the genome size of 115 dipterocarp species and examine the variation and evolution of genome size in this family.Methods: Genome size was estimated using flow cytometry. Both the rpoB and trnL intron were sequenced to uncover the evolution of genome size within a phylogenetic framework.Results: The 1C genome size varied between 0.267 and 0.705 pg in Shorea hemsleyana and Shorea ovalis, respectively, a 2.64-fold variation across the family. Most dipterocarps are characterised by very small genomes with a mean 1C value of 0.416 pg (sd = 0.075) and five polyploids are recorded. The ancestral genome size for dipterocarps was reconstructed as 1Cx = 0.481 pg (95% CI = 0.433–0.534).Conclusions: Genome size variation in dipterocarps was characterised by very small v...

Taxonomic classification of the important medicinal plant, Ficus deltoidea (Moraceae), is challenging because of the variability of its leaves and fig forms that occur within the species. We developed 16 nuclear Simple Sequence Repeat (nSSR) markers, and characterized them using 24 individuals from a natural population. We then studied the intraspecific variation of F . deltoidea subsp. deltoidea in Peninsular Malaysia using morphological and molecular approaches. Based on the morphological variations, we further determined the varieties that occur regionally under the above subspecies based on the leaf characteristics. As for molecular data sets, we used both chloroplast DNA (cpDNA) and nSSR markers to elucidate the phylogenetic relationship among the varieties. The cpDNA dendrogram yielded poorer resolution where most of the clades were forming paraphyletic complex. The cluster analysis based on nSSR is largely congruent with the morphological classification, with F . deltoidea subsp. deltoidea classified into four main varieties, namely var. deltoidea , var. angustifolia , var. kunstleri and var. lutescens . Our study demonstrates the applicability of molecular approach in complementing the conventional taxonomic classification.

Illegal logging and smuggling of Gonystylus bancanus (Thymelaeaceae) poses a serious threat to this fragile valuable peat swamp timber species. Using G. bancanus as a case study, DNA markers were used to develop identification databases at the species, population and individual level. The species level database for Gonystylus comprised of an rDNA (ITS2) and two cpDNA ( trnH-psbA and trnL ) markers based on a 20 Gonystylus species database. When concatenated, taxonomic species recognition was achieved with a resolution of 90% (18 out of the 20 species). In addition, based on 17 natural populations of G. bancanus throughout West (Peninsular Malaysia) and East (Sabah and Sarawak) Malaysia, population and individual identification databases were developed using cpDNA and STR markers respectively. A haplotype distribution map for Malaysia was generated using six cpDNA markers, resulting in 12 unique multilocus haplotypes, from 24 informative intraspecific variable sites. These unique haplotypes suggest a clear genetic structuring of West and East regions. A simulation procedure based on the composition of the samples was used to test whether a suspected sample conformed to a given regional origin. Overall, the observed type I and II errors of the databases showed good concordance with the predicted 5% threshold which indicates that the databases were useful in revealing provenance and establishing conformity of samples from West and East Malaysia. Sixteen STRs were used to develop the DNA profiling databases for individual identification. Bayesian clustering analyses divided the 17 populations into two main genetic clusters, corresponding to the regions of West and East Malaysia. Population substructuring ( K =2) was observed within each region. After removal of bias resulting from sampling effects and population subdivision, conservativeness tests showed that the West and East Malaysia databases were conservative. This suggests that both databases can be used independently for random match probability estimation within respective regions. The reliability of the databases was further determined by independent self-assignment tests based on the likelihood of each individual's multilocus genotype occurring in each identified population, genetic cluster and region with an average percentage of correctly assigned individuals of 54.80%, 99.60% and 100% respectively. Thus, after appropriate validation, the genetic identification databases developed for G. bancanus in this study could support forensic applications and help safeguard this valuable species into the future.

The development of timber tracking methods based on genetic markers can provide scientific evidence to verify the origin of timber products and fulfill the growing requirement for sustainable forestry practices. In this study, the origin of an important Dark Red Meranti wood, Shorea platyclados, was studied by using the combination of seven chloroplast DNA and 15 short tandem repeats (STRs) markers. A total of 27 natural populations of S. platyclados were sampled throughout Malaysia to establish population level and individual level identification databases. A haplotype map was generated from chloroplast DNA sequencing for population identification, resulting in 29 multilocus haplotypes, based on 39 informative intraspecific variable sites. Subsequently, a DNA profiling database was developed from 15 STRs allowing for individual identification in Malaysia. Cluster analysis divided the 27 populations into two genetic clusters, corresponding to the region of Eastern and Western Malaysia. The conservativeness tests showed that the Malaysia database is conservative after removal of bias from population subdivision and sampling effects. Independent self-assignment tests correctly assigned individuals to the database in an overall 60.60−94.95% of cases for identified populations, and in 98.99−99.23% of cases for identified regions. Both the chloroplast DNA database and the STRs appear to be useful for tracking timber originating in Malaysia. Hence, this DNA-based method could serve as an effective addition tool to the existing forensic timber identification system for ensuring the sustainably management of this species into the future.

Orthosiphon stamineus (Lamiaceae) is an important medicinal plant in Malaysia that has great potential in the herbal medicine industry. In this study, we developed and characterized ten microsatellites for O. stamineus. The microsatellite loci were checked for variability using 28 individuals of O. stamineus sampled from 10 nurseries. The number of alleles ranged from two to four, and the observed heterozygosity ranged from 0.143 to 0.963. Neighbor-joining analysis revealed two main genetic clusters corresponding to the two varieties (white and purple). The application of these microsatellites will facilitate the cultivar/variety identification and germplasm management in the species.

Hopea bilitonensis is an extremely rare and predominantly selfing dipterocarp in Peninsular Malaysia. A comprehensive research was initiated to assess the ecological genetics of H. bilitonensis to elucidate specific ecological and genetic requirements and subsequently to recommend conservation strategies. The objective for conservation of a rare plant such as H. bilitonensis differs from that of a common plant. For common plants, the conservation strategies are to prevent the species from becoming endangered. In contrast, for rare plants, the final race against extinction is being fought. Tropical forests are rich in plant species diversity and obtaining adequate knowledge to set conservation strategies for the majority of these species might be difficult. Thus, it is suggested that for the conservation of tree species, the species can be grouped according to their life history traits. The information generated for a species can then be adapted to species that have similar types of life history traits. We have recently generated the ecological genetics information for a rare and predominantly outcrossed dipterocarp (Shorea lumutensis). This study on H. bilitonensis will provide ecological genetics information for the conservation of rare and predominantly selfing dipterocarps.

Full-sib families are produced from artificially controlled pollination in tree breeding. This mating design is, however, very costly and logistically difficult as most tree species are large in size. With the development of molecular markers, known relationships among the offspring could be established from the maximum likelihood in paternity analysis. In this study, we successfully established full-sib families on the basis of paternity analysis of offspring derived from two Shorea platyclados seed parents from the natural forest. A total of 2,049 and 970 offspring were collected from two mother trees M01 and M06, respectively. Potential pollen donors surrounding the mother trees were sampled, specifically a total of 77 adult trees within the 10-ha plot for M01 and 28 adult trees within the 4-ha plot for M06. For mother tree M01, parentage was assigned to 45.4% of the offspring at the 95% confidence level with 59 full-sib families established. For mother tree M06, parentage was assigned to 19.9% of the offspring at the 95% confidence level with 19 full-sib families established. The establishment of full-sib families in S. platyclados enables breeding in dipterocarp tree species, once a decade-long proposition, to become more efficient in a cost-saving manner.

We demonstrate the usage of meniscus pinning by surface relief boundaries to control in-plane orientation of monolayer colloidal crystals without the interruption of grain disorientation. By optimizing the pinning boundary and withdrawal speed, a well controlled linear meniscus contact line offers unidirectional growth of a colloidal crystal-densely packed crystal direction ⟨11⟩ and ⟨10⟩ parallel to linear edge-giving rise to a single domain crystal with only twins and vacancies present as residual defects. The pinning effect works by eliminating the wavy contact line induced by fingering instability which is commonly found in liquid wetting film. It is found that surfactants and colloidal particles play significant roles to enhance edge pinning, increasing the distance traveled by receding bulk meniscus (during substrate withdrawal) before liquid depinning or rupturing.

This paper reports 10 polymorphic microsatellite markers for a valuable peat swamp timber species, Gonystylus bancanus (Thymelaeaceae). The primers were designed from a genomic library enriched with dinucleotide (CT) repeats and screened on 24 samples from a natural population. The number of alleles detected per locus ranged from two to nine while the observed and expected heterozygosities ranged from 0.455 to 0.864 and from 0.476 to 0.863, respectively. No significant deviation from Hardy–Weinberg equilibrium (P

The mating system and seed variation of Acacia hybrid (A. mangium × A. auriculiformis) were studied using allozymes and random amplified polymorphic DNA (RAPD) markers, respectively. Multi-locus outcrossing rate estimations indicated that the hybrid was predominantly outcrossed (mean±s.e. t m = 0.86±0.01). Seed variation was investigated using 35 polymorphic RAPD fragments. An analysis of molecular variance (AMOVA) revealed the highest genetic variation among seeds within a pod (66%–70%), followed by among pods within inflorescence (29%–37%), and the least variation among inflorescences within tree (

Simple sequence repeats (SSRs) derived from expressed sequence tags (ESTs) are valuable markers because they represent transcribed regions and often transferable to related taxa. Here, we report the development and characterization of EST-SSRs from Shorea leprosula. Fifty-four sequences containing SSRs were identified in 2003 unigenes assembled from 3159 ESTs. Twenty-four EST-SSRs were developed, of which four gave multiple amplifications, five were found to be monomorphic and 15 showed polymorphism, with allele numbers ranging from two to 17 in a single Pasoh Forest Reserve population of 24 individuals. The observed and expected heterozygosities ranged from 0.05 to 0.91 and from 0.16 to 0.93, respectively. Cross-species transferability of the 15 loci to 36 species within Dipterocarpaceae revealed between four and 14 loci that gave positive amplification and 10 loci were found to be transferable to more than 15 species.

Intsia palembanica is a high-value tropical hardwood species of the family Leguminosae. A total of 16 microsatellite markers were developed for this important timber species using an enrichment approach. These markers were screened on 24 samples from a natural population and subsequently tested for reproducibility, ease of scoring and locus-specificity, across five populations. The observed and expected heterozygosities ranged from 0.026 to 0.976 and 0.026 to 0.928, respectively, while the mean number of alleles per locus per population was 8.73. These microsatellite markers are informative and will be useful for conservation genetic study, individual identification and timber tracking.

The inheritance of glyphosate-resistant goosegrass was studied by making reciprocal crosses between resistant (R) and susceptible (S) biotypes. Eighty-four F1hybrids were confirmed using isozyme analyses. Reciprocal F1hybrids displayed uniform levels of resistance intermediate (I) to that of the parental types, with no indication of maternal inheritance. The F1hybrids were selfed to produce F2populations. F3populations were produced by selfing resistant and intermediate F2phenotypes. A segregation ratio of 1:2:1 (S:I:R) was observed in the F2and subsequently in the F3generations derived from selfing intermediate F2phenotypes. Individuals in F3families derived from selfing resistant F2phenotypes were resistant. Results from the present study show that glyphosate resistance in goosegrass is inherited as a single, nuclear, and incompletely dominant gene.

Premise of the study Aggressive collections and trade activities in recent decades have resulted in heavy pressure on the natural stands of Aquilaria malaccensis and concerns over its long-term survival potential. To aid DNA profiling and assessment of its genetic diversity, microsatellite markers were developed for the species. Methods and results Seventeen polymorphic microsatellite markers were developed for A. malaccensis using an enrichment protocol. The markers were screened on 24 samples from a natural population. The number of alleles ranged from two to 11, and the observed heterozygosity ranged from 0.042 to 0.957. No significant deviation from Hardy-Weinberg equilibrium was detected after conservative Bonferroni correction. Conclusions This is the first report on the development of microsatellite markers in A. malaccensis. The markers will be used to establish a DNA profiling database and to estimate the genetic diversity and population genetic structure of the species.

 Premise of the study : Microsatellite markers of an important medicinal plant, Eurycoma longifolia (Simaroubaceae), were developed for DNA profi ling and genetic diversity studies.  Methods and Results : Eighteen polymorphic microsatellite loci were developed for E. longifolia . The primers were designed from a genomic library enriched for dinucleotide (CT) repeats and screened on 32 samples from a natural population. The number of alleles detected per locus ranged from four to 16, while the observed heterozygosity ranged from 0.097 to 0.938. No signifi cant deviation from Hardy – Weinberg equilibrium was detected in all the 18 loci, and no linkage disequilibrium was found between these loci after conservative Bonferroni correction.  Conclusions : The 18 microsatellite markers of E. longifolia are highly polymorphic and informative. These markers would serve as an important tool for DNA profi ling and genetic diversity studies.

Nine polymorphic microsatellite markers were isolated and characterized in Shorea platyclados (Dipterocarpaceae) using CT-enriched library method. The polymorphism of the microsatellite loci was analyzed by screening 98 samples from a natural population. The number of alleles per locus ranged from 4 to 12, with an average of 8.22 per locus, and the observed heterozygosity ranged from 0.204 to 0.888 (average 0.562). These microsatellite loci will be useful for population genetic studies on S. platyclados and adding genetic information for hill dipterocarps.

Premise of the study: Microsatellite markers were isolated and characterized in Shorea platyclados (Dipterocarpaceae) for DNA profiling and genetic diversity assessment of this tropical timber species. Methods and Results: Fifteen polymorphic microsatellite loci were developed and characterized in S. platyclados using a genomic library enriched for dinucleotide (CT) repeats. The primers amplified dinucleotide repeats with 3–14 alleles per locus across four natural populations. The observed and expected heterozygosities ranged from 0.292 to 1.000 and from 0.301 to 0.894, respectively. No significant deviation from Hardy–Weinberg equilibrium was detected in the 15 loci. Four loci pairs displayed linkage disequilibrium. Conclusions: These highly polymorphic markers are adequate for DNA profiling and studies of population genetics in S. platyclados.

Premise of the study: The exploitation of Labisia pumila for commercial demand is gradually increasing. It is therefore important that conservation is prioritized to ensure sustainable utilization. We developed microsatellites for L. pumila var. alata and evaluated their polymorphism across var. alata, var. pumila, and var. lanceolata. Methods and Results: Ten polymorphic microsatellites of L. pumila were developed using the magnetic bead hybridization selection approach. A total of 84, 48, and 66 alleles were observed in L. pumila var. alata, var. pumila, and var. lanceolata, respectively. The species is likely a tetraploid, with the majority of the loci exhibiting up to four alleles per individual. Conclusions: This is the first report on the development of microsatellites in L. pumila. The microsatellites will provide a good basis for investigating the population genetics of the species and will serve as a useful tool for DNA profiling.

The in-house production of fluorescently labelled internal size standard offers the advantage of cost saving over the commercial size standard in microsatellite genotyping. Based on the reported in-house internal size standard protocol, we have improved the method by generating 21 DNA fragments (in a standard named as HM- 400) with each size similar to that of the commercial size standard. The consistent amplification of the correct fragment size was optimised via primer modulation for non-templated nucleotide addition by Taq DNA polymerase. A total of six microsatellite loci were used to assess the accuracy of HM-400 and the mean standard deviation of the size data was 0.19. The differences between the fragment size means for samples sized using HM-400 and commercial size standard were small with an average of 0.29 bp. The production cost of HM- 400 was only 10% of the cost of commercial size standard.