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Abstract International timber trade communities are increasingly demanding that timber in the wood supply chain be sourced from sustainably harvested forests and certified plantations. This is to combat illegal logging activities to prevent further depletion of our precious forests worldwide. Hence, timber tracking tools are important to support law enforcement officials in ensuring only sustainably harvested timbers are traded in the market. In this study, we developed chloroplast DNA (cpDNA) and simple sequence repeat (SSR) databases as tracking tools for an important tropical timber tree species, Shorea leprosula from Peninsular Malaysia. A total of 1410 individual trees were sampled from 44 natural populations throughout Peninsular Malaysia. Four cpDNA regions were used to generate a cpDNA haplotype database, resulting in a haplotype map comprising 22 unique haplotypes derived from 28 informative intraspecific variable sites. This cpDNA database can be used to trace the origin of an unknown log at the regional level. Ten SSR loci were used to develop the SSR allele frequency database. Bayesian cluster analysis divided the 44 populations into two genetic clusters corresponding to Region A and Region B. Based on conservativeness evaluation of the SSR databases for individual identification, the coancestry coefficients (θ) were adjusted to 0.1900 and 0.1500 for Region A and B, respectively. These databases are useful tools to complement existing timber tracking systems in ensuring only legally sourced timbers are allowed to enter the wood supply chain.

Ng, Kobayashi, et al. present the genome assembly for the dipterocarp Shorea leprosula and present transcriptome data for ten more dipterocarp species of seven genera. The Shorea leprosula genome, along with drought stress experiments, demonstrate evidence for a whole-genome duplication (WGD) event dated to the Cretaceous-Paleogene boundary, with WGD duplicates enriched in genes upregulated during the drought response.

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.

The maintenance of mixed mating was studied in Shorea curtisii, a dominant and widely distributed dipterocarp species in Southeast Asia. Paternity and hierarchical Bayesian analyses were used to estimate the parameters of pollen dispersal kernel, male fecundity and self-pollen affinity. We hypothesized that partial self incompatibility and/or inbreeding depression reduce the number of selfed seeds if the mother trees receive sufficient pollen, whereas reproductive assurance increases the numbers of selfed seeds under low amounts of pollen. Comparison of estimated parameters of self-pollen affinity between high density undisturbed and low density selectively logged forests indicated that self-pollen was selectively excluded from mating in the former, probably due to partial self incompatibility or inbreeding depression until seed maturation. By estimating the self-pollen affinity of each mother tree in both forests, mother trees with higher amount of self-pollen indicated significance of self-pollen affinity with negative estimated value. The exclusion of self-fertilization and/or inbreeding depression during seed maturation occurred in the mother trees with large female fecundity, whereas reproductive assurance increased self-fertilization in the mother trees with lower female fecundity.

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.

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.

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

To evaluate the effect of flowering tree density on genetic variation in a dominant tree species, genetic diversities and outcrossing rates of Shorea curtisii (Dipterocarpaceae) were compared between undisturbed and selectively logged forests using microsatellite markers. The mean heterozygosity and the effective number of alleles per locus in the selectively logged plot were not significantly different from those of the undisturbed plot. However, the average number of alleles derived from the pollen donor was significantly lower in the selectively logged forests, indicating the possibility of a loss of genetic variation in future generations. The average outcrossing rate for 11 trees in an undisturbed plot was 96.3%, which was similar to other reports from dipterocarp species based on isozyme analysis. However, the outcrossing rate in the selectively logged plot was 52.2% for five trees, which was significantly lower than that in the undisturbed plot. This decline of outcrossing rate in the selectively logged plot may result from the much lower density of conspecific flowering trees, and the high rate of selfing may result in inbreeding depression and/or a decrease in genetic variation of this forest in future generations. [ABSTRACT FROM AUTHOR]

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-einberg 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. [ABSTRACT FROM AUTHOR]

• Premise of the study: Microsatellite markers of an important medicinal plant, Eurycoma longifolia (Simaroubaceae), were developed for DNA profiling 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 significant 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 profiling and genetic diversity studies. [ABSTRACT FROM AUTHOR]

Premise of the study: Microsatellite markers were developed for Johannesteijsmannia lanceolata to assess the genetic diversity and mating system of this alarmingly endangered species. Methods and Results: A total of 31 polymorphic microsatellite markers were developed for J. lanceolata using the enrichment protocol. These markers were screened on 24 samples from a natural population. The number of alleles ranged from four to 20, while the observed heterozygosity ranged from 0.391 to 1.000. The 31 loci were further tested for transferability on J. altifrons , J. magnifi ca , and J. perakensis . Generally, all loci showed positive amplifi cations in these three Johannesteijsmannia species, except Jla 124 ( J. magnifica ) and Jla 168b ( J. magnifi ca and J. perakensis ). Conclusions: These microsatellite markers could be employed to study the population genetics and mating system of J. lanceolata and other Johannesteijsmannia species. [ABSTRACT FROM AUTHOR]