Illegal logging poses a significant threat to the sustainability of Malaysian forest
ecosystems. Presently, foresters have to depend on wood anatomical evidences to
link the suspected timber thefts to the source trees but this is inconclusive. This study
was aimed to utilize DNA markers in plant DNA fingerprinting for forensic
applications using Neobalanocarpus heimii as a model. To generate a comprehensive
DNA database of N. heimii for individual identification, 30 natural populations were
identified from 27 forest reserves, and a total of 1081 individuals were collected
throughout Peninsular Malaysia. An extensive evaluation of 51 short tandem repeat
(STR) loci developed for Dipterocarpaceae managed to identify 12 STR loci, which
showed specific amplification, absence of null alleles, single-locus mode of
inheritance, and absence of mononucleotide repeat motifs in N. heimii. Cluster
analyses via assignment test and genetic distance divided the 30 populations into
three genetic clusters, corresponding to three geographical regions: Region A (west),
Region B (central and south) and Region C (northeast). DNA databases of N. heimii
were constructed and characterized at the levels of population, region and Peninsular
Malaysia. Independence tests showed that the majority of the loci significantly deviated from Hardy-Weinberg equilibrium due to population substructuring and
inbreeding. Thus, the match probability of N. heimii should be estimated using the
‘subpopulation-cum-inbreeding model’ that adjusted for coancestry (θ) and
inbreeding (f) coefficients. The conservativeness tests showed that both the regional
and Peninsular Malaysian databases were conservative and should be adequate to
predict allele and genotype frequencies of N. heimii throughout Peninsular Malaysia.
With a combined power of discrimination of more than 0.99999999999999999, the
Peninsular Malaysian database should be able to provide legal evidences for court
proceedings against illegal loggers on N. heimii. The comprehensive DNA
fingerprinting databases developed for N. heimii are the first reported for a tropical
tree species and the methodology developed should be able to serve as a model for
the study of other important timber species in Malaysia. The availability of DNA
fingerprinting databases for the majority of important timber species in Malaysia
would enhance the capacity of Forest Department officials to curb the problem of
illegal logging and this would indirectly ensure the conservation and sustainable
utilization of forest resources in Malaysia