Estimation of genetic diversity and evaluation of plant germplasm is the most important step in
collection and management of plant genetic resources. Also, comparison of different DNA-based
genetic markers in diversity evaluation and then advising the most efficient markers is very important.
In order to investigate genetic variation among Persian oak (Quercus brantii Lindi.) populations of
Lorestan province (Iran), 20 genotypes were collected from different geographical and climatic
regions. After DNA extraction, polymerase chain reactions (PCR) were used for study of
polymorphism using three markers including ISJ, ISSR and SCoT. Genotyping was performed using
the polymorphic bands obtained from all three markers separately, and also by combining the data of
three markers. PCR results of the primers showed 91 polymorphic bands with an average of 71% per
locus. The ISSR marker with 44 bands had the most polymorphic bands. Genotypes were
discriminated by ISJ, ISSR and SCoT markers in 5, 6 and 5 groups, respectively, and using the
combined data of three markers, genotypes were classified in 5 groups (each group included more than
one genotype) and 3 group (each group included one genotype). The results showed that the obtained
clustering by different markers were nearly consistent with clustering of genotypes based on the
climatic origin of genotypes. The most similarity between the groupings was between ISJ and ISSR
markers with 89%. Overall, the results indicated the usefulness of markers used to estimate genetic
distances between different oak communities.