Comparison of ISSR and RAPD markers to characterize three Chilean Nothofagus species

The present study is the first report of fingerprinting on three Chilean Nothofagus species using ISSR and RAPD markers; 61 Nothofagus nervosa, 32 Nothofagus obliqua and 32 Nothafagus dombeyi individual trees, sampled from collection and natural sites, were analyzed. Among 45 primers tested, the 6 ISSR and 6 RAPD primers selected for the analysis generated a total of 63 ISSR and 42 RAPD fragments. A high proportion of polymorphic bands, ranging from 97% and 80%, was found using both markers. A similar number of private and marker bands was generated by both markers in all the species examined and one discriminant ISSR fragment was obtained for N. dombeyi. Jaccard and Dice similarity indices were used to evaluate pairwise genetic divergence; cluster analysis of the similarity matrices was performed to estimate the intra- and inter-specific genetic diversity, and PCA analysis was employed to evaluate the resolving power of the markers to differentiate between the species. These analyses, carried out for both markers, allowed us to identify three main groups corresponding to the three Nothofagus species. The results of the present study can be seen as a starting point for future researches on the population and evolutionary genetics of these species.