The demand for blackberries (Rubus spp.) has increased in Costa Rica, which represents an important income for small farmers in the country. The material grown in Costa Rica consists of four species and nine genotypes, mostly landraces of R. adenotrichos and is grown from southern Mexico, to northern South America. Costa Rica possesses diversity of Rubus with desirable economic traits, such as high ORAC values, but little is known about their genetics and genomics. In this study, genotypes were analyzed using 9 RAPD, and 13 SSR markers as well as using preliminary flow cytometry work. Nei’s genetic distances were calculated, and the UPGMA procedure was used. ‘Qualicum’, ‘Tulameen’ and ‘Navaho’ were comparative controls. Both RAPD and SSR analyses concurred with morphological data except for R. urticifolius ld. ‘Caballo’, which showed a closer relationship to R. adenotrichos landraces than R. urticifolius ld. ‘Ratón’. Although, R. urticifolius was reported as a diploid, allelic patterns were similar to that of a tetraploid. R. glaucus was reported as a blackberry-raspberry hybrid; both RAPD and SSR analyses support this as the genotype showed the closest relationship to R. idaeus. Flow cytometry analyses showed that R. adenotrichos landraces were diploid. Ploidy measurements for all other genotypes are underway to determine whether different ploidy levels can be found in R. urticifolius, or that ‘Caballo’ is a different species from ‘Ratón’. Genetic relationships and ploidy information is crucial to breeders for determining crossing compatibly among the genotypes, and initializing a competent breeding program in the future.
