The objective of this work is to present an appropriate set of RAPD (random amplified polymorphic DNA) markers using single and multiplex PCR analysis suitable for the characterization of the endemic Cuban species Carica cubensis and the establishment of genetic relationships with the cultivated species Carica papaya. RAPD markers presented a high level of polymorphism. In addition, the incorporation of more than one RAPD primer in the PCR analysis increased the number of obtained bands and the polymorphism of these bands. A total of 73 RAPD bands were detected (45 of them polymorphic) with the nine RAPD markers assayed using single and multiplex PCR analysis. Results demonstrated a reduced genetic variability within the tested Carica cubensis accessions. The observed clustering in this species could be better explained according to geographic proximity and can indicate the similar precedence of the isolated studied populations. C. cubensis seem to be subspecies of C. papaya adapted to the environmental conditions of the mountains of Cuba or a endemic species close to C. papaya. The implications of these results in the creation of effective germplasm core collection in Carica species have been also discussed.
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