Comparative assessment of microsatellite and retrotransposon-based markers for genetic characterization of commercial banana cultivars (Musa spp.)

Abstract

Banana cultivars of agronomic interest have been genetically characterized using two different molecular markers. On the one hand, a panel of 14 trinucleotide single sequence repeats (SSRs or microsatellites) was optimized for homogeneous PCR conditions. It was tested with 50 individuals from seven cultivars, yielding 76 alleles and 5.4 ± 1.8 alleles per locus, while the presence of cultivar-exclusive alleles allowed the discrimination of all cultivars. On the other hand, a retrotransposon-based marker system named inter-primer binding site (iPBS) was implemented for the first time in the Musa genus. A total of 120 bands were detected in eight different Musa cultivars, from which 65.8% were polymorphic and 23.3% were cultivar exclusive. Both techniques allowed a cut-off identification of all cultivars studied, but overall, iPBS analysis was a more straightforward and economical choice. Despite the fact that we were unable to distinguish local banana varieties belonging to the same cultivar, new cultivar-specific molecular markers have been developed for the Musa genus, which could be used to guide new breeding programmes and maintain high quality of Plátano de Canarias.