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Elodia Sánchez, William Solano, Andrés Gatica-Arias, Max Chavarría and Emanuel Araya-Valverde

Abstract: A large collection of coffee genetic resources is conserved in Costa Rica.
In this study, microsatellite DNA fingerprinting of coffee through singleplex and
multiplex PCR approaches coupled with capillary electrophoresis are described.
To validate both methods, germplasm of Coffea spp. (Arabica and non-Arabica)
and intraspecific F1 hybrids were analyzed using fourteen microsatellite markers.
It was observed that through both PCR methods the fingerprinting profile of a
subset of samples was identical. The genetic analyses revealed that non-Arabica
coffee displayed greater genetic variation than Arabica coffee did. In addition,
microsatellite analyses allowed the separation of C. arabica from other species
using the principal coordinate analysis (PCoA) approach. The neighbor-joining
tree clustering analysis revealed either a grouping of wild genotypes separated
from cultivars of C. arabica, or a relation of intraspecific F1 hybrids with parental
lines. The utility of our methodology for the characterization of F1 hybrids not
previously analyzed through SSR (Simple Sequence Repeats) fingerprinting is
demonstrated.

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