Genetic diversity of a Coffea Germplasm Collection assessed by RAPD markers

Genetic diversity and relationships within and among nine species of Coffea, one species of Psilanthus and the Piatã hybrid from the Coffee Germplasm Collection of Instituto Agronômico de Campinas (IAC), Brazil were assessed using RAPD markers. Genetic diversity and relationships were evaluated by proportion of polymorphic loci (P), Shannon’s genetic index (H′ and G′ST) and clustering analysis. The overall RAPD variation among all accessions was mostly partitioned between rather than within species. However, C. canephora and C. liberica showed a high genetic diversity within the species ( $${\underline{\hbox{H}'}} $$ sp = 0.414 and $${\underline{\hbox{H}'}} $$ sp = 0.380, respectively) and this was highly structured (high $${\underline{\hbox{G}'}} $$ ST). Genetic diversity from C. congensis and C. arabica was also structured, but with lower levels of genetic diversity ( $${\underline{\hbox{H}'}} $$ sp = 0.218 and $${\underline{\hbox{H}'}} $$ sp = 0.126, respectively). The results were consistent with agronomic and molecular studies and demonstrated that the IAC Coffea Collection is representative of the phylogenetic structure observed in the genera. This study devises sampling strategies for coffee germplasm collections and provides genetic diversity parameters for future comparisons among them.