Unlike other important crops analyzed so far for genetic diversity and population structure, the brief
history and particularities of the genetics of the cultivated strawberry (Fragaria ·ananassa Duchesne) have limited its
genetic characterization. The genomic composition and the pattern of inheritance have not been fully elucidated,
although a number of studies have suggested a highly diploidized genome. In this study, the similarity relationships
and structure of 92 selected strawberry cultivars with widely diverse origins have been established using simple
sequence repeat (SSR) markers derived from expressed sequence tags (EST-SSR markers). Genetic analysis
performed by the unweighted pair group method with arithmetic mean clustering revealed a distribution according
to both date of cultivar release and breeding for a specific climatic adaptation. Additionally, a model-based clustering
approach identified three populations among the strawberry cultivars with an overall FST value of 0.15 to 0.16. Both
analyses support a limited differentiation of modern cultivars, most probably as a consequence of the methodology of
strawberry breeding. Interestingly, the collection of strawberry cultivars here analyzed showed comparable genetic
differentiation to that observed in natural populations of Fragaria chiloensis (L.) Mill., one of its wild ancestors. Our
results suggest that breeding has produced a small but significant reduction on the genetic diversity of F. ·ananassa.
The panel of 10 EST-SSRs described in this work provided an extremely low probability of confusion (less than 10–11),
offering an efficient and accurate method for cultivar identification.