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The construction of a reference map of the complex octoploid cultivated strawberry was optimized by comparative mapping between Fragaria showing different levels of ploidy. In addition, this approach is a powerful tool for improving the detection of QTLs, and for a better understanding of the organization of these QTLs. By identifying the homoeologous linkage groups in the complex octoploid cultivated strawberry, potential homoeologous QTLs in Fragaria can be detected. The comparative mapping was based on two populations belonging to two different levels of Fragaria. The linkage map of the complex octoploid cultivated strawberry (Fragaria x ananassa Duch., 2n=8x=56) was based on a segregating population of 213 individuals of a cross between ‘Capitola’ and ‘CF1116’, two genotypes with many contrasting traits. This genetic map was compared to the diploid one, obtained from an interspecific cross between F. vesca and F. bucharica (Sargent et al., 2006). Based on 56 SSR markers common to both diploid and octoploid genetic maps, almost all linkage groups of the genetic octoploid map were arranged into the seven homoeologous groups (HGs) expected for the genus Fragaria, which belongs to the tribe Rosoideae. For each trait, QTLs can potentially be detected on each linkage group belonging to the same HG. Results showed detection of homoeologous chromosomal regions potentially involved in viability of the plant.