AbstractBackgroundThe Rosaceae encompass a large number of economically-important diploid and polyploid fruit and ornamental species in many different genera. The basic chromosome numbers of these genera arex= 7, 8 and 9 and all have compact and relatively similar genome sizes. Comparative mapping between distantly-related genera has been performed to a limited extent in the Rosaceae including a comparison betweenMalus(subfamily Maloideae) andPrunus(subfamily Prunoideae); however no data has been published to date comparingMalusorPrunusto a member of the subfamily Rosoideae. In this paper we compare the genome ofFragaria, a member of the Rosoideae, toPrunus, a member of the Prunoideae.ResultsThe diploid genomes ofPrunus(2n=2x= 16) andFragaria(2n=2x= 14) were compared through the mapping of 71 anchor markers – 40 restriction fragment length polymorphisms (RFLPs), 29 indels or single nucleotide polymorphisms (SNPs) derived from expressed sequence tags (ESTs) and two simple-sequence repeats (SSRs) – on the reference maps of both genera. These markers provided good coverage of thePrunus(78%) andFragaria(78%) genomes, with maximum gaps and average densities of 22 cM and 7.3 cM/marker inPrunusand 32 cM and 8.0 cM/marker inFragaria.ConclusionOur results indicate a clear pattern of synteny, with most markers of each chromosome of one of these species mapping to one or two chromosomes of the other. A large number of rearrangements (36), most of which produced by inversions (27) and the rest (9) by translocations or fission/fusion events could also be inferred. We have provided the first framework for the comparison of the position of genes or DNA sequences of these two economically valuable and yet distantly-related genera of the Rosaceae.