Map-based cloning (MBC) strategies have been successfully used in the stone fruits to narrow in on the target genes (Bielenberg et al. 2004; Romero et al. 2004; Boudehri et al. 2009; Esmenjaud et al. 2009; Sajer et al. 2012) and will be even more useful, now that the genome sequence of peach (Prunus persica) is available (https://www.jgi.doe.gov/; https://services. applied genomics.org/projects/drupomics/). However, there have been two limitations of this strategy. Firstly, MBC approaches have always been extremely time-consuming. Secondly, if the function of the gene of interest is unknown or no corresponding gene has been isolated from another species, either because it is not present in other species or has not been investigated so far, there are not many options open in stone fruits. Nevertheless, there are some advantages for map-based cloning approaches in stone fruits. Most Prunus species are diploid, peach as a model species within the Rosaceae has a small genome size and is rich in simple sequence repeat (SSR) markers, which showed a high transferability in the genus Prunus (Genome Database for Rosaceae, www.rosaceae.org; Mnejja et al. 2010). The high level of colinearity among genomes of different Prunus species (Dirlewanger et al. 2004) allowed the construction of a Prunus reference genetic and framework physical map (Dirlewanger et al. 2004; Zhebentyayeva et al. 2008), which proved to be very useful tools in MBC approaches. Since 1st April 2010 the peach genome sequence can be publicly accessed (https:// www.jgi.doe.gov/), which will be considerably helpful for ongoing and future MBC approaches. Apart from simple genetic traits, polygenic traits or traits with large natural variation in the phenotype, which can only be addressed by quantitative trait loci (QTL) analyses, simply require MBC to identify the genes behind the trait (Peters et al. 2003). With the peach genome sequence and effi cient marker technologies available, MBC has become a very powerful tool for isolation of genes in stone fruits.