The second generation reference genetic map of B. rapa and its alignment onto the Arabidopsis genome sequence (linkage groups A1, A2, A3, A4 and A5). Cumulative recombination distances are shown to the left and marker loci to the right of the linkage groups. SSR markers developed from the BAC sequences are designated in bold strokes. The correspondence between the SSR markers and the BAC clones is given in Additional file 2. The colored bars to the right of the linkage groups indicate Arabidopsis chromosomes (chromosome 1: light blue; chromosome 2: yellow; chromosome 3: dark blue; chromosome 4: green; chromosome 5: red), representing the synteny blocks between the two genomes. The synteny blocks identified by Schranz et al.  are embedded in the colored bars. New blocks proposed in this study, not identified by Schranz et al. , are marked with red lines. The numbers to the right of the colored bars indicate aligned positions on Arabidopsis chromosomes in megabase pairs (Mb). Arabidopsis chromosomes are not to scale.