AbstractBackgroundThe large number of genetic linkage maps representingBrassicachromosomes constitute a potential platform for studying crop traits and genome evolution withinBrassicaceae. However, the alignment of existing maps remains a major challenge. The integration of these genetic maps will enhance genetic resolution, and provide a means to navigate between sequence-tagged loci, and with contiguous genome sequences as these become available.ResultsWe report the first genome-wide integration ofBrassicamaps based on an automated pipeline which involved collation of genome-wide genotype data for sequence-tagged markers scored on three extensively used amphidiploidBrassica napus(2n = 38) populations. Representative markers were selected from consolidated maps for each population, and skeleton bin maps were generated. The skeleton maps for the three populations were then combined to generate an integrated map for each LG, comparing two different approaches, one encapsulated in JoinMap and the other in MergeMap. The BnaWAIT_01_2010a integrated genetic map was generated using JoinMap, and includes 5,162 genetic markers mapped onto 2,196 loci, with a total genetic length of 1,792 cM. The map density of one locus every 0.82 cM, corresponding to 515 Kbp, increases by at least three-fold the locus and marker density within the original maps. Within theB. napusintegrated map we identified 103 conserved collinearity blocks relative toArabidopsis, including five previously unreported blocks. The BnaWAIT_01_2010a map was used to investigate the integrity and conservation of order proposed for genome sequence scaffolds generated from the constituent A genome ofBrassica rapa.ConclusionsOur results provide a comprehensive genetic integration of theB. napusgenome from a range of sources, which we anticipate will provide valuable information for rapeseed and Canola research.