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Background  The complex genome of rapeseed ( Brassica napus ) is not well understood despite the economic importance of the species. Good knowledge of sequence variation is needed for genetics approaches and breeding purposes. We used a diversity set of  B. napus  representing eight different germplasm types to sequence genome-wide distributed restriction-site associated DNA (RAD) fragments for polymorphism detection and genotyping.    Results  More than 113,000 RAD clusters with more than 20,000 single nucleotide polymorphisms (SNPs) and 125 insertions/deletions were detected and characterized. About one third of the RAD clusters and polymorphisms mapped to the  Brassica rapa  reference sequence. An even distribution of RAD clusters and polymorphisms was observed across the  B. rapa  chromosomes, which suggests that there might be an equal distribution over the  Brassica oleracea  chromosomes, too. The representation of Gene Ontology (GO) terms for unigenes with RAD clusters and polymorphisms revealed no signature of selection with respect to the distribution of polymorphisms within genes belonging to a specific GO category.    Conclusions  Considering the decreasing costs for next-generation sequencing, the results of our study suggest that RAD sequencing is not only a simple and cost-effective method for high-density polymorphism detection but also an alternative to SNP genotyping from transcriptome sequencing or SNP arrays, even for species with complex genomes such as  B. napus .

High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing