<p>Abstract</p> <p>Background</p> <p>The complex genome of rapeseed (<it>Brassica napus</it>) 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 <it>B. napus</it> representing eight different germplasm types to sequence genome-wide distributed restriction-site associated DNA (RAD) fragments for polymorphism detection and genotyping.</p> <p>Results</p> <p>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 <it>Brassica rapa</it> reference sequence. An even distribution of RAD clusters and polymorphisms was observed across the <it>B. rapa</it> chromosomes, which suggests that there might be an equal distribution over the <it>Brassica oleracea</it> 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.</p> <p>Conclusions</p> <p>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 <it>B. napus</it>.</p
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