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Background  Several major crop species are current or ancient polyploids. To better describe the genetic factors controlling traits of agronomic interest (QTL), it is necessary to understand the structural and functional organisation of these QTL regions in relation to genome duplication. We investigated quantitative resistance to the fungal disease stem canker in  Brassica napus,  a highly duplicated amphidiploid species, to assess the proportion of resistance QTL located at duplicated positions.    Results  Genome-wide association analysis on a panel of 116 oilseed rape varieties genotyped with 3228 SNP indicated that 321 markers, corresponding to 64 genomic regions, are associated with resistance to stem canker. These genomic regions are relatively equally distributed on the A (53%) and C (47%) genomes of  B. napus . Overall, 44% of these regions (28/64) are duplicated homoeologous regions. They are located in duplications of six (E, J, R, T, U and W) of the 24 ancestral blocks that constitute the  B. napus  genome. Overall, these six ancestral blocks have 34 duplicated copies in the  B.napus  genome. Almost all of the duplicated copies (82% of the 34 regions) harboured resistance associated markers for stem canker resistance, which suggests structural and functional conservation of genetic factors involved in this trait in  B. napus.Conclusions  Our study provides information on the involvement of duplicated loci in the control of stem canker resistance in  B. napus . Further investigation of the similarity/divergence in sequence and gene content of these duplicated regions will provide insight into the conservation and allelic diversity of the underlying genes.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-498) contains supplementary material, which is available to authorized users.

Homoeologous duplicated regions are involved in quantitative resistance of Brassica napus to stem canker