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Background  The amphiploid species  Brassica napus  (oilseed rape, Canola) is a globally important oil crop yielding food, biofuels and industrial compounds such as lubricants and surfactants. Identification of the likely ancestors of each of the two genomes (designated A and C) found in  B. napus  would facilitate incorporation of novel alleles from the wider  Brassica  genepool in oilseed rape crop genetic improvement programmes. Knowledge of the closest extant relatives of the genotypes involved in the initial formation of  B. napus  would also allow further investigation of the genetic factors required for the formation of a stable amphiploid and permit the more efficient creation of fully fertile re-synthesised  B. napus . We have used a combination of chloroplast and nuclear genetic markers to investigate the closest extant relatives of the original maternal progenitors of  B. napus . This was based on a comprehensive sampling of the relevant genepools, including 83 accessions of A genome  B. rapa  L. (both wild and cultivated types), 94 accessions of  B. napus  and 181 accessions of C genome wild and cultivated  B. oleracea  L. and related species.    Results  Three chloroplast haplotypes occurred in  B. napus . The most prevalent haplotype (found in 79% of accessions) was not present within the C genome accessions but was found at low frequencies in  B. rapa . Chloroplast haplotypes characteristic of  B. napus  were found in a small number of wild and weedy  B. rapa  populations, and also in two accessions of cultivated  B. rapa  'brocoletto'. Whilst introgression of the  B. napus  chloroplast type in the wild and weedy  B. rapa  populations has been proposed by other studies, the presence of this haplotype within the two brocoletto accessions is unexplained.    Conclusions  The distribution of chloroplast haplotypes eliminate any of the C genome species as being the maternal ancestor of the majority of the  B. napus  accessions. The presence of multiple chloroplast haplotypes in  B. napus  and  B. rapa  accessions was not correlated with nuclear genetic diversity as determined by AFLPs, indicating that such accessions do not represent recent hybrids. Whilst some chloroplast diversity observed within  B. napus  can be explained by introgression from inter-specific crosses made during crop improvement programmes, there is evidence that the original hybridisation event resulting in to  B. napus  occurred on more than one occasion, and involved different maternal genotypes.

Origins of the amphiploid species Brassica napus L. investigated by chloroplast and nuclear molecular markers