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<p>Abstract</p> <p>Background</p> <p>The gene <it>FLOWERING LOCUS T </it>(<it>FT</it>) and its orthologues play a central role in the integration of flowering signals within <it>Arabidopsis </it>and other diverse species. Multiple copies of <it>FT</it>, with different <it>cis</it>-intronic sequence, exist and appear to operate harmoniously within polyploid crop species such as <it>Brassica napus </it>(AACC), a member of the same plant family as <it>Arabidopsis</it>.</p> <p>Results</p> <p>We have identified six <it>BnFT </it>paralogues from the genome of <it>B. napus </it>and mapped them to six distinct regions, each of which is homologous to a common ancestral block (E) of <it>Arabidopsis </it>chromosome 1. Four of the six regions were present within inverted duplicated regions of chromosomes A7 and C6. The coding sequences of <it>BnFT </it>paralogues showed 92-99% identities to each other and 85-87% identity with that of <it>Arabidopsis</it>. However, two of the paralogues on chromosomes A2 and C2, <it>BnA2.FT </it>and <it>BnC2.FT</it>, were found to lack the distinctive CArG box that is located within intron 1 that has been shown in <it>Arabidopsis </it>to be the binding site for theFLC protein. Three <it>BnFT </it>paralogues (<it>BnA2.FT</it>, <it>BnC6.FT.a </it>and <it>BnC6.FT.b</it>) were associated with two major QTL clusters for flowering time. One of the QTLs encompassing two <it>BnFT </it>paralogues (<it>BnC6.FT.a </it>and <it>BnC6.FT.b</it>) on chromosome C6 was resolved further using near isogenic lines, specific alleles of which were both shown to promote flowering. Association analysis of the three <it>BnFT </it>paralogues across 55 cultivars of <it>B. napus </it>showed that the alleles detected in the original parents of the mapping population used to detect QTL (NY7 and Tapidor) were ubiquitous amongst spring and winter type cultivars of rapeseed. It was inferred that the ancestral <it>FT </it>homologues in <it>Brassica </it>evolved from two distinct copies, one of which was duplicated along with inversion of the associated chromosomal segment prior to the divergence of <it>B. rapa </it>(AA) and <it>B. oleracea </it>(CC). At least ten such inverted duplicated blocks (IDBs) were identified covering a quarter of the whole <it>B. napus </it>genome.</p> <p>Conclusion</p> <p>Six orthologues of <it>Arabidopsis FT </it>were identified and mapped in the genome of <it>B. napus </it>which sheds new light on the evolution of paralogues in polyploidy species. The allelic variation of <it>BnFT </it>paralogues results in functional differences affecting flowering time between winter and spring type cultivars of oilseed <it>Brassica</it>. The prevalent inverted duplicated blocks, two of which were located by four of the six <it>BnFT </it>paralogues, contributed to gene duplications and might represent predominant pathway of evolution in <it>Brassica</it>.</p>