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

The evolution of Brassica napus FLOWERING LOCUST paralogues in the context of inverted chromosomal duplication blocks