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<p>Abstract</p> <p>Background</p> <p>Rapeseed (<it>Brassica napus</it> L<it>.</it>) has spring and winter genotypes adapted to different growing seasons. Winter genotypes do not flower before the onset of winter, thus leading to a longer vegetative growth period that promotes the accumulation and allocation of more resources to seed production. The development of winter genotypes enabled the rapeseed to spread rapidly from southern to northern Europe and other temperate regions of the world. The molecular basis underlying the evolutionary transition from spring- to winter- type rapeseed is not known, however, and needs to be elucidated.</p> <p>Results</p> <p>We fine-mapped the spring environment specific quantitative trait locus (QTL) for flowering time, <it>qFT10-4</it>,in a doubled haploid (DH) mapping population of rapeseed derived from a cross between Tapidor (winter-type) and Ningyou7 (semi-winter) and delimited the <it>qFT10-4</it> to an 80-kb region on chromosome A10 of <it>B. napus</it>. The <it>BnFLC.A10</it> gene, an ortholog of <it>FLOWERING LOCUS C</it> (<it>FLC</it>) in <it>Arabidopsis</it>, was cloned from the QTL. We identified 12 polymorphic sites between <it>BnFLC.A10</it> parental alleles of the TN-DH population in the upstream region and in intron 1. Expression of both <it>BnFLC.A10</it> alleles decreased during vernalization, but decreased more slowly in the winter parent Tapidor. Haplotyping and association analysis showed that one of the polymorphic sites upstream of <it>BnFLC.A10</it> is strongly associated with the vernalization requirement of rapeseed (r^<it>2</it> = 0.93, <it>χ</it>^<it>2</it> = 0.50). This polymorphic site is derived from a <it>Tourist</it>-like miniature inverted-repeat transposable element (MITE) insertion/deletion in the upstream region of <it>BnFLC.A10</it>. The MITE sequence was not present in the <it>BnFLC.A10</it> gene in spring-type rapeseed, nor in ancestral ‘A’ genome species <it>B. rapa</it> genotypes. Our results suggest that the insertion may have occurred in winter rapeseed after <it>B. napus</it> speciation.</p> <p>Conclusions</p> <p>Our findings strongly suggest that (i) <it>BnFLC.A10</it> is the gene underlying <it>qFT10-4</it>, the QTL for phenotypic diversity of flowering time in the TN-DH population, (ii) the allelic diversity caused by MITE insertion/deletion upstream of <it>BnFLC.A10</it> is one of the major causes of differentiation of winter and spring genotypes in rapeseed and (iii) winter rapeseed has evolved from spring genotypes through selection pressure at the <it>BnFLC.A10</it> locus, enabling expanded cultivation of rapeseed along the route of <it>Brassica</it> domestication.</p>