Sequence variation and functional analysis of a <italic>FRIGIDA</italic> orthologue (<italic>BnaA3.FRI</italic>) in <italic>Brassica napus</italic>.

Background: Allelic variation at the <italic>FRIGIDA</italic> (<italic>FRI</italic>) locus is a major contributor to natural variation of flowering time and vernalization requirement in <italic>Arabidopsis thaliana</italic>. Dominant <italic>FRI</italic> inhibits flowering by activating the expression of the MADS box transcriptional repressor <italic>FLOWERING LOCUS C</italic> (<italic>FLC</italic>), which represses flowering prior to vernalization. Four <italic>FRI</italic> orthologues had been identified in the domesticated amphidiploid <italic>Brassica napus</italic>. Linkage and association studies had revealed that one of the <italic>FRI</italic> orthologues, <italic>BnaA3.FRI</italic>, contributes to flowering time variation and crop type differentiation. Results: Sequence analyses indicated that three out of the four <italic>BnaFRI</italic> paralogues, <italic>BnaA3.FRI</italic>, <italic>BnaA10.FRI</italic> and <italic>BnaC3.FRI</italic>, contained a large number of polymorphic sites. Haplotype analysis in a panel of 174 <italic>B. napus</italic> accessions using PCR markers showed that all the three paralogues had a biased distribution of haplotypes in winter type oilseed rape (<italic>P</italic> < 0.01). Association analysis indicated that only <italic>BnaA3.FRI</italic> contributes to flowering time variation in <italic>B. napus</italic>. In addition, transgenic functional complementation demonstrated that mutations in the coding sequence of <italic>BnaA3.FRI</italic> lead to weak alleles, and subsequently to flowering time variation. Conclusion: This study for the first time provides a molecular basis for flowering time control by <italic>BnaA3.FRI</italic> in <italic>B. napus</italic>, and will facilitate predictive oilseed rape breeding to select varieties with favorable flowering time and better adaption to latitude and seasonal shifts due to changing climate. [ABSTRACT FROM AUTHOR]