Natural variation in autumn expression is the major adaptive determinant distinguishing Arabidopsis FLC haplotypes.

In winter is registered during vernalization through the temperature-dependent repression and epigenetic silencing of floral repressor . Natural Arabidopsis accessions show considerable variation in vernalization. However, which aspect of the repression mechanism is most important for adaptation to different environments is unclear. By analysing dynamics in natural variants and mutants throughout winter in three field sites, we find that autumnal expression, rather than epigenetic silencing, is the major variable conferred by the distinct Arabidopsis haplotypes. This variation influences flowering responses of Arabidopsis accessions resulting in an interplay between promotion and delay of flowering in different climates to balance survival and, through a post-vernalization effect, reproductive output. These data reveal how expression variation through non-coding cis variation at has enabled Arabidopsis accessions to adapt to different climatic conditions and year-on-year fluctuations.