We found that, besides the FLM promoter, also intron 1 sequences were essential for FLM basal expression and subsequently identified by phylogenomic footprinting a conserved 373 bp intron 1 region essential for FLM basal expression (Figure 2). Further, through association analyses using genomic sequence information, we uncovered FLM regulatory regions (PRO2+ and INT6+) that control temperature-dependent FLM expression in a haplotype-specific manner (Figure 4). While most PRO2+ and INT6+ haplotypes displayed differential basal but temperature-sensitive FLM expression, correlating strongly with changes in flowering time, one INT6+ variant, INT6+CAA, was strongly compromised in temperature-sensitive FLM regulation and flowering pointing at the importance of this intronic region for flowering time adaptation (Figures 4 and 6).