To find polymorphisms regulating FLM expression and splicing, we performed a genotype-phenotype association analysis. Since the vernalization pathway strongly delayed flowering in 24 of the 54 accessions and consequently suppressed FLM effects, we used FLM expression as a phenotype for the association analysis (Figure 3—figure supplement 2A). To ascertain that FLM expression was not affected by FLC, we examined FLM in non-vernalized wild type Col-0 and flc-3 mutants as well as in Col-0 carrying a functional vernalization module (Michaels and Amasino, 1999). Concurrent with previous reports, we did not detect an influence of FLC on FLM transcript abundance in our conditions (Figure 3—figure supplement 2B) (Scortecci et al., 2001; Ratcliffe et al., 2001). We then obtained FLM expression data from the FLM haplotype set and measured total FLM transcript levels as well as FLM-ß and FLM-δ levels at 15°C or 23°C (Supplementary file 3). In line with the reported behaviour of FLM in Col-0, we observed that FLM-ß expression decreased (on average 0.6 fold) and FLM-δ increased (on average 1.4 fold) with increasing temperature in most accessions (Figure 3B and Supplementary file 3) (Lee et al., 2013; Posé et al., 2013; Lutz et al., 2015). At the same time, we also observed substantial variation in FLM-ß and FLM-δ expression between the accessions of the FLM haplotype set, inviting the conclusion that non-coding sequence variation modulates FLM expression (Figure 3B and Supplementary file 3). Since total FLM transcript levels strongly correlated with FLM-ß but not with FLM-δ abundance at 15°C and at 23°C, it could be suggested that FLM-ß represents the major FLM form among the FLM transcripts (Figure 3—figure supplement 3A,B).