Whereas the PRO2+ and INT6+ polymorphisms tested affected FLM transcript abundance, the molecular causes of these transcription changes varied among the different polymorphisms (Figures 4 and 7). Deletion of a 225 bp promoter region including the PRO2+ polymorphic site was associated with tenfold reduced levels of FLM pre-mRNA indicating that this promoter region was essential for FLM expression (Figure 7). A twofold relative difference of FLM-ß levels was found when comparing the PRO2+GATAC and PRO2+AAACC variants with the lowest and highest FLM-ß expression, respectively, and our linear model would predict a flowering time difference of 14.4 leaves at 15°C (Figures 4 and 5). The PRO2+ region harbours a predicted MADS-box transcription factor binding site and several instances of auto- or cross-regulation of MADS-box factors have been described (de Folter et al., 2005; Kaufmann et al., 2009; Smaczniak et al., 2012). It can therefore be envisioned that FLM expression is regulated by MADS-box transcription factors and that PRO2+ polymorphisms modulate the efficiency or specificity of these binding events and thereby modulate basal FLM expression.