The nine PRO2+/INT6+ haplotype combinations included in our transgenic experiments represent 69% of the world-wide PRO2+/INT6+ variation (Figure 8—figure supplement 1A,B). We found, that FLM-ß explained around 21% of flowering time in a genetically heterogeneous population of summer-annual Arabidopsis accessions (Figure 8). Hence, PRO2+ and INT6+ haplotypes regulate FLM-ß abundance and, in turn, contribute to flowering time regulation in Arabidopsis accessions (Figures 8 and 9). We consider it not surprising that the correlation of flowering time with FLM-ß levels (21% versus 94%) as well as the responsiveness of flowering time to FLM-ß levels differ between a genetically heterogeneous natural population and the homogenous transgenic population. First, we showed that residual FLC transcript may also slightly contribute to variation of flowering time of summer-annual accessions, possibly interfering with the effects of FLM-ß (Balasubramanian et al., 2006; Li et al., 2006). Further, additional sequence variation in FLM in natural accessions may contribute to relevant expression changes, e.g. in the part of intron 1 identified as essential for FLM expression but not analysed in further detail here (Figure 2). Then, it is possible that these accessions harbour variation in the FLM-related MAF2 - 4, and this variation may differentially affect flowering time, in isolation or in combination with variation of their common interaction partner SVP (Ratcliffe et al., 2003; Airoldi et al., 2015; Scortecci et al., 2003). Bearing these possible genetic and environmental interferences in mind, we regard the detected effect of FLM-ß on flowering (21%) in cool (15°C) temperatures as considerable and suggest that it is rather an underestimation.