To examine the effects of the non-coding sequence variations in a homogenous background, we transformed the deletion accession Nd-1 with FLMCol-0 variants carrying the PRO1, PRO2+ and INT6+ polymorphisms or deletions of PRO2+ (PRO2+Δ16bp) and INT6+ (INT6+Δ17bp) (Figure 4C,D). Additionally, we transformed variants with deletions of between two and six PolyA stretches (PolyA_2xΔa, PolyA_2xΔb, PolyA_3xΔ, PolyA_4xΔ, PolyA_5xΔ, PolyA_6xΔ; Figure 4D and Figure 4—figure supplement 1A). Using pooled T2 segregating lines (n = 18–45) for each of the transgenes, we analysed the effects of the sequence variation on FLM-ß and FLM-δ expression at 15°C and 23°C. The PRO1- deletion, as present in the FLMCol-0 reference, did not reveal differences in FLM transcript levels when compared to PRO1T (FLMCol-0) (Fig. Figure 4—figure supplement 1B,C). However, two PRO2+ (PRO2+GGAAC, PRO2+AAACC) and three INT6+ variants (INT6+ACA, INT6+CAC and INT6+AAA) displayed an upregulation of FLM-ß at 15°C when compared to FLMCol-0 (Figure 4E). Increases and decreases of FLM-δ levels largely followed those of FLM-ß levels except for INT6+AAA, which showed an upregulation exclusively of FLM-ß (Figure 4E,F). The deletion variant PRO2+Δ16bp showed upregulation of FLM-ß but INT6+Δ17bp did not have significantly altered FLM-ß and FLM-δ levels when compared to FLMCol-0 (Figure 4E,F). We concluded that the identity of these regions rather than their presence controlled FLM expression and temperature-sensitive FLM regulation. The PolyA motif deletion variants showed gradually decreasing FLM-ß and FLM-δ levels with an increasing number of deletions while the deletion of all six PolyA motifs (PolyA_6xΔ) had an especially strong effect on FLM-ß expression and its temperature-sensitive expression (Figure 4E,F and Figure 4—figure supplement 1B,C). Thus, the PolyA motifs possess a regulatory role but may function in a redundant manner.