Temperature-dependent changes in FLM abundance and alternative splicing are critical for flowering time control in ambient temperatures in Arabidopsis. How FLM expression is regulated and whether Arabidopsis accessions have employed differential FLM expression and splicing to adapt to different temperature climates remained to be shown. We previously found that Arabidopsis transgenic lines expressing an intronless FLM from a functional FLM promoter fragment cannot express FLM to detectable levels and fail to rescue the flowering time phenotype of a flm-3 loss-of-function mutant (Lutz et al., 2015). We subsequently compared FLM expression in transgenic lines expressing a genomic FLM fragment, obtained from the Columbia-0 (Col-0) wild type, containing all six introns (pFLM::gFLM; FLMCol-0) with lines expressing the FLM-ß (pFLM::FLM-ß) or FLM-δ (pFLM::FLM-δ) splice variants retaining intron 1 but lacking all other introns (Figure 1A). The presence of intron 1 was sufficient to restore the basal expression of FLM at the ambient temperatures 15°C, 21°C, and 27°C, but introns 2–6 were required for the temperature-sensitive regulation of the splice variants FLM-ß and FLM-δ (Figure 1B). We concluded that intron 1 may contain critical information for FLM expression and introns 2–6 may contribute to temperature-dependent FLM expression.10.7554/eLife.22114.002Figure 1.FLM intronic sequences determine basal and temperature-dependent FLM expression.(A) Schematic representation of the pFLM::gFLM (FLMCol-0), pFLM::FLM-ß, and pFLM::FLM-δ constructs. Scale is set to 1 according to the A of the ATG start codon. Black boxes represent exons, grey lines 5’- or 3’-untranslated regions, dark-grey lines introns. Arrows indicate primer binding sites; the forward primer F1 was used to amplify FLM-ß and FLM-δ with reverse primers R1 and R2, respectively. (B) Mean and SD (three biological replicates) of qRT-PCR analyses of FLM-ß and FLM-δ expression in ten day-old plants harbouring the transgenes shown in (A). For normalization, the respective values measured at 21°C were set to 1.DOI: http://dx.doi.org/10.7554/eLife.22114.002