Figure 4: Lateral root phenotypes of circadian clock mutants.

(a) TOC1 gene expression in the basal meristem is induced in response to auxin treatment of whole seedlings in Col-0, as well as arf7arf19 mutant plants. Expression intensities are on a log2 scale and are based on transcriptomics data with an ATH1 chip (Affymetrix), three independent biological replicates each. Error bars indicate s.d.; asterisks indicate a significant difference (P<0.05, Student’s t-test) from wildtype. (b–d) All seedlings were grown in constant light conditions, without previous entrainment. N=20 for all experiments. Error bars indicate s.d.; asterisks indicate a significant difference from wildtype. (b) Emerged lateral root density of 10-day-old C24 and toc1-1 seedlings in cm⁻¹ revealed a strong phenotype for toc1-1. (c,d) Ten-day-old seedlings were fixed and the primordium density of different developmental stages (stage I to emerged (E)) of wild-type (C24) and toc1-1 mutant seedlings in cm⁻¹ was determined. (e) Comparison of oscillating gene expression patterns from the lateral root transcriptomic time course of the circadian clock genes CCA1 and TOC1 and auxin signalling genes IAA14 and AtDAO2, demonstrate gating of auxin signalling by the circadian clock during lateral root primordium development. Expression intensities are on a log2 scale. Red vertical bars indicate peak times of TOC1 expression. All seedlings were grown in constant light conditions, without previous entrainment. The mean of the gene expression is given by the solid line and the error bars show the mean±2 s.e. N=4. (f) IAA and oxIAA accumulations exhibit circadian rhythms in roots under free-running conditions. Seedlings were germinated and entrained under 12 h light/dark cycle before transfer to constant darkness. Tissue was harvested starting at subjective dawn for 5-day seedlings. The experiment was repeated three times. White bars, light period; dark bars, dark period. Error bars indicate s.d.; N=3.