Organ-specific clocks show phase differences under constant environmental conditions and LD cycles.

(A) Schematic depicting the experimental conditions used. Seedlings were grown for 4 d under LD cycles and imaged either under constant light (LD-to-LL) or LD (LD-to-LD). The white triangle represents the beginning of imaging. (B) Expression of GI::LUC from different organs imaged under the LD-to-LL condition. Data represent the mean ± standard error of organs scored as rhythmic. Luminescence counts were normalized to the minimum and maximum values of the time series. (C) Times of peaks of GI::LUC expression in different organs under the LD-to-LL condition. Plots represent the 25th percentile, median, and the 75th percentile for the peak times of organs scored as rhythmic. Organs show significant phase differences, ***p < 0.001, by Kruskal-Wallis ANOVA. Pairwise comparisons are shown in S1 Fig. (D) Period estimates of GI::LUC for different organs imaged under the LD-to-LL condition. The means of organs are statistically different (p < 0.05, by one-way ANOVA, Tukey post hoc tests) if they do not have a letter in common. (E) Expression of GI::LUC from different organs imaged under the LD-to-LD condition. Data represent the mean ± standard error of organs scored as rhythmic. Luminescence counts were normalized to the minimum and maximum values of the time series. Color legend is as in B. (F) Times of peaks of GI::LUC expression in different organs imaged under the LD-to-LD condition. Plots represent the 25th percentile, median, and the 75th percentile for the peak times of organs scored as rhythmic. Organs show significant phase differences, ***p < 0.001, by Kruskal-Wallis ANOVA. Pairwise comparisons are shown in S3 Fig. Color legend is as in C. (G) Period estimates of GI::LUC for different organs imaged under the LD-to-LD condition. The means of organs are statistically different (p < 0.05, by one-way ANOVA, Tukey post hoc tests) if they do not have a letter in common. (H, I) Representative phase plot of GI::LUC expression across longitudinal sections of the cotyledon (top), hypocotyl (middle), and root (bottom) of a single seedling under LD-to-LL (H) and LD-to-LD (I) conditions. Color bars are as in H. For LD-to-LL data, N = 4; LD-to-LD, N = 3; for both, n = 26–35. N represents the number of independent experiments and n the total number of organs tracked. See S1 and S2 Files for exact n, test statistics, and percentage rhythmicity of each organ. Box plots indicate the median and upper and lower quartiles, and whiskers the 9th and 91st percentiles of organs scored as rhythmic. Underlying data are available from https://gitlab.com/slcu/teamJL/greenwood_etal_2019. GI, GIGANTEA; LD, light-dark; LL, constant light; LUC, LUCIFERASE.