Transcriptome changes of tomato internode elongation induced by far-red light 3 61 0d 10:30am 0d 4:30pm 1d 10:30am 1d 4:30pm 2d 10:30am 2d 4:30pm 3d 10:30am 3d 4:30pm 4d 10:30am 4d 4:30pm 0 20 40 60 80 time Stem length (mm) MM WL+FR MM WL M82 WL+FR M82 WL * ** *** *** *** ** ** *** *** *** *** *** 0d 10:30am 0d 4:30pm 1d 10:30am 1d 4:30pm 2d 10:30am 2d 4:30pm 3d 10:30am 3d 4:30pm 4d 10:30am 4d 4:30pm 0 5 10 15 20 time Internode1 length (mm) WL+FR MM WL MM WL+FR M82 WL M82 * *** *** *** *** *** * * ** ** ** *** *** *** (a) (b) Figure 3.3. Stem and first internode length for 4 days in WL+FR treatment. (a) The stem length of MM and M82 in WL and WL+FR. (b) The first internode length of MM and M82 in WL and WL+FR. The seedlings were grown in WL for 1 week, and 0 day 10:30 am in the morning we started supplemental FR treatment, the lengths were measured at 0, 6, 24, 30, 48, 52, 64, 70, 94 hours that correspond to day 0 at 10:30am, day 0 at 4:30 pm, day 1 at 10:30 am, and so on. Asterisks indicate significance between WL and WL+FR as follows: p≤0.05 ,** p≤0.01, *** p≤0.001.Upper significance indicates comparison in MM, lower significance indicates comparison in M82. Figure 3.4. Experimental design for time series and tissue-specific RNA sequencing on tomato internode elongation in WL vs WL+FR treatment. Plants were grown for 7 days in WL before the WL+FR treatment. The whole internodes were harvested at all timepoints, and pith tissue only at the two latest timepoints. In order to capture the early events in the first internode elongation, we designed the RNA-sequencing timepoints leading to the point where the elongation phenotype was observed, specifically: 6 hours (16:30 day 0), 24 hours (10:30 day 1), 30 hours (16:30 day 1), and 48 hours (10:30 day 2). The samples harvested were the first internode and the central cylinder (pith) of the first internode. The pith was only successfully sectioned at the two later timepoints (Figure 3.4) where the stem is thick enough for accurate dissection. The experiment consisted of two light treatments, two cultivars, two tissue
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