Chapter 3 56 ABSTRACT Plants utilize especially red and blue light for the essential activity of photosynthesis. Also, the plant sensing mechanisms for light can detect these wavelengths: red by phytochrome, and blue by the cryptochromes and phototropins. Phytochrome can also sense far-red light (FR) as a signal for detecting light reflected from neighboring plants and leaves. Changes in the ratio of red and far-red light alter the ratio of phytochrome active and inactive forms, leading to stem elongation in tomato as described in Chapter 2. Despite being a well-known phenomenon for decades, the cellular level regulatory mechanisms in stem-forming plants have not been fully resolved. To address this, we designed a time series RNA-seq at a tissue-specific level in tomato. The transcriptome data indicated regulation of auxin during internode elongation in the first few hours which had a lasting effect on cell elongation. We also found that internode and pith cells exhibit a strong auxin response during the afternoon FR treatment timepoints. Moreover, through GO analysis, we observed indications for changes in cell division and elongation, including cell wall formation. The role of auxin and other hormones is followed up experimentally in Chapter 4. We also analyzed expression modules through WGCNA, which identified FR-responsive transcription factors (TFs) that are our putative key regulators. We reviewed the known roles for these TFs from the literature and selected three candidate TFs that may play a role in shade avoidance syndrome (SAS)-linked cell division in stem tissues for further study (Chapter 5). In conclusion, this chapter has successfully identified potential candidate TFs and highlighted the crucial role of auxin in the examined context.
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