Chapter 4 144 4.3 DISCUSSION In this chapter, we have provided insights into the hormone dynamics governing shade avoidance syndrome (SAS) in tomato. Our investigation shed light on the role of the hormones, auxins (IAA), gibberellins (GA), and brassinosteroids (BR), in mediating internode 1 elongation responses under changing light conditions. Our findings contribute to a deeper understanding of the regulatory mechanisms that plants employ to optimize growth in response to reduced red-to-far-red (R:FR) ratio. 4.3.1 The FR-responsive transcriptome included IAA and GAresponsive genes We initiated our analysis using the multi-blast method to identify IAA, GA, and BRrelated genes that were absent in the tomato (ITAG4.1) GO annotation, and then visualized the FR-responsive log foldchanges in a heatmap (Figure 4.2). We observed IAA-responsive SAURs displaying notable up- and downregulation, hinting at functional redundancy between SAUR genes. Other IAA-related genes had very mild changes except for few genes such as IAA10 (Figure 4.2, red boxes). SAURs have been shown to respond not only to auxin, but also GA and BR (Luo et al., 2018; Stortenbeker and Bemer, 2019). GA-related genes, particularly GA oxidases, showed a pattern of FR-response. The fold change in their expression hinted at an underlying GA function in SAS. In the gene responses to the hormone and light treatments (Figures 4.22-4.23), we observed a surprisingly similar expression pattern between FR-, IAA- and GA-treated plants. The inducive expression patterns of GA and IAA exhibit a strong positive correlation, with IAA showing the highest correlation with FR responsiveness, followed by GA+IAA and GA alone. This suggests that the influence of GA inducive expression cannot be reversed by IAA. On the other hand, BR functions independently by inducing negative regulation, and combining it with GA and IAA does not reverse this effect. Due to the limitation of the number of genes that could be included in our analysis, these interpetations need to be taken cautiously. In contrast, BR-treated plants displayed a unique expression pattern not resembling any other of our treatments (Figure 4.24). This divergence might be for the same reason as the fact that BR-related pathways did not exhibit significant up- or downregulation in our FR RNA-seq data (Figure 4.2b). Consequently, the gene expression patterns caused by BR treatment would be also different from FR treatment. Overall, this would indicate that the BR pathway would be either distinct from, or only a small part of the FR response in the tomato internode.
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