General discussion 6 219 To overcome the limitations of the GO enrichment and to gain insight into the hormonal signatures in the transcriptome data, we curated lists of hormone responsive and related genes, identified their tomato homologs, and visualized these as heatmaps (Figures 4.2). Specifically in the case of GA and BR that are missing from tomato GO, we identified several genes, which show more pronounced FR effects on gene regulation in GA genes compared to BR-related genes, with up to a 4-fold change. BR-related genes show no significant change. Notably, GA oxidase genes, crucial in GA biosynthesis, are significantly upregulated. In other words, IAA and GA-related genes exhibit a remarkably similar expression pattern, with numerous genes showing high upregulation and downregulation, indicating that that IAA and GA play roles in the FR response in the stem, while BR response is not evident. When we consider these results in the light of the hormone treatments, a new nuance emerges. GA and BR are necessary and sufficient for the internode elongation (Figures 4.13,14,16), while the role of IAA remains unsolved. Looking at the hormone treatment qPCR data (Figure 4.22-4.23), the story is complicated even further. IAA and GA give more similar responses, resembling that of FR-response, while BR application also leads to a substantial gene expression alteration, however with opposing effects to IAA and GA. Note that BR effects are clear in genes that are not annotated as BR-related, indicating that looking at proposed BR-related genes to infer BR function (e.g. GO enrichment, Figure 4.2b BR-heatmap) is not very effective. In conclusion, the gene expression responses of IAA and GA demonstrate an increase in response to FR, whereas BR exhibit no alteration. Regarding the recapitulation of FR effects with exogenous hormone treatments, IAA has a minor impact, while GA and BR fully recapitulate the effect. From our inhibitor work, we saw that blocking GA and BR also blocks the FR response, indicating them being necessary for the FR-induced elongation. These effects are different from Arabidopsis SAS where auxin plays a core role, being the mobile signal, necessary and sufficient, to induce the petiole and hypocotyl elongation responses. It is likely that the relative hormonal regulation balances in SAS has diverged between tomato and Arabidopsis, and this will complicate translation of Arabidopsis SAS findings to crop applications.
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