Hormone interplay in the regulation far-red-responsive stem elongation in tomato 4 113 4.2 RESULTS 4.2.1 IAA and GA-related transcripts show a robust fold change response to FR, while BR-related genes exhibit a muted response We wanted to explore how hormone-related genes were responding to FR in our tomato RNAseq data (described in detail in Chapter 3). Given the shortness of tomato gene lists for hormone responses in the current (ITAG4.1) tomato GO annotation, we used Arabidopsis Gene Ontology (GO) annotations (Table 4.1) from TAIR (The Arabidopsis Information Resource)(Lamesch et al., 2012) to identify the genes of interest. Then, we employed a multi-blast strategy against the tomato transcripts in the Solgenomics database (https://solgenomics.net/tools/blast/). This approach allowed us to identify putative tomato genes responsive to hormones in our RNA-seq dataset. This was also supplemented by tomato hormone literature (Li et al., 1994; Knauss et al., 2003; Wu et al., 2012; Stortenbeker and Bemer, 2019). We visualized the FR-responsiveness of these genes of interest in our transcriptome data (Figures 4.2, S4.1, S4.2). Figure 4.2. FR response of IAA, BR and GA-related genes in tomato. Heatmap generated from RNAseq data illustrates the log fold change in gene expression associated with (a) IAA, (b) GA and BR. Upregulation is represented in red, while downregulation in blue. FR-responsive DEGs are boxed in red.
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