Hormone interplay in the regulation far-red-responsive stem elongation in tomato 4 139 IAA19 expression in low R:FR, and other studies have published gene expression work for IAA19 in low R:FR in Arabidopsis, also being confirmed by GUS expression (Pierik et al., 2009; Keuskamp et al., 2010a; de Wit et al., 2016). PIN3 is a protein that regulates auxin transport and has been found to relocate in response to shade, inducing an increase in auxin concentration in Arabidopsis hypocotyls (Keuskamp et al., 2010b). Previous studies have demonstrated that shade promotes SAUR expression in Arabidopsis, suggesting that SAURs play a role in SAS (Ren and Gray, 2015). GA20ox2 expression patterns are more complex. We found no expression change in GA20ox1 in both the FR and GA treatments, while the IAA and GA+ IAA-treatment show downregulation of GA20ox1. These results also further reinforce that pith cells respond differently to entire internode to FR treatment or to hormones. Pith exhibits distinct responsiveness to FR depending on the hormone treatment, as well as in comparison to supplemental FR alone. In supplemental FR, HY5, SAUR, PIN3, PIN9, IAA22, YUC9, and GA20 ox show higher expression in pith compared to the entire internode, suggesting an augmented IAA signaling and GA influence. However, for HY5, only GA and IAA induce upregulation, with pith showing a less pronounced response compared to the entire internode. The responsiveness of pith varies more widely in other treatments, further emphasizing complexity in the hormone network. To analyse the expression pattern similarities between treatments and to identify which hormone(s) were most similar to FR treatment, we performed Pearson correlation analysis (Figure 4.24). The regression fit parameters indicated that IAA exhibited the most similar pattern compared to FR among these genes, followed by GA and GA+IAA. The fact that IAA treatment led to a gene expression pattern most similar to far-red light (Figure 4.24) suggests that auxin plays a significant role in mediating the elongation response. From the correlations it was also apparent that the BR treatment induced a very strong expression pattern different to the other hormones and FR. Also, this strong effect of BR overcame the effects of the two other hormones, as the BR treatment pattern correlated highly with that of BR+GA+IAA treatment. Our qPCR data also suggests an opposing expression shift for many transcription factors in BR-treated plants compared to farred treatment (Figures 4.23, 4.24). Overall, the qPCR results indicate that while BR is necessary for the FR-induced internode elongation in tomato, it is not able to induce the FR-like gene expression patterns, while IAA and GA are able to induce some of these changes. However, before overinterpreting this data, we need to keep in mind that a large portion of the qPCR targets are auxin responsive genes.
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