Chapter 3 72 3.2.9 Diurnal expression patterns are associated with defence, light, and metabolism In our data there is a clear pattern of diurnal rhythm. The morning (10am) timepoints (24h, 48h) and the afternoon (6h, 30h) timepoints cluster together in the PCA (Figure S3.1), and the afternoon 4 pm timepoints tend to show clearer FR-responses than the morning 10 am timepoints (Figure 3.7). In the afternoon, methyltransferase activity was enriched in the FR-upregulated DEGs (Figure 3.7) and trehalose biosynthetic process was enriched in FR-downregulated DEGs. We assume methyltransferase activity upregulation indicates significant molecular modifications, possibly involving epigenetic and protein-level changes. Simultaneously, the downregulation of genes associated with trehalose biosynthesis hints at a recalibration of stress protection mechanisms. While trehalose typically safeguards plants from environmental stresses, vascular plants like tomatoes have shifted towards regulating carbon assimilation and sugar status, indicating a divergence in stress response strategies (Grennan, 2007; Paul et al., 2010; Lunn et al., 2014). This strategic switch may prioritize growth over stress tolerance. Moreover, trehalose’s involvement in signaling during interactions with microorganisms, responses to cold, salinity, and the regulation of stomatal conductance and water-use efficiency underscores its multifaceted role in plant biology. This interplay reflects the plant’s adaptive response to shifting environmental conditions, enhancing our understanding of its intricate survival strategies (Finnegan and Kovac, 2000; Lunn et al., 2014). To investigate which genes in our data followed diurnal regulation, we analysed the DEGs between morning and afternoon for each tissue and treatment, and carried out GO enrichment analyses (Figure 3.10 and Figure 3.11). In the internode WL conditions, we observe that auxin is enriched in afternoon up DEGs, while other treatments and tissues do not show the same response. Simultaneously, we see an increase in activities related to photosynthesis in internode WL in the morning.. Concurrently, the upregulation of polysaccharide catabolic processes indicates an increased energy demand to support DNA binding, translation and more. Morning downregulation of photosynthesis and DNA binding activities in both the whole internode and pith reflects the natural influence of the diurnal rhythm on shade avoidance (GO: DNA-binding transcription factor activity, histone acetyltransferase activity, sequence-specific DNA binding, photosynthesis, chlorophyllide a oxygenase [overall] activity, photosystem II). Collectively, these responses signify the plant’s adaptation to morning light conditions, allowing it to effectively capture and convert light energy into chemical energy for growth and maintenance. And light treatment did make a major change to diurnal cycle in general.
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