Transcriptome changes of tomato internode elongation induced by far-red light 3 87 3.3.3 Stable photosynthesis expression showed in the internode and pith We identified distinct modules representing clusters of nodes with shared attributes or connectivity patterns (Figure 3.12). Heatmaps revealed consistent FR-upregulation of genes in specific modules, including mediumpurplegrey3, enriched in GO terms relating to photosynthesis and protein synthesis. Conversely, salmon and lightsteelblue1 modules showed downregulation. Additionally, genes within the turquoise module, mainly downregulated over time, play pivotal roles in plant development and maintenance, particularly in ribosome, nucleosome, and photosystem I-related functions. Stems possess a notable photosynthetic activity (Hetherington et al., 1998). The stems capture and fix carbon dioxide generated during respiration concurrent with photosynthesis, yet there is a lack of observable carbon exchange (Xu et al., 1997). Under high R:FR ratios, stems exhibit enhanced photosynthetic capacity compared to lower R:FR conditions (Hattrup et al., 2007). Our WGCNA modules, specifically the blue and green modules, align with these observations. These modules reveal stable expression patterns of photosynthesis-related genes over time, with a distinct downregulation in FR compared to WL conditions (Figure 3.12). Intriguingly, key regulators, primarily from the turquoise module and yellow modules (as seen in Figures 3.12-3.14), maintain little fold change between FR and WL. However, at certain timepoints, we observed the absence of GO terms associated with carbon dioxide or carbohydrate exchange which was enriched in the morning timepoint especially in pith (Figures 3.9-3.11). This discovery suggests that the plant’s inherent homeostatic mechanisms governing photosynthesis may also support respiration processes, thereby stabilizing internal metabolism. This dynamic interplay between gene modules and metabolic processes underscores the plant’s remarkable ability to maintain equilibrium in response to shifting environmental conditions. 3.3.4 Summary In the face of low R:FR conditions, we observed a significant upregulation of auxinresponsive genes, particularly SAURs. The diurnal rhythm emerged as a key regulator, influencing various pathways such as hormone response, sugar metabolism, and respiration. A detailed examination of pith tissue-specific transcriptomes revealed substantial differences comparable to the whole internode, unveiling specific regulatory pathways. Notably, several transcription factors previously mentioned were identified in the differentially expressed genes, underscoring their role in the response to low R:FR. Subsequently, our focus shifted to hormones and these transcription factors in the subsequent chapters for a deeper exploration of their regulatory roles.
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