Transcriptome changes of tomato internode elongation induced by far-red light 3 85 where stem elongation is distinguishable at two days, we selected earlier timepoints, including two different times of day for the diurnal rhythm to understand the response. When we analyzed the transcriptome data the major effect (Montavon et al., 1983) is coming from diurnal rhythm in the first few principle components (PC1, PC2, PC3) in PCA analysis and DE analysis (Figure S1, Figure 3.4c). Diurnal rhythm adaptation could have been important for tomato (Xiang et al., 2022). In Figures 3.10 and 3.11, we found that some clear diurnal rhythm responses when comparing morning vs afternoon transcriptomes. In the previous research into tomato diurnal rhythm, the elongation of stems declined during the day while the soluble sugars increased in the morning and decreased from afternoon till night (Went, 1944). During our observations, the expression of gene Solyc08g082860 related to the sugar trehalose showed a reduction in levels during the afternoon, suggesting less protein from trehalose from damaging cellular structures and molecules caused by environmental stress (Lunn et al., 2014). Additionally, we observed an activation of sugar transfer processes, particularly involving the activity of methyltransferases, indicating an increase in sugar transfer activities during the afternoon period. These findings collectively indicate dynamic changes in sugar metabolism and transfer processes over the course of the day. Therefore, the response of tomato stem elongation to far-red light unveils dynamic changes in sugar metabolism influenced by diurnal rhythm. In the context of WGCNA, we observed intriguing patterns across multiple gene modules (Figures 3.12-3.14, S3.3). One of the standout findings is within the green module, where FR response exhibits a diurnal rhythm in the internode. These genes are functionally associated with essential processes such as photosynthesis and protein translation. It’s worth noting that the impact of FR on this module may be limited, as key regulators could have already reached their peak expression levels due to diurnal clock influences, darkolivegreen module associated with intracellular carbohydrate metabolism, shows a clearer diurnal pattern in WL but not that obvious in FR, even though the expression value is higher (Figure 3.19). The diverse responses of various gene modules shed light on the intricate regulatory mechanisms at play in plant adaptation to changing light environments and provide insights for further investigation.
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