Transcriptome changes of tomato internode elongation induced by far-red light 3 69 The lyase activity is enriched in the downregulated FR-responsive DEGs (Figure 3.7) is attributed to genes Solyc05g010320 and Solyc05g052240, both annotated to encode chalcone-flavanone isomerase (CHI) on Solgenomics.net. CHI is a crucial enzyme in plant biology, converting chalcones into flavanones, vital compounds in plants (Moustafa and Wong, 1967). CHI downregulation reduces flavonoid levels in plant tissues, impacting functions such as UV protection, pollinator attraction, and pathogen defence. Additionally, it can alter tissue pigmentation, potentially resulting in different colours and patterns (Ryan et al., 2002). This downregulation affects a plant’s stress response and pathogen resistance, as flavonoids attribute in part to their antioxidative effects, involve the non-specific quenching of reactive oxygen species (ROS) generated by both the pathogens and the plant in response to infection and stress (Mierziak et al., 2014). There is an enrichment of hydrolase activity targeting ester bonds. Ester bonds are the connections that link a carboxylic acid group to an alcohol group, forming a molecule known as an ester. Hydrolases break these bonds apart, releasing the carboxylic acid and alcohol components. Alcohols, particularly ethanol, may contribute to defense mechanisms by participating in the synthesis of secondary metabolites like lignin and flavonoids, strengthening cell walls, and inducing stress-related genes. Additionally, alcohol accumulation can serve as an indicator of stress or pathogen attack (Bashir et al., 2022; Matsui et al., 2022). In all pith FR-upregulated DEGs (Figure 3.7), there are two specific genes of interest: Solyc06g008870 and Solyc09g075680, both annotated to encode the gibberellin receptor, GIBBERELLIN INSENSITIVE DWARF 1 (GID1) on Solgenomics.net. GID1 is involved in the plant’s response to gibberellin hormones, regulating growth and development. The downregulation of GID1 in the pith may have various change on gibberellin pathway involving cell division and elongation (Ueguchi-Tanaka et al., 2007; Murase et al., 2008). Downregulation of various pathways involved in the synthesis of compounds with diverse functions, such as the NAD biosynthetic process, carbon fixation (photosynthesis), and nicotianamine biosynthetic process, can have far-reaching effects. These pathways being downregulated in response to FR treatment suggests that the plants may be building up secondary metabolites, considered to be a stress hallmark. These pathways are reported to involved in many crucial functions such as defense mechanism which was reported in previous research (Courbier et al., 2020).
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