Chapter 3 60 vulgaris ‘Kentucky Wonder’) during the internode elongation (Beall et al., 1996). In Chapter 2, we also observed elongation and cell layer increase in pith, thickness increase in interfascicular cambium, and longer epidermis cells in response to FR. Distinguishing gene expression in specific cell types is an effective way to reveal cell functions of individual cell types in plants without the noise from surrounding tissue. High-resolution gene expression profiling methods to understand SAS have been conducted in Arabidopsis and other models, including tomato (Li et al., 2012; Bolger et al., 2014; Bush et al., 2015; Kohnen et al., 2016a; Gommers et al., 2017; Pantazopoulou et al., 2017; Molina-Contreras et al., 2019; Courbier et al., 2020; Küpers et al., 2023). Profiling the cell type and organ-specific gene expression changes in the stem SAS would aid understanding the pith elongation, division, and expansion in secondary growth. In this chapter, we present time course transcriptomes from tomato first internode and its inner cylinder (pith & vasculature) for FR response. We found that in the young seedlings of 14 dag, auxin was the major growth regulation response, upregulated at our earliest timepoint of 6 hours of FR treatment. Auxin response was enriched in upregulated genes of both internode and pith, and however, no other hormonal regulation pathways were enriched in FR-responsive genes. Meanwhile, the metabolic changes such as amine metabolic process and catalytic activity were enriched in pith differentially expressed genes. These tissue-specific transcriptional signatures often predict previously unknown cell-type-specific functions, and the results could lead to the discovery of unknown pathways in tomato and unknown characteristic in pith. 3.2 RESULTS 3.2.1 First internode elongation was visible from the second day after the supplemental FR treatment started In the previous chapter, we demonstrated that tomato first internode was significantly longer after 7-day whole-plant FR-treatment (WL+FR) compared to the control white light (WL) treatment. In this chapter, we set out to investigate the molecular mechanisms of elongation on tissue level in first internode by conducting a time course RNA seq analysis. Initially we investigated the elongation of first internode from the start of the FR exposure at 7 dag (Figure 3.3). At the start of FR supplementation, the first internode already existed, but was still very small and closely connected with the meristem. We observed that at 48 hours, the elongation of the first internode started to show increase in WL+FR compared to WL. This increase was observed for the elongation of the total stem as well. Both tomato cultivars MM and M82 show very similar response pattern for the duration we investigated.
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