Chapter 3 64 comparing the DEGs in the pith and internode at both 30 and 48 hours, we observed that the pith exhibits a higher count of unique DEGs. These findings suggest a distinctive pattern of gene expression regulation in the pith, potentially highlighting its specialized role in SAS. In 06h In 24h In 30h In 48h Pith 30h Pith 48h response to auxin cellular iron ion homeostasis acireductone dioxygenase [iron(II)-requiring] activity protein dimerization activity ferric iron binding nucleoside triphosphate catabolic process mitochondrial pyruvate transmembrane transport methyltransferase activity nucleoside-triphosphate diphosphatase activity DNA binding 4-alpha-glucanotransferase activity galactosyltransferase activity carbohydrate metabolic process enzyme inhibitor activity copper ion binding anion transport oxidoreductase activity hydrolase activity- hydrolyzing O-glycosyl compounds FAD binding checkpoint clamp complex DNA damage checkpoint signaling transaminase activity glycopeptide alpha-N-acetylgalactosaminidase activity endoplasmic reticulum nucleic acid binding small-subunit processome intramolecular lyase activity thiamine biosynthetic process chitin binding RNA-directed 5'-3' RNA polymerase activity trehalose biosynthetic process hexosyltransferase activity phosphorelay signal transduction system O-methyltransferase activity anion transport calcium-dependent phospholipid binding catalytic activity oxidoreductase activity- acting on the CH-CH group of donors quinolinate synthetase A activity NAD biosynthetic process 4 iron- 4 sulfur cluster binding phosphoenolpyruvate carboxylase activity carbon fixation tricarboxylic acid cycle chitin catabolic process cell wall macromolecule catabolic process chitinase activity serine-type endopeptidase inhibitor activity phosphatase activity glycolipid biosynthetic process phosphatidylinositol phospholipase C activity xenobiotic transmembrane transport antiporter activity intracellular signal transduction cation transmembrane transporter activity oxidoreductase activity nicotianamine biosynthetic process nicotianamine synthase activity protein dimerization activity acyltransferase activity- transferring groups other than amino-acyl groups defense response transmembrane transport membrane transmembrane transporter activity lyase activity oxidoreductase activity- acting on paired donors- with incorporation or reduction of molecular oxygen terpene synthase activity oxidoreductase activity- acting on the CH-OH group of donors- NAD or NADP as acceptor lipid biosynthetic process steroid biosynthetic process 3-beta-hydroxy-delta5-steroid dehydrogenase activity iron ion binding hydrolase activity- acting on ester bonds heme binding cytochrome-c oxidase activity aerobic respiration Tissue and treated hours -log(q value) Up DEGs Down DEGs -5 0 5 10 15 Figure 3.7. Gene ontology (GO) enrichment analysis of FR-responsive DEGs in whole internode or pith. Heatmap of the -log of adjusted p-values (q-value) for each enriched GO category. Red color scheme for upregulated DEGs, and blue for downregulated. The color scale is capped the at 15 to ensure clearer visualization of all GO details.
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