Integrated Transcriptomic and Metabolomic Profiling of Paclobutrazol-Induced Dwarfism in Tomato Epicotyls

Tomato (<i>Solanum lycopersicum</i> L.) seedlings are prone to excessive growth in summer, especially severe overgrowth of the embryo axis. Paclobutrazol is a plant growth inhibitor that regulates the balance of hormones in plants and delays their growth. In this study, 200 mg·L^-1 paclobutrazol was sprayed onto highly homozygous inbred strain DH tomato seedlings at the two-leaf stage, which led to a significant reduction in the length of the epicotyl, an increase in the number of cells, a close cell arrangement, and a reduction in cell size. To study the mechanism by which paclobutrazol dwarfs the epicotyl of tomatoes, we utilized a combined analysis of the transcriptome and metabolome to identify potential candidate genes and regulatory pathways. The results revealed that after paclobutrazol treatment, both the flavonoid and phenylpropanoid biosynthesis pathways were jointly annotated. In addition, plant hormones and sucrose metabolism pathways were also discovered using transcriptome analysis. Xyloglucan endotransglucosylase/hydrolases (<i>XTHs</i>), small auxin-up RNAs (<i>SAURs</i>) and invertase family-related genes were detected, which can serve as key candidate genes for the subsequent analysis of epicotyl dwarfism in tomato plants. These results provide a framework for understanding the metabolic processes underlying epicotyl dwarfism and a foundation for preventing tomato seedling overgrowth.