Integrated Transcriptomic and Metabolomic Analysis Reveals a Role of SlTPR4 in Enhancing Resistance to <i>Botrytis cinerea</i> in Tomato ( <i>Solanum lycopersicum</i> )

<i>Solanum lycopersicum</i> (Tomato) is an important economic crop that is frequently susceptible to gray-mold disease caused by <i>Botrytis cinerea</i>. However, the mechanism through which tetratricopeptide repeat (TPR) proteins participate in the tomato response to <i>Botrytis cinerea</i> remains unclear. In this study, we found that <i>SlTPR4</i>-overexpressing plants exhibited enhanced resistance to <i>Botrytis cinerea</i>, whereas <i>sltpr4</i> mutants showed increased sensitivity to the pathogen. By integrating transcriptomic and metabolomic analyses, we observed significant alterations in phenylpropanoid biosynthesis in <i>SlTPR4</i>-overexpressing plants. RT-qPCR analysis further revealed up-regulation of key flavonoid biosynthetic genes: <i>SlPAL</i>, <i>SlC4H</i>, <i>SlCHS</i>, and <i>SlCHI</i>. Yeast two-hybrid assays demonstrated interactions between SlTPR4 and both SlPAL and SlCHI, indicating that SlTPR4 enhances disease resistance by activating the phenylpropanoid-flavonoid pathway. In summary, this study elucidates the role of SlTPR4-mediated flavonoid metabolism in enhancing tomato resistance to <i>Botrytis cinerea</i> and provides novel targets and a theoretical basis for breeding disease-resistant cultivars.