Abstract
The Mediterranean Basin, a hotspot for tomato production, is one of the most vulnerable areas to climate change, where rising temperatures and increasing soil and water salinization represent major threats to agricultural sustainability. Thus, to understand the molecular mechanisms behind plant responses to this stress combination, an RNA-Seq analysis was conducted on roots and shoots of tomato plants exposed to salt (100 mM NaCl) and/or heat (42°C, 4 h each day) stress for 21 days. The analysis identified over 8000 differentially expressed genes (DEGs) under combined stress conditions, with 1716 DEGs in roots and 2665 in shoots being exclusively modulated in response to this specific stress condition. Functional enrichment analysis revealed an apparent downregulation of genes associated with cell cycle progression, differentiation, and cell wall organization in both roots and shoots. This may explain the impaired plant growth and reduced performance observed under stress co-exposure. On the other hand, combined stress triggered a marked upregulation of genes involved in hormone signaling, protein stability, heat shock response, antioxidant defense, glutathione metabolism, and enzymatic regulation, suggesting a well-coordinated activation of protective mechanisms. Additionally, upregulation of genes related to RNA modification and ribosome-related processes indicates a tight transcriptional control over these responses, enabling plants to manage resources effectively and prioritize stress acclimation at the expense of growth. Overall, the data gathered in our study provide important insights into the complex molecular adjustments deployed by tomato plants under combined heat and salt stress, offering a foundation for future approaches to enhance tomato plants' resilience to climate change.