The Translational Landscape of Tomato Seedlings under Salt Stress

• Salt stress profoundly remodels the tomato translatome to prioritize adaptive pathways. • Translational control provides a rapid and dominant mechanism for crop stress adaptation. • uORFs (repressive) and dORFs (enhancing) act as key regulators of protein synthesis. • This regulatory network provides novel targets for improving crop salt tolerance. While gene expression under salt stress has been extensively studied at the transcriptional level, the translational regulatory mechanisms that rapidly influence protein synthesis for enhanced organismal plasticity remain less understood. Here, we employed ribosome profiling and RNA sequencing to construct a comprehensive translatome of tomato seedlings under salt stress. Our results reveal that salt stress profoundly alters gene expression at both transcriptional and translational levels. We observed a general inhibition of translational efficiency, yet a subset of genes exhibited significant expression changes exclusively at the translational level. Further analysis of genome-wide translation dynamics uncovered stage- and pathway-specific expression patterns of key functional genes. Moreover, we systematically identified small open reading frames (ORFs) and characterized the dynamic expression of upstream (uORFs) and downstream (dORFs) ORFs, highlighting their strong associations with translational control. Importantly, based on our multi-omics integration, we propose a model wherein uORFs, dORFs, and miRNAs exhibit highly coordinated patterns, suggesting a potential synergistic interplay during salt stress adaptation. In summary, this study provides a high-resolution overview of the translational landscape in salt-stressed tomato, offering novel insights into the molecular mechanisms of plant salt tolerance. The generated translatomic resource is a valuable asset for future crop improvement.