Abstract

BACKGROUND Silicon (Si) has shown potential in mitigating salt stress in cotton, but the underlying mechanisms remain not fully understood. In this study, hydroponic experiments assessed effects of exogenous Si (0.4 mmol L −1 ) on growth, water status, and related physiology indexes of cotton seedlings under 150 mmol L −1 NaCl stress. We investigated whether Si enhances salt tolerance via water balance maintenance and transcriptional regulation using RNA-Seq. RESULTS Salt stress significantly inhibited cotton seedlings growth, reducing plant height, leaf area, and root dry weight by 31.8%, 36.5%, and 40.0%, respectively. Exogenous Si application alleviated the inhibitory effects of salt stress on these growth parameters. The positive effects of Si were primarily credited to increasing root aquaporin (AQP) content, which facilitates improved root hydraulic conductance (Lpr) and ultimately improves leaf water status. Under salt stress, Si elevated leaf water content by 51.8%, bound water by 186.9%, and leaf water potential by 31.0%. Moreover, Si increased abscisic acid (ABA) content at the early stage of salt stress, promoting stomatal closure to reduce water loss. Furthermore, we identified 81 differentially expressed genes shared among CK_ versus _NaCl, CK_ versus _NaCl+Si and NaCl_ versus _NaCl+Si comparisons (where CK is control), with significant enrichment in pathways related to ABA metabolism (NECD and CYP707A4), ABA signal transduction (YR1/PYLs and ABI5), and water transport (such as plasma membrane intrinsic proteins). CONCLUSION These results suggested that exogenous Si enhances salt tolerance by regulating ABA and AQP levels, promoting early stomatal closure, increasing Lpr, and thus maintaining leaf water content, which collectively support cotton seedling growth under salt stress. © 2026 Society of Chemical Industry.