Comprehensive DIA-MS Proteomics of Root Basal Nodes Elucidates Mechanisms of Salt Tolerance in Rice

Soil salinity severely affects rice growth, yield, and quality, posing a global food security challenge. Rice is particularly vulnerable to high salinity, which restricts growth and tolerance to other stresses. To address this, breeding efforts have been made in the past, leading to the generation of multi-stress-tolerant rice lines. A key achievement is the introgression of Submergence 1 (Sub1), Anaerobic Germination 1 (AG1), and Pi9 QTLs into the Indonesian variety Ciherang, generating the CSA-Pi9 line with improved tolerance to submergence, salinity, and blast disease. In this study, we applied data-independent acquisition mass spectrometry (DIA-MS)–based proteomics of root basal nodes to explore salt tolerance in three rice cultivars, including CSA-Pi9, CSA (Ciherang+Sub1+AG1), and Dongjin (DJ). We identified 3016 differentially modulated proteins under salinity. Functional annotation revealed that CSA-Pi9 activates coordinated protective processes contributing to superior performance, such as sodium exclusion with potassium retention, membrane remodeling, and cuticle reinforcement via lipid and sterol metabolism, and sustained energy production with balanced sugar, nitrogen, and water metabolism, compared to the sensitive cultivar DJ under salt stress. These proteome-wide insights highlight complex regulatory networks underlying salinity tolerance in rice and provide potential molecular targets for breeding strategies to enhance crop resilience under adverse environments.