Transcriptomic analysis of Thai rice varieties at the reproductive stage uncovers potential genetic determinants of salt tolerance

Soil salinity represents a major environmental constraint limiting crop productivity and threatening global food security. Previous evaluation of Thai rice varieties under reproductive stage salinity stress revealed a substantial genetic variation in salt tolerance, providing valuable germplasm for identifying novel tolerance genes. This study aimed to characterize molecular mechanisms underlying salt tolerance differences among contrasting Thai rice varieties through comparative transcriptome analysis. Four local Thai rice varieties with distinct salt tolerance phenotypes were subjected to transcriptomic analysis during their reproductive stages. Physiological and yield-related parameter assessment under salt stress confirmed that ‘Daw Dawk Mai (DD)’, ‘Nahng Nuan (NN)’, and ‘Tah Bahn (TB)’ exhibited greater tolerance than ‘Ta Pow Lom (TP)’ under extreme salt stress conditions. RNA sequencing of flag leaves on days 1 and 3 following salt treatment revealed 5975, 2620, 1017, and 958 differentially expressed genes in ‘TP’, ‘TB’, ‘NN’ and ‘DD’, respectively, indicating salt-sensitive varieties exhibit more extensive transcriptional perturbation. Gene ontology (GO) enrichment and pathway analysis demonstrated that all salt-tolerant varieties (DD, NN, and TB) shared uniquely enriched GO terms, including cold acclimation, protein folding and response to reactive oxygen species (ROS) in the biological process category; chitinase activity in the molecular function category; and cell wall and external encapsulating structure in the cellular component category. Comparative transcriptome analysis indicated three potential salt-tolerant genes, including receptor-like protein kinase (Os07g0534100), OsEULD2 (Os07g0683600), and hypothetical protein (Os11g0160400) that were significantly upregulated under salinity stress uniquely in all three salt-tolerant varieties and exhibited higher expression relative to the salt-sensitive variety (‘TP’) under salt stress conditions. Furthermore, cis-element analysis revealed that an indel within the OsEULD2 promoter may have affected its expression and salt tolerance. Comparative transcriptome analysis successfully identified three salt tolerance candidate genes with potential applications in rice breeding programs. The discovery of conserved stress response pathways and variety-specific regulatory elements advances our understanding of reproductive-stage salt tolerance mechanisms in rice. These findings provide molecular tools for developing salt-tolerant cultivars through marker-assisted selection and contribute to global efforts addressing salinity challenges in rice production systems.