Aconserved salt-stress co-expression network in japonica rice reveals partially dissociated hub gene connectivity and transcriptional induction.

Introduction: Soil salinity severely compromises rice ( Methods: We performed integrated RNA sequencing and weighted gene co-expression network analysis (WGCNA) on three japonica rice varieties under control (0 mM), moderate (85.6 mM), and severe (136.9 mM) NaCl stress. Results: All three varieties exhibited basal salt tolerance. Differential expression analysis identified 2,067 and 4,900 non-redundant differentially expressed genes (DEGs) under moderate and severe stress, with 205 and 1,093 DEGs shared across the three varieties, respectively. WGCNA identified 32 co-expression modules. The brown module showed the strongest dose-dependent response to salt stress and was enriched in phenylpropanoid biosynthesis, plant hormone signal transduction, and MAPK signaling; its eigengene was highly concordant across varieties (mean r = 0.987), consistent with a shared leaf-level transcriptional program. Across brown-module genes, intramodular connectivity and salt-induced fold change were positively but only moderately correlated (Pearson r = 0.377): Discussion: Connectivity and induction thus reflect complementary aspects of the salt-stress response, and candidate hub genes for molecular breeding should be prioritized by both criteria jointly, followed by validation across diverse genetic backgrounds.