Ion-structured transcriptional network reorganization is associated with tissue-specific adaptation to saline-alkaline stress in sorghum.

Saline-alkaline stress imposes complex ionic and high-pH constraints that disrupt cellular homeostasis and metabolic stability in crops. Here, we suggest that in Sorghum bicolor, ionic imbalance is associated with coordinated transcriptional network patterns. Integrating ion homeostasis measurements, antioxidant enzyme profiling, and weighted gene co-expression network analysis (WGCNA), we characterized tissue-specific responses to saline-alkaline stress induced by 50 mM Na₂CO₃ (pH ≥ 10.5) after 24 and 72 h of exposure. Stress induced pronounced Na⁺ accumulation in both leaf and root tissues, whereas K⁺ levels remained stable in leaves but declined markedly in roots, revealing divergent ionic regulation strategies. Transcriptomic analysis uncovered distinct temporal dynamics, with roots exhibiting broader and more sustained reorganization. WGCNA identified Na⁺- and K⁺-associated co-expression modules whose eigengene expression closely paralleled ion dynamics. In leaves, a Na⁺-correlated module enriched for endoplasmic reticulum protein folding components underwent coordinated repression. In roots, a K⁺-associated module enriched for plastid metabolism and ion transport declined in parallel with K⁺ depletion. Hub gene connectivity strongly aligned with ion traits, supporting structured and ion-associated network patterns. Together, these findings suggest that ionic imbalance is closely associated with tissue-specific stress responses and provide candidate modules and hub genes for future functional validation of saline-alkaline tolerance in sorghum.