Supplementary file 2_Differential physiological responses and transcriptome co-expression networks of salt-tolerant and salt-sensitive foxtail millet (Setaria italica (L.)) under salt stress.xlsx

IntroductionSalt stress severely limits crop productivity by disrupting ion homeostasis and cellular metabolism. Foxtail millet (Setaria italica (L.)), a stress-resilient cereal, exhibits marked natural variation in salt tolerance, yet the regulatory mechanisms underlying this divergence remain unclear.
MethodsHere, we integrated physiological assessments, time-course transcriptome profiling, and weighted gene co-expression network analysis (WGCNA) to dissect salt stress responses in a salt-tolerant accession (SDT80) and a salt-sensitive accession (SDS81). Key indicators of ion balance and oxidative damage were measured, and co-expression modules and hub genes associated with salt tolerance were identified.
ResultsUnder salt stress, SDT80 maintained lower Na+ accumulation, a more stable Na+ /K+ ratio, and reduced membrane lipid peroxidation compared with SDS81. Transcriptomic analyses revealed dynamic and genotype-dependent expression patterns: SDT80 preferentially activated abiotic stress-related pathways, whereas SDS81 showed enrichment in processes linked to photosynthetic inhibition and cellular injury. WGCNA identified 23 co-expression modules, among which two key modules were strongly correlated with treatment duration, ion contents, and oxidative stress indices. Hub-gene analysis suggested that one module functions as a regulatory core integrating transcriptional control, calcium signaling, and metabolic adjustment, while the other is mainly involved in detoxification, energy metabolism, and cell wall remodeling.
DiscussionCollectively, our integrative network analyses indicate that salt tolerance in foxtail millet arises from coordinated regulatory networks coupling ion homeostasis, stress signaling, and metabolic reprogramming rather than single-gene effects, providing candidate targets for improving salt tolerance in millet and other crops.