ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Crop and Product Physiology
Differential physiological responses and transcriptome co-expression networks of salt-tolerant and salt-sensitive foxtail millet (Setaria italica (L.)) under salt stress
Provisionally accepted
- Shandong Academy of Agricultural Sciences, Jinan, China
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Salt stress severely constrains crop productivity by disrupting ion homeostasis and cellular metabolism. Foxtail millet (Setaria italica (L.)), a stress-resilient cereal, exhibits substantial variation in salt tolerance among accessions, yet the regulatory basis of this divergence remains unclear. Here, we combined physiological measurements, time-course transcriptome profiling, and weighted gene co-expression network analysis (WGCNA) to investigate salt stress responses in a salt-tolerant accession (SDT80) and a salt-sensitive accession (SDS81). SDT80 maintained lower Na+ accumulation, a more stable Na+/K+ ratio, and reduced membrane lipid peroxidation compared with SDS81 under salt stress. Transcriptome analysis revealed dynamic and genotype-specific gene expression patterns, with SDT80 preferentially activating abiotic stress–related pathways, whereas SDS81 showed enrichment in processes associated with photosynthetic impairment and cellular damage. WGCNA identified 23 co-expression modules, among which two key modules were strongly associated with treatment duration, ion contents, and oxidative stress indices. Hub-gene analysis suggested that one module acts as a central regulatory hub coordinating transcriptional regulation, calcium signaling, and metabolic adjustment, whereas the other is primarily involved in detoxification, energy metabolism, and cell wall remodeling. Integrative accession-specific and combined network analyses further indicate that salt tolerance in foxtail millet arises from coordinated, genotype-dependent regulatory networks coupling ion homeostasis, stress signaling, and metabolic reprogramming rather than from single-gene effects. Collectively, these findings provide a modular network framework and candidate targets for improving salt tolerance in millet and other crops.
Keywords: co-expression network, foxtail millet, Salt-sensitive, Salt-tolerant, Setaria italica, WGCNA
Received: 21 Dec 2025; Accepted: 22 Jan 2026.
Copyright: © 2026 Liu, Wang, Hou, Tian, Xie, Bai, Cong, Yang and Liu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Min Liu
Wei Liu
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