Multi-omics and physiological analyses reveal drought-resilience mechanisms in foxtail millet (Setaria italica)

Climate change has increased both the frequency and intensity of droughts, leading to fluctuations in global crop production and posing a threat to agricultural stability and the supply of raw materials in drought-prone areas. Foxtail millet, known for its exceptional drought resistance, water-saving abilities, and a short growth cycle, is an ideal drought-tolerant crop for water-efficient agriculture. This study explores the physiological and molecular mechanisms underlying drought stress resistance in foxtail millet by examining germplasm with varying levels of drought tolerance. A comprehensive approach integrating physiological profiling, transcriptomic, and proteomic analyses was employed to identify key drought-responsive regulators and to validate the role of SiMAPKKK17 in drought tolerance. Under drought stress, phenotypic traits such as plant height were reduced, with a more significant decrease observed in the drought-sensitive accession ‘CMG46’. Drought stress reduced antioxidant enzyme activity (SOD, POD, and CAT) and increased osmotic regulators (proline and soluble sugars) and stress markers (H₂O₂ and MDA) in accessions. Differential expression analysis identified 2181 differentially expressed genes (DEGs) and 249 differentially expressed proteins (DEPs) in ‘CMG46’, while 659 DEGs and 435 DEPs were detected in the drought-tolerant accession ‘JMK10’. KEGG enrichment analysis revealed significant enrichment in the MAPK signalling pathway, a finding that was confirmed by CASE analysis. A differential expression regulation network highlighted SiMAPKKK17 as a novel drought-resistant gene within this pathway. Transgenic lines overexpressing SiMAPKKK17 demonstrated improved growth, enhanced antioxidant defence (increased SOD, POD, and CAT activity), better osmotic regulation, and reduced accumulation of stress markers (H₂O₂ and MDA) under drought stress. qRT-PCR analysis confirmed that SiMAPKKK17 upregulated drought-responsive genes in the MAPK pathway. These results suggest that SiMAPKKK17 functions as a positive regulator of drought tolerance in foxtail millet, integrating MAPK signalling with ROS homeostasis and osmotic adjustment. This study offers valuable insights into the molecular mechanisms of drought tolerance and identifies potential targets for genetic improvement, aiming to enhance drought resilience in foxtail millet. • Investigated the phenotypic and physiological mechanisms of millet’s response to drought stress. • Systematically studied the molecular mechanisms of millet’s response to drought stress through transcriptomic and proteomic analyses. • Identified the MAPK signaling pathway as a key pathway contributing to millet’s adaptation to drought stress. • Validated that overexpression of SiMAPKKK17 in wild-type plants significantly enhances drought tolerance in millet.