Integrated transcriptome and proteome analysis reveals mechanisms underlying salt and alkali stress responses in Miscanthus

Salt and alkali stresses represent significant abiotic factors that adversely affect plant growth and yield. Despite their prevalence, the molecular mechanisms governing plant responses to these stressors remain inadequately understood. This study sought to explore the responses of Miscanthus lutarioriparius , a promising bioenergy crop, to individual and combined salt & alkali stresses through transcriptomic and proteomic profiling. The analyses identified 8150 differentially expressed genes (DEGs) and 2204 differentially expressed proteins (DEPs), with 583 overlapping members. Enrichment analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) highlighted a significant presence of DEGs and DEPs in pathways associated with oxidative metabolism of organic compounds, as well as pathways involving oxidoreductase and transferase activities. Moreover, the construction of a protein-protein interaction network of DEPs identified 12 pivotal proteins that formed four subclusters . The reliability of the transcriptome data was substantiated by validating the expression dynamics of eight identified DEGs utilizing real-time quantitative PCR (RT-qPCR). Additionally, the functional role of a specific dehydrin protein, MlDHN1, in enhancing salt and alkali stress tolerance was verified using the virus-induced gene silencing (VIGS) technique. The results provide valuable insights into the adaptive strategies of Miscanthus to saline and alkaline stresses, pinpointing potential targets for genetically enhancing stress resilience.