Time-course transcriptomic and proteomic analysis reveals dynamic regulation landscape of maize salt-alkali tolerance

Soil salinization and alkalinity are major threats to maize production worldwide. To dissect the dynamic molecular responses and co-expression network underlying salt-alkali tolerance, we conducted a time-series multi-omics study using two maize inbred lines contrasting in salt tolerance: HCL195 (tolerant) and HCL660 (sensitive). Root samples were collected at 0, 12, 24, 48, and 72 h after treatment with 100 mmol/L saline-alkali solution for RNA sequencing, and at 0, 24, and 72 h for protein quantification. HCL195 showed superior growth and a markedly stronger and sustained transcriptional response, with 2,492 genes differentially expressed at all stress time points, compared to 700 in HCL660. KEGG enrichment analysis revealed that phenylpropanoid and diterpenoid biosynthesis pathways were significantly enriched in both lines across all time points. Most genes in these pathways exhibited overall upregulation with temporal dynamics in response to salt-alkali stress. Proteomic profiles corroborated the transcriptomic result that HCL195 maintained a higher proportion of up-regulated proteins. Joint transcriptome-proteome analysis identified 36 up- and 142 down-regulated concordant genes at 72 h in HCL195. Through construction of a transcription factor (TF)–target gene co-expression network, we identified seven hub TFs that collectively regulate 271 genes, three of which are known to be related to salt tolerance. These results highlight that sustained activation of key secondary metabolic pathways and antioxidant modules, driven by a core set of TFs, underpins maize salt tolerance.