Metabolic Trade-Off Between Carbon and Phenylpropanoid Pathways in Wheat Under Saline-Alkali Stress Revealed by Multi-Omics Analysis.

Wheat production is severely limited by soil salinity-alkalinity, yet the molecular mechanisms governing seed germination under such stress remain largely unelucidated. This study employed integrated transcriptomics, metabolomics, and WGCNA to decipher the adaptation strategies of germinating wheat seeds to gradient saline-alkali stress. Our results showed that stress induced a functional differentiation in carbon metabolism: fructose and mannose metabolism was enhanced, whereas starch and sucrose metabolism was inhibited. Concurrently, the phenylpropanoid defense network was differentially regulated, with the upstream backbone suppressed but the downstream stilbenoid biosynthesis branch specifically activated. WGCNA identified a core co-expression module (MEblue) enriched in these pathways, from which nine candidate hub genes, including SNL3 and TPS1, were identified based on their strong correlations with key metabolites. These findings provide crucial candidate gene targets for molecular breeding of saline-alkali tolerant wheat.