Integrative transcriptome and metabolome analysis reveal key pathways in combined salt-alkali tolerance of wheat (Triticum aestivum L.)

• Two salt-alkali-tolerant (ST) and two sensitive (SS) wheat genotypes showed contrasting growth and stress responses under sodium sulfate. • ST wheat had higher soluble sugars, proline, and SOD activity, with lower MDA, reflecting better osmotic and oxidative stress management. • Transcriptome–metabolome analysis revealed DEGs and pathways—amino acid metabolism, ABC transporters, and glutathione—underpinning ST tolerance, offering targets for breeding resilient wheat. Wheat production in southern Xinjiang is severely limited by sulfate-dominated saline–alkali soils, which are characterized by high salinity and alkalinity, yet the molecular mechanisms underlying varietal differences in tolerance remain poorly understood. Here, we evaluated 120 wheat varieties under sodium sulfate stress and identified two salt-alkali-tolerant (ST) and two salt-alkali-sensitive (SS) genotypes. Compared with SS wheat, ST wheat maintained higher root and shoot growth, accumulated more soluble sugars and antioxidant enzymes (SOD), and exhibited lower membrane damage (MDA) under stress. Transcriptome analysis revealed that key genes such as P5CS/P5CR, SOS1/NHX1 , ABC transporters, and GSHS/GST were significantly upregulated. Metabolomic profiling demonstrated significant enrichment in pathways associated with ABC transporters (67 metabolites), glutathione metabolism (GSH/GSSG, 47 metabolites), and related amino acid metabolism pathways (48 metabolites). Integrated network analysis revealed that the amino acid metabolism-ion transport-glutathione metabolism module represents the central regulatory network associated with stress tolerance. This study provides new insights into the mechanisms of wheat tolerance to sulfate-type saline-alkali stress and offers candidate genes, metabolites, and physiological traits for marker-assisted selection, germplasm screening, and targeted breeding to improve crop performance in saline-alkali soils.