Unraveling the Saline–Alkali–Tolerance Mystery of Leymus chinensis Nongjing–4: Insights from Integrated Transcriptome and Metabolome Analysis

Soil salinization–alkalization is a critical abiotic constraint on global agriculture, threatening agroecosystem sustainability. Leymus chinensis, a high–quality perennial forage with strong stress resilience, is an ideal model for studying saline–alkali tolerance in graminaceous crops. We integrated physiological, transcriptomic, and metabolomic profiling to dissect its responses under moderate vs. severe carbonate stress, mimicking natural saline–alkali soils rather than single salt stress treatments. Multi–omics analysis revealed drastic reprogramming of energy metabolism, carbohydrate homeostasis, water transport, and secondary metabolism. Our novel finding reveals that L. chinensis uses stress–severity–dependent mechanisms, with flavonoid biosynthesis as a central “regulatory hub”: moderate saline–alkali stress acts as a stimulus for “Adaptive Activation” (energy + antioxidants), promoting growth, while severe stress exceeds tolerance thresholds, causing “systemic imbalance” (oxidative damage + metabolic disruption) and growth retardation. Via WGCNA and metabolome–transcriptome modeling, 22 transcription factors linked to key flavonoid metabolites were identified, functioning as molecular switches for stress tolerance. Our integrated approach provides novel insights into L. chinensis’ tolerance networks, and the flavonoid biosynthesis pathways and regulatory genes offer targets for precision molecular breeding to enhance forage stress resistance and mitigate yield losses from salinization–alkalization.