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. <i>Leymus chinensis</i>, 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 <i>L. chinensis</i> 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 <i>L. chinensis</i>' 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.