Salt-alkali stress critically limits plant growth and agriculture. Leymus chinensis, a dominant perennial grass in the saline-alkali soils of the Songnen Plain in Northeast China, possesses strong environmental adaptability and high forage value. Two natural ecotypes, Yellow-Green (YG) and Gray-Green (GG), are found in this region, yet their morphological and adaptive differences have not been systematically elucidated. This study compared the physiological responses and transcriptome changes of these ecotypes under neutral salt and alkaline salt treatments to evaluate their salt-alkali tolerance. The GG ecotype accumulated more hemicellulose and total pectin in its roots. Under low salt-alkali stress, photosynthetic pigment synthesis and ion accumulation were promoted in both ecotypes. However, under high stress, the GG ecotype exhibited significantly higher activities of Na⁺-K⁺-ATPase and Ca²⁺-Mg²⁺-ATPase compared to YG, supporting superior ion homeostasis. Concurrently, the maximum photochemical efficiency of photosystem II remained stable in GG, with non-photochemical quenching increasing, yielding superior photosynthetic protection. Salt-alkali stress caused reactive oxygen species (ROS) accumulation in both ecotypes, especially in YG. The GG ecotype maintained a more efficient antioxidant defense system by significantly enhancing antioxidant enzyme activities and antioxidant content. Transcriptome analysis revealed that under high stress, key pathways (e.g., MAPK signaling, phenylpropanoid metabolism, starch and sucrose metabolism) were activated in GG leaves. In roots, mitochondrial oxidative phosphorylation and the tricarboxylic acid cycle were enhanced. Thus, the GG ecotype exhibits an efficient regulatory network for coping with salt-alkali stress by regulating ion homeostasis, photosynthetic protection, ROS scavenging, and multiple metabolic pathways, thereby conferring greater tolerance.
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