Methyl jasmonate enhances rice tolerance to alkaline stress via the auxin pathway

•Alkaline stress significantly increased methyl jasmonate (MeJA) in rice seedlings.•Jasmonate-responsive genes were consistently activated by alkaline stress.•MeJA enhanced rice tolerance to alkaline stress through the auxin pathway. Soil alkalization is a major challenge for global crop production. This study reveals a novel defense mechanism in rice seedlings against alkaline stress, involving methyl jasmonate (MeJA) and auxin pathways. Under alkaline stress (15 mM Na2CO3), rice seedlings exhibited elevated levels of endogenous MeJA and upregulation of JA-responsive genes. Pre-treatment with MeJA (50 µM) significantly improved seedling survival, growth, and mitigated root damage under alkaline stress. This treatment also upregulated genes associated with cell death suppression (OsBI1) and stress tolerance (OsJRL, OsNAC). Notably, MeJA pre-treatment increased auxin (indole-3-acetic acid, IAA) levels in roots, and upregulated genes involved in IAA synthesis (OASA1, OASA2) and auxin signaling (Aux/IAA, ARFs). Blocking auxin transport with N-1-naphthylphthalamic acid intensified root damage under alkaline stress and diminished the protective effect of MeJA. These results highlight the crucial role of MeJA-induced activation of auxin pathway in enhancing rice tolerance to alkaline stress, and provide valuable insights for developing strategies to improve crop resilience in alkaline soils.