Integrated Physiological, Transcriptomic, and Proteomic Analyses Reveal Alkali Stress Response and Tolerance Mechanisms of Rhododendron obtusum ‘Fenzhuanglou’ Seedlings

Soil alkalization limits the cultivation of Rhododendron, an acidophilic ornamental genus, yet the alkali tolerance threshold of R. obtusum ‘Fenzhuanglou’ remains undefined. Seedlings were exposed for 40 d to mixed alkali (NaHCO3:Na2CO3 = 9:1; 0, 50, 60, and 70 mmol·L−1), combining physiological assays with RNA-seq and DIA proteomics of control and 60 mmol·L−1 leaves. The 50 mmol·L−1 treatment caused no visible injury, 60 mmol·L−1 defined the visible-injury threshold, and 70 mmol·L−1 caused severe, progressive damage. Chlorophyll b fell to about 20% of the control by 40 d under 60–70 mmol·L−1; antioxidant enzymes peaked at 20 d and then collapsed, while malondialdehyde accumulated dose-dependently, indicating late-stage failure of reactive oxygen species scavenging. Transcriptomics identified 7214 differentially expressed genes enriched in MAPK signaling, hormone signal transduction, and circadian rhythm; proteomics quantified 7452 proteins, including 1093 differentially expressed proteins enriched in flavonoid biosynthesis and α-linolenic acid metabolism. The low mRNA–protein correlation (ρ = 0.14–0.20) is consistent with transcript–protein decoupling potentially involving post-transcriptional regulation, protein stability, and turnover. These results define 60 mmol·L−1 as the tolerance limit of this cultivar and, to our knowledge, provide the first integrated multi-omics framework for alkali adaptation in Rhododendron.