Defining seedling stage-specific metabolic adaptations to salinity in landrace Pokkali and cultivated rice IR64

Understanding the biochemical basis of salinity tolerance in naturally evolved landraces cultivated in seawater along coastal India is key to improving elite rice (Oryza sativa L.) genotypes. We conducted a detailed time-course metabolome profiling of two contrasting genotypes: the salt-sensitive IR64 and the salt-tolerant wild rice Pokkali. Principal component analysis revealed distinct metabolic profiles under control and stress, with salinity inducing significant, time-dependent reprogramming. The genotypes showed clear metabolic distinctions between early and prolonged stress phases, highlighting osmotic vs. ionic responses. Pokkali accumulated protective metabolites like proline and glutathione, while IR64 showed elevated tricarboxylic acid cycle intermediates. Differential buildup of phytohormone precursors-azelaic acid, phenylalanine, and tryptophan-suggested their roles in salinity response. Pokkali rapidly restored cellular homeostasis via rapid accumulation of trehalose (4.3×), tryptophan (6.2×), proline (2.2×), glutamate (3.2×), and hydroxyproline (3.3×). Glutamate, a central amino acid metabolism regulator, accumulated prominently in Pokkali, whereas IR64 exhibited higher γ-aminobutyric acid (GABA) (9×) and phenylalanine (4×), indicating cellular stress damage. Exogenous proline application and GABA biosynthesis inhibition confirmed their contrasting roles in stress response and genotype-specific salinity tolerance. Our extensive metabolic dataset and salt-tolerance biomarkers offer valuable insights for developing resilient rice cultivars for saline environments.