Journal of Agronomy and Field Innovations

Background: Soil salinization poses a threat to rice (Oryza sativa L.) productivity in coastal and irrigated lowland agro-ecosystems threatening food security of billions of people depending on rice as a dietary staple. Physiological and molecular studies have revealed ion-transport and antioxidant mechanisms associated with salt tolerance. However, the metabolic reprogramming connecting genotype to phenotype under salinity is poorly understood. 
Objective: The objectives of this study were to characterize the metabolomic responses of contrasting rice genotypes to graded salt stress using complementary liquid chromatography-tandem mass spectrometry (LC-MS/MS) and gas chromatography-mass spectrometry (GC-MS) platforms, and to identify candidate biomarkers of salt tolerance. 
Methods: Both salt-sensitive (IR64) and salt-tolerant (Pokkali) varieties were subjected to treatments with different concentrations of NaCl (0, 100 and 150 mM) in controlled hydroponic conditions. The leaf and root tissues were subjected to analysis for untargeted and targeted metabolomics and the physiological traits were recorded. The metabolic profiles specific to the genotype and treatment were successfully obtained using multivariate statistical techniques like PCA, HCA, and pathway enrichment analysis. 
Results: The salinity stress induced significant concentrations of osmoprotectants such as proline, glycine betaine, and gamma-aminobutyric acid along with shifts in the levels of carbohydrates, organic acids, and flavonoids, while the tolerant genotype exhibited a greater metabolic flexibility than the sensitive genotype. Comparative metabolome analysis revealed prominent markers related to the mechanisms of tolerance and revealed correlations of specific metabolites with indicators of the physiological response to stress. Moreover, the metabolic pathways being enriched indicate that processes of amino acids metabolism, tricarboxylic acid cycle, and flavonoid biosynthesis are important parts of the metabolic adaptation. 
Significance and Conclusion: The above studies show that the merged metabolomic findings from LC-MS/MS and GC-MS can support the identification of biochemical mechanisms underlying the salinity tolerance of rice genotypes, with the identification of potential biomarkers of relevance for breeding programs based on metabolomics.