Untargeted metabolomics reveals key metabolites and genes underlying salinity tolerance mechanisms in maize

Abstract

Understanding the physiological, metabolic, and genetic mechanisms underlying salt tolerance is essential for improving crop resilience and productivity, yet their complex interactions remain poorly defined. We compared physiological and metabolic responses to salinity between two contrasting maize inbred lines: the salt-sensitive C68 and the salt-tolerant NC326. The senstitivity of C68 was characterized by reduced shoot and root dry weights and plant height, high tissue accumulation of Na and Cl, but low K, and lower leaf proline accumulation compared to the salt-tolerant NC326. Untargeted metabolomics identified 56 metabolites categorized as constitutively upregulated or salt-responsive. In NC326, constitutive accumulation of flavonoids, including schaftoside, tricin, and kaempferol-related compounds in leaves suggests adaptive priming against oxidative stress, while constitutively higher lipids and fatty acids in roots may enhance membrane stability. Salt-responsive metabolites, notably antioxidants and lanosterol, highlighted inducible oxidative-stress mitigation and membrane-stabilization strategies. By integrating metabolomic and genetic analyses, we identified 10 candidate genes involved in the biosynthesis of key metabolites. These findings establish a comprehensive platform for functional validation of metabolites and candidate genes for developing maize varieties with improved resilience to soil salinity through targeted breeding or biotechnological strategies. Plane Language SummarySalinity, or high salt content in soil, is a major challenge to crop growth worldwide, reducing food production. Maize, an important crop globally, struggles to grow under salty conditions. This study compared two maize types--one that grows well in salty soil and one that struggles--to understand how maize plants adapt to salt stress. Using advanced techniques, we measured hundreds of compounds (metabolites) in plant tissues to identify protective substances. We discovered that plants resistant to salt stress naturally produce higher amounts of protective substances, helping them avoid damage from salt. Additionally, we found specific metabolites that plants produce when exposed to salty conditions to protect their cells. We also identified genes that control the production of these important metabolites. This research provides new insights into how maize plants manage salt stress and highlights potential targets for developing crops that grow better in saline soils. Core IdeasO_LIMaize genotypes differ in growth, ion balance, and proline under salt stress. C_LIO_LIMetabolomics reveals pre-stress buildup of protective flavonoids and fatty acids. C_LIO_LISalt triggers metabolic changes like sterol increase to protect membranes. C_LIO_LIGenetic analysis links genes to key metabolites controlling salt tolerance. C_LIO_LIMetabolite-gene insights guide breeding of maize for salt resilience C_LI