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SUMMARY  Inorganic phosphorus (Pi) is an essential element in numerous metabolic reactions and signaling pathways, but the molecular details of these pathways remain largely unknown. In this study, metabolite profiles of maize ( Zea mays  L.) leaves and roots were compared between six low‐Pi‐sensitive lines and six low‐Pi‐tolerant lines under Pi‐sufficient and Pi‐deficient conditions to identify pathways and genes associated with the low‐Pi stress response. Results showed that under Pi deprivation the concentrations of nucleic acids, organic acids and sugars were increased, but that the concentrations of phosphorylated metabolites, certain amino acids, lipid metabolites and nitrogenous compounds were decreased. The levels of secondary metabolites involved in plant immune reactions, including benzoxazinoids and flavonoids, were significantly different in plants grown under Pi‐deficient conditions. Among them, the 11 most stable metabolites showed significant differences under low‐ and normal‐Pi conditions based on the coefficient of variation ( CV ). Isoleucine and alanine were the most stable metabolites for the identification of Pi‐sensitive and Pi‐resistant maize inbred lines. With the significant correlation between morphological traits and metabolites, five low‐Pi‐responding consensus genes associated with morphological traits and simultaneously involved in metabolic pathways were mined by combining metabolites profiles and genome‐wide association study ( GWAS ). The consensus genes induced by Pi deficiency in maize seedlings were also validated by reverse‐transcription quantitative polymerase chain reaction ( RT ‐ qPCR ). Moreover, these genes were further validated in a recombinant inbred line ( RIL ) population, in which the glucose‐6‐phosphate‐1‐epimerase encoding gene mediated yield and correlated traits to phosphorus availability. Together, our results provide a framework for understanding the metabolic processes underlying Pi‐deficient responses and give multiple insights into improving the efficiency of Pi use in maize.

Metabolite profiling and genome‐wide association studies reveal response mechanisms of phosphorus deficiency in maize seedling