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In this study, metabolite profiles of maize (<jats:italic>Zea mays<\/jats:italic> L.) leaves and roots were compared between six low\u2010Pi\u2010sensitive lines and six low\u2010Pi\u2010tolerant lines under Pi\u2010sufficient and Pi\u2010deficient conditions to identify pathways and genes associated with the low\u2010Pi 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\u2010deficient conditions. Among them, the 11 most stable metabolites showed significant differences under low\u2010 and normal\u2010Pi conditions based on the coefficient of variation (<jats:styled-content style=\"fixed-case\">CV<\/jats:styled-content>). Isoleucine and alanine were the most stable metabolites for the identification of Pi\u2010sensitive and Pi\u2010resistant maize inbred lines. With the significant correlation between morphological traits and metabolites, five low\u2010Pi\u2010responding consensus genes associated with morphological traits and simultaneously involved in metabolic pathways were mined by combining metabolites profiles and genome\u2010wide association study (<jats:styled-content style=\"fixed-case\">GWAS<\/jats:styled-content>). The consensus genes induced by Pi deficiency in maize seedlings were also validated by reverse\u2010transcription quantitative polymerase chain reaction (<jats:styled-content style=\"fixed-case\">RT<\/jats:styled-content>\u2010<jats:styled-content style=\"fixed-case\">qPCR<\/jats:styled-content>). Moreover, these genes were further validated in a recombinant inbred line (<jats:styled-content style=\"fixed-case\">RIL<\/jats:styled-content>) population, in which the glucose\u20106\u2010phosphate\u20101\u2010epimerase encoding gene mediated yield and correlated traits to phosphorus availability. Together, our results provide a framework for understanding the metabolic processes underlying Pi\u2010deficient responses and give multiple insights into improving the efficiency of Pi use in maize.<\/jats:p>","DOI":"10.1111\/tpj.14160","type":"journal-article","created":{"date-parts":[[2018,11,25]],"date-time":"2018-11-25T10:29:48Z","timestamp":1543141788000},"page":"947-969","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":116,"title":["Metabolite profiling and genome\u2010wide association studies reveal response mechanisms of phosphorus deficiency in maize seedling"],"prefix":"10.1111","volume":"97","author":[{"given":"Bowen","family":"Luo","sequence":"first","affiliation":[{"name":"Maize Research Institute Sichuan Agricultural University 611130 Sichuan Chengdu China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Ma","sequence":"additional","affiliation":[{"name":"Maize Research Institute 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