Plants can produce metabolites to directly involve in various biological pathways. Obtaining variations of specific metabolites in different genotypes would facilitate the understanding underlying complex genetic architecture of maize. One of most representative natural diversity panel, 282 Goodman Diversity Panel, was used to perform LC-MS on tips and bases of leaves of each genotype. In total, 7,000 mass features were survived after filtering. Based on the retention time, three major metabolites were separated, phenylpropanoids, benzoxazinoid-like and flavonoid-like absorbance profiles. Using these metabolites, GWAS results shew that the majority of metabolites were controlled as significantly associated with genomic loci. This massive information from metabolomic side can be served as a valuable source for bridging the gap between genotype and phenotype, which provides an opportunity to explain phenotypic variants. The Plant Cell: