Plants produce a vast array of chemically and biologically different compounds.These compounds are not only important for plant themselves and their interactions with the environment,but also provide indispensable resources for humans as sources for nutrition,energy,and medicine.Understanding the genes involved in metabolism and dissection of the metabolic pathway are essential to improve plant adaptation to environmental stresses,to improve food quality,and to increase the yield of major crops such as rice and maize through metabolomics-based breeding.Here we report the genetic studies of crop metabolomes combining both metabolic quantitative trait locus (QTL) mapping and metabolic genome-wide association study (GWAS).Hundreds of loci with high resolution and large effects were uncovered.Data mining revealed a large number of candidate genes underlying metabolites that are of physiological and agronomical importance.Our forward-genetics-based strategy provides a powerful tool for large-scale gene-metabolite annotation and identification,pathway elucidation and knowledge about crop improvement.