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Metabolic genome-wide association studies (mGWAS),whereupon metabolite levels are regarded as traits,can help unravel the genetic basis of metabolic networks.A total of 309Arabidopsis accessions were grown under two independent environmental conditions (control and stress) and subjected to untargeted LC-MS-based metabolomic profiling;levels of the obtained hydrophilic metabolites were used in GWAS.Our twocondition-based GWAS for more than 3000 semi-polar metabolites resulted in the detection of 123 highly resolved metabolite quantitative trait loci (p ≤ 1.0E-08),24.39％ of which were environment-specific.Interestingly,differently from natural variation in Arabidopsis primary metabolites,which tends to be controlled by a large number of small-effect loci,we found several major large-effect loci alongside a vast number of small-effect loci controlling variation of secondary metabolites.The two-condition-based GWAS was followed by integration with network-derived metabolite-transcript correlations using a time-course stress experiment.Through this integrative approach,we selected 70 key candidate associations between structural genes and metabolites,and experimentally validated eight novel associations,two of them showing differential genetic regulation in the two environments studied.We demonstrate the power of combining large-scale untargeted metabolomics-based GWAS with time-course-derived networks both performed under different abiotic environments for identifying metabolite-gene associations,providing novel global insights into the metabolic landscape of Arabidopsis.