Understanding the mechanisms of adaptation to the environment in cultivated plants is a promising way to meet the challenge of maintaining food security in the context of global warming. In the case of maize, high-throughput sequencing has revealed that structural variations represent a large part of the genome and could have huge phenotypic effects. Among these, Presence Absence Variants (PAVs) may be involved in adaptation of maize to its environment, but their contribution to the genetic determinism of traits and genotype by environment interactions remains largely unknown. To address this issue, we performed a genome-wide association study between two types of polymorphisms, SNPs and Insetions/Deletions (InDels), and molecular traits obtained from proteomics and metabolomics analyses. The genetic panel used for this study was composed of 254 dent inbred lines genotyped with 978,134 SNPs and 72,041 InDels. The latter encompassed from 37 to 129,700 pb, including thousands of PAVs that are not present in the B73 reference genome. Proteins and metabolites were quantified by mass spectrometry in leaf samples from F1 hybrids obtained by crossing the inbred lines with one flint tester line. Hybrid plants were grown under two watering conditions (well-watered and water deficit) in greenhouse. In total, we detected 61,225 QTLs associated with proteome or metabolome variations. Among these, 4,766 QTLs were exclusively detected by InDels. To take into account the difference of marker density between InDels and SNPs, we used a re-sampling approach which showed that there is no difference for effect size distribution of QTLs between InDels and SNPs and for the number of QTLs detected by InDels or SNPs. Additionally, the QTLs detected by the two types of polymorphism were equally distributed in the two watering conditions. Our results suggest that InDels and SNPs equally contributed to molecular trait variation and response to drought stress.< Réduire