The evolution of maize yields under water deficit conditions is of particular concern in the context of climate change and human population growth. However, the multiplicity and versatility of drought-response mechanisms make the design of new drought-tolerant varieties a complex task that would greatly benefit from a better understanding of the genotype-phenotype relationship. To provide novel insight into this relationship, we integrated high-throughput phenotypic, proteomics, and genomics data acquired on 254 maize hybrids grown under well-watered (WW) and water deficit (WD) conditions by using association genetics and protein co-expression analysis. By first analyzing the data obtained in each watering condition, we showed that water deficit, even mild, induced a deep proteome remodeling which affected the structure of the protein co-expression network. We also highlighted a reprogramming of the genetic architecture of the abundance of many proteins that may affect the phenotypic traits. We then focused on the plants' response to water deficit by analyzing the plasticity of the different genotypes at the proteome and phenotype levels. We showed that the genetic architecture of plasticity indices, computed as WD/WW log ratios for protein abundances and WD/WW ratios for phenotypic traits, do not overlap with those obtained for the same proteins and traits in each the WW and WD conditions. Work is currently in progress to build molecular networks linking the genome to the phenotype through the proteome based on the data collected in the WW and WD conditions and the plasticity indices.