A proteomics-based systems genetics approach reveals environment-specific loci modulating protein co-expression and drought-related traits in maize

ABSTRACT The evolution of maize yields under drought is of particular concern in the context of climate change and human population growth. To better understand the mechanisms associated with the genetic polymorphisms underlying the variations of traits related to drought tolerance, we used a systems genetics approach integrating high-throughput phenotypic, proteomics and genomics data acquired on 254 maize hybrids grown under two watering conditions. We show that water deficit, even mild, induced a strong proteome remodeling and a reprogramming of the genetic control of the abundance of many proteins. We identify close co-localizations between QTLs and pQTLs, thus highlighting environment-specific pleiotropic loci associated to the co-expression of drought-responsive proteins and to the variations of phenotypic traits. These findings bring several lines of evidence supporting candidate genes at many loci and provide novel insight into the molecular mechanisms of drought tolerance.