RT Journal
A1 Blein-Nicolas, Mélisande
A1 Negro, Sandra Sylvia
A1 Balliau, Thierry
A1 Welcker, Claude
A1 Cabrera-Bosquet, Llorenç
A1 Nicolas, Stéphane Dimitri
A1 Charcosset, Alain
A1 Zivy, Michel
T1 A systems genetics approach reveals environment-dependent associations between SNPs, protein coexpression, and drought-related traits in maize
JF Genome Research 
JO Genome Research 
YR 2020 
FD November 01 
VO 30 
IS 11 
SP 1593 
OP 1604 
DO 10.1101/gr.255224.119 
UL http://genome.cshlp.org/content/30/11/1593.abstract 
AB The effect of drought on maize yield is of particular concern in the context of climate change and human population growth. However, the complexity of drought-response mechanisms makes the design of new drought-tolerant varieties a difficult task that would greatly benefit from a better understanding of the genotype–phenotype relationship. To provide novel insight into this relationship, we applied a systems genetics approach integrating high-throughput phenotypic, proteomic, and genomic data acquired from 254 maize hybrids grown under two watering conditions. Using association genetics and protein coexpression analysis, we detected more than 22,000 pQTLs across the two conditions and confidently identified 15 loci with potential pleiotropic effects on the proteome. We showed that even mild water deficit induced a profound remodeling of the proteome, which affected the structure of the protein coexpression network, and a reprogramming of the genetic control of the abundance of many proteins, including those involved in stress response. Colocalizations between pQTLs and QTLs for ecophysiological traits, found mostly in the water deficit condition, indicated that this reprogramming may also affect the phenotypic level. Finally, we identified several candidate genes that are potentially responsible for both the coexpression of stress response proteins and the variations of ecophysiological traits under water deficit. Taken together, our findings provide novel insights into the molecular mechanisms of drought tolerance and suggest some pathways for further research and breeding.