Conclusion
We aimed to dissect the genetic architecture of tomato response to different environments involving control and stress growing conditions. The MAGIC population demonstrated a large genetic variability in response to abiotic stresses which was reflected by the identification of 63 plasticity QTLs. This was achieved through the use of different plasticity parameter highlighting the importance of plasticity quantification for deciphering its genetic basis. The plasticity QTLs were in majority (65% of the plasticity QTLs) located in distinct regions than the QTLs detected for the mean phenotypes, suggesting a specific genetic control of mean trait variation and plasticity at some extent. Using plasticity as a trait per se in mapping analysis turned out to be a good method for identifying genetic regions underlying GxE. Almost all the QEI were also identified for at least one of the plasticity parameters. Overall, this study presents the MAGIC population as a powerful resource for tomato breeding under abiotic stress conditions, as well as for understanding the genetic mechanisms regulating tomato response to environmental variation.