Genomic location of the MAGIC-MET QTLs
The availability of substantial genomic information in tomato enabled the identification of different genomic regions which have undergone selective sweeps which were strongly selected during the domestication and improvement process (Lin et al. 2014; Zhu et al. 2018). When projected on the physical positions of the tomato reference genome (SL2.50 version), most of the plasticity QTLs we identified were located within the sweep regions defined by Zhu et al. (2018). It therefore suggests that plasticity might have been selected together with other interesting agronomic traits during tomato domestication and improvement. For instance, this is corroborated by the positive correlation between slope (from the Finlay-Wilkinson regression model) and mean fruit weight variation. Indeed, genotypes with higher FW slope are characterized by good adaptability in high quality environments and will likely be intended to selection. Co-selection of allelic variants leading to higher performance in optimal condition together with plasticity alleles is a realistic assumption that would explain the significant correlation that we observed between the genotypic means and plasticity. In rice for instance, GhD7 has been described as a key high-yield gene simultaneously involved in the regulation of plasticity of panicle and tiller branching and involved in abiotic stress response (Herath 2019). This example highlights a gene carrying different allelic variants affecting together plasticity and mean phenotypes. Further investigations are needed to assess how domestication and breeding have affected plasticity in tomato and other crop species.
An important genomic region involved in the genetic regulation of plasticity for six different traits was identified in chromosome 11 (Supplemental Figure 9). This region is obviously a regulatory hub carrying interesting plasticity genes. It remains to determine if the co-localization of the different plasticity QTLs in this region is due to the action of a pleiotropic gene or different linked genes. Nevertheless, the chromosome 11 region highlighted here is an interesting target for breeding as well as for understanding the functional mechanisms of plasticity genes.