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.