Genetic location of the MAGIC-MET QTLs
The physical positions based on the SL2.50 version of the reference genome, were used to compare the position of the different QTL category (genotypic means, plasticity or QEI). Indeed, a recent study has identified different tomato regions (Sweep regions) that were selected during domestication and improvement events (Zhu et al., 2018). These regions were cross checked against the positions of our QTLs. Some QTLs detected in the MAGIC-MET design were located in large regions thus colocating with a high number of Sweep regions (Figure 5 & Supplemental Figure 7). Thus, considering only the QTLs with CI lower than 2Mbp intervals and all QEI, a total of 61 QTLs were selected and compared with the Sweep regions. Plasticity QTLs appeared to be in majority located within the Sweep regions and only 6% of the selected plasticity QTLs were outside the domestication/improvement selective sweeps (Supplemental Figure 8). Interestingly, the Sweep region SW75 located in chromosome 3 (between 64.76 and 65.01 Mbp) carried a total of five QTLs (ht3.1, fset3.1, flw3.2, leaf3.1, fset3.1). The Supplemental Table 5 presents all the Sweep regions holding at least one MAGIC-MET QTL. Chromosome 11 was highlighted as holding a number of plasticity QTLs for different traits (Figure 3). Indeed, seven different QTLs all identified with plasticity parameters, were located within the Sweep regions SW254 and SW255, from 53.81 – 55.62 Mbp on chromosome 11 (Supplemental Figure 9). Among the ten QTLs that were outside the Sweep regions, one QTL was identified for mean FW and located on chromosome 5 (fw5.1) in position 4.52 Mbp. This QTL was mapped in a region holding other QTLs segregating in the MAGIC population for fruit size, fruit width and fruit length (Supplemental Table 6; data from the experiment in Pascual et al. (2015)).