Plant material and phenotyping
The MAGIC population was derived from a cross between eight parental lines that belong to Solanum. lycopersicum and Solanum lycopersicum cerasiforme groups. More details about the population development can be found in Pascual et al. (2015). Briefly, the population was composed of about 400 8-way MAGIC lines that underwent three generations of selfing before greenhouse evaluations were carried out. In this study, a subset of 241 to 397 lines was grown in each environment (Supplemental Table 1).
The full genome of each parental line was re-sequenced and their comparison with the reference tomato genome (‘Heinz 1706’) yielded 4 millions SNPs (Causse et al., 2013). From these polymorphisms, a genetic map of 1345 discriminant SNPs was developed (Pascual et al., 2015) and used in the present study for the QTL analysis.