QTL mapping
We used genotypic means and plasticity measurements for every trait as
input phenotypes to decipher the genetic architecture of tomato response
to abiotic stresses. Considering the 10 traits evaluated, a total of 104
unique QTLs were identified for genotypic means and the plasticity
parameters (Supplemental Table 4). The proportion of QTLs shared between
mean and plasticity was about 21%, lower than QTLs that were plasticity
or mean specific (79%). Considering only the 63 plasticity QTLs, 11 and
7 QTLs were specifically detected with the SCv and VAR plasticity
parameters. Plasticity QTLs were detected on every chromosome (Figure
3); however, the chromosome 1 showed the highest number with 12
plasticity QTLs. In this chromosome, plasticity QTLs were detected at
least once for every trait. The chromosome 11 carried a total of 11
plasticity QTLs and interestingly all these QTL (except ppnflw11.1)
co-localized in a short region of the chromosome between 52 and 55 Mbp.
The chromosomes 5, 6 and 10 showed the lowest number (only 3) of
plasticity QTLs. For QTLs detected on genotypic means, the number of
QTLs per chromosome varied from 2 QTLs on chromosomes 6 and 10 to one
QTL on chromosome 1.