Figure 3. Exploration and statistical significance of the landscape of multiple agronomic properties of interest for tomato fruit applying local perturbations in its effective TRN.

(A) Agronomic properties improved by perturbing a single gene as function of efficiency reached by that transcriptional perturbation with respect to the wild-type scenario; only perturbations causing positive mean efficiencies are plotted. Both agronomic properties and efficiencies of a single perturbation are tested on the 169 RILs and error bars represent their minimum and maximum values in both axis. (B) Relationship between agronomic properties in the wild-type genome and the average of the agronomic properties resulting of all single perturbations in the wild-type TRN for each RIL; vertical error bars represent the best and worst optimized re-engineered TRN for a given RIL. (C) Average number of single gene perturbations that overcome a given efficiency threshold in the 169 RILs (light bars; error bars represent standard deviation for the 169 RILs) and average probability of selecting the same gene-perturbation in a set of RILs (dark bars; error bars show standard deviation for all genes of the TRN). Left and right columns represent perturbations of single gene in case of knockout or over-expression, respectively. (A, B) show fitness as related to the acceptability of tomato fruit (blue) and production vs. quality (red); (C) and fitness values associated to maximize only fruit quality (green). Agronomic properties are plotted in arbitrary units.