Plant development represents a balance between phenotypic stability and plasticity in response to genetic and environmental perturbations. This balance was termed canalization - the property of a developmental process of being to some extent modifiable but to some extent resistant to modification. In light of global climatic changes and the need to maintain our current crop productivity rates we aim to better understand the factors that regulate phenotypic canalization. We explored the pattern of canalization of 16 “homologous” traits in 31 varieties of tomato, pepper, eggplant, melon, watermelon, sunflower and maize. We found remarkable similarity in trait canalization patterns where those associated with reproduction and yield were plastic and the rest were consistently stable in all crops. For a particular genotype the highest variation was found for seed number produced per plant while single seed weight was the most stable trait for all entries. These conserved ancestral canalization patterns in higher plants indicated that tomato is as good a system as any to investigate the genetic basis of canalization. Meta analysis of 20 years of “historic” tomato data which is publically available via ‘Phenome Networks’ led to the identification of a number of quantitative trait loci (QTL) of Solanum pennellii origin that affected yield stability. In some hybrids heterosis was shown to be a factor that induced yield stability, an observation that is well documented in modern agriculture. Validation of the effect of these historic QTL was done using a new experimental design that generates multiple estimates of the coefficient of variation of traits as well as their reaction norms in optimal and water stress environments. For example, the introgression line IL10-2-2 did not affect mean yield but doubled its stability in three years of consecutive trials as well as in fine mapping analysis. This 2 Mbp genomic segment is the first QTL identified for yield stability in any plant and we hope that further studies of stable and plastic genotypes will allow us to address the long-standing question of the genetic basis of Waddindton’s theory of canalization.