Genomics of trait canalization in tomato

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Plant development represents a balance between phenotypic robustness and flexibility (canalization) in response to genetic and environmental perturbations. In light of global climatic changes and the decreasing availability of usable water, maintaining our current crop production rate will depend on understanding the mechanisms that regulate phenotypic stability. We propose to develop a genomic perspective on trait canalization in tomato by focusing our phenotyping efforts on common genetic resources using a common ontology. We will explore canalization of cultivated tomato (Solanum lycopersicum) in comparison with Solanum pennellii, making use of previous and newly developed populations such as F2, introgression lines and backcross inbred lines. With these genetic resources, in homozygous and heterozygous states (in F1 hybrids), we will fine-map quantitative trait loci (QTL) and epistatic genomic regions for development, physiology, metabolism and yield. All data will be linked via ontology descriptors, map positions, and mode of inheritance of QTL, and uploaded to Phenom Networks, which is a WEB2 platform for statistical genomics of complex phenotypes. The ability to probe the phenotypic diversity in multiple genetic and environmental layers, combined with the available genome sequences of both parental species, will allow us to identify and clone QTL, genes and microRNAs that impact canalisation. This will enable breeding for yield stability as well as addressing the long-standing question on the genetic bases of the canalization stream that modulates phenotypes to follow a restricted path.