Exploring Genetic Diversity in Tomato Fruit with a System Biology Approach

Dissection of the genetic variation and inheritance of phenotypic trait is the first step for plant improvement. The cascade of effects from DNA variation to trait phenotype is organized in complicated biological networks, where intermediate molecular phenotypes such as transcript and protein abundance also vary in populations. However, most of the omics studies developed in crops species focused on one or two genotypes and failed to provide an insight into this natural variation. Tomato (Solanum lycopersicum) is a model organism for the fleshy–fruited plants. Its genome has been fully sequenced and annotated, opening new prospects for analysing biological systems and their complex functions at different levels including genomics, transcriptomics, proteomics, and metabolomics.

In our study a set of 8 tomato lines, which represent 96% of the genetic diversity identified in a collection of 360 accessions was employed to characterize the fruit at different omics levels. Fruits were harvested and pericarp samples analysed at cell expansion stage. Transcriptome profiles obtained by Digital Gene Expression analysis allowed us to identify more than 3000 genes differentially expressed. Proteome profiles revealed by 2D-PAGE revealed more than 300 spots showing quantitative variations between genotypes.

All these data revealed the high natural variation present in the tomato species, in spite of its low genetic diversity. Besides, they permitted the discovery of several correlations within and between levels of analysis revealing the regulatory networks operating during fruit development.

This information will be especially useful to analyse a multiallelic genetic intercross population derived from the 8 lines. The detailed description provided here will help us to identify the genes under the QTL, relating the polymorphisms at the sequence levels with their expression.