Analysis of DNA methylation levels in wild and cultivated tomato species

Tomato plants are used as a model system to study fruit development and quality. Tomato fruit development can be divided into three main phases: cell division, cell elongation and fruit ripening. All these phases are associated with deep changes at the gene expression as well as at the epigenetic level. Cytosine methylation is an epigenetic mark associated with genetic inactivity and heterochromatin state in higher eukaryotes, including plants. In plants cytosines are mainly methylated at CG and CXG contexts and, at low levels, at CXX. These methylated sequences are widespread in the whole genome, but are present at higher density at LTR-retrotransposons. Using genomic DNA methylation assays, we analysed the global and locus specific variations of CG and CXG methylation patterns to understand the potential role of epigenetic mechanisms during the development of tomato plants. The analysis showed changes in the cytosine methylation pattern at CG and CXG sites in fruits of the cultivated tomato Ailsa Craig (Teyssier et al., 2008, Planta 228: 391-9). Domesticated and wild tomato species do show remarkable differences in terms of shape, colour, timing and development of fruits, therefore it is very interesting to compare these species also in terms of epigenetic variations. The preliminary comparative analysis of DNA methylation in wild and cultivated tomato species indicated contrasting situations, characterized by different patterns of DNA methylation at repetitive loci such as the 5S rDNA, various retrotransposons and at single loci. Furthermore, the analysis of the abundance of retrotransposons between species revealed differences in distribution and amount between wild and cultivated tomato species. A specific transposon-related case will be described, suggesting that the domestication process of tomato cultivated species might have been associated with DNA epigenetic variations.