The Role of DNA Methylation in the Domestication of Tomato

Epigenetic modifications contribute to phenotypic variation through their effect on phenomena such as genome stability and patterns of gene expression.  Large scale epigenome studies have been carried out on both model and non-model plant species but little is known about the role of epigenetics in the phenotypic changes that occur during the domestication process.  We used bisulfite sequencing to compare DNA methylation patterns in two accessions of cultivated tomato (Solanum lycopersicum) and three accessions of its putative wild ancestor (S. pimpinellifolium).  All epigenomes were aligned with the reference genome of S. lycopersicum 2.50 from the Sol Genomics database using Bismark. Mapping efficiency was high for all libraries. Patterns of cytosine methylation were similar in all accession: 52%, 45% and 3% for CpG, CHG and CHH respectively.  Cytosines in the CpG and CHG contexts were highly methylated (95% and 88% respectively). Overall cytosine methylation patterns were not correlated with repeat or centromere regions. Despite similar overall methylation rates, several genes were shown to be differentially methylated between the domesticated and wild accessions, including genes implicated in transcription regulation, flower development, and fruit development and ripening, as well as genes involved in metabolism, histone modification, and other cellular processes.  To determine if the differences in methylation are correlated with differences in expression, we used quantitative RT-PCR to compare the expression of these genes in wild and cultivated accessions.  Results will be presented and the potential role of these genes in domestication traits will be discussed.