Abstract

Eukaryotic genomes are covalently modified with a diverse set of chromatin marks, which are present on both the DNA and the associated histones (Bird., 2007). These are often linked to silencing of transposable elements (TEs) as part of a genome defence system (Law et al., 2011). There are also effects of these modifications on gene expression, chromosome behaviour and differentiation of pericentric heterochromatin and distal euchromatin. Although these changes do not alter the primary DNA sequence, they are frequently heritable through cell division, sometimes for multiple generations, and can thus often be classified as epigenetic marks. These conserved epigenetic marks have been found to influence many aspects of gene expression and chromosome biology, and they have characteristic genomic distributions. In plants, the regions of methylated DNA are epigenetic marks and have potential to affect gene expression that are transmitted between dividing cells of the same generation. Unlike mammals, DNA methyltransferases in plants are active during gametogenesis and embryogenesis so that patterns of DNA methylation can persist from parent to progeny and do not need to be reset.

Heritable epigenetic features can be gained and lost, similarly to mutational change and they will have been selected by plant breeders and during adaptive change of natural populations. The epigenetic features, however, may not be obviously associated with genetic markers and so they contribute to hidden heritability. In our project, we will find out the regions in tomato that are epigenetically heritable. We will also find why there is DNA methylation in different regions of the genome and which of these regions are likely to influence gene expression. We will then define why it is that heritable stability of DNA methylation varies at different loci. We believe this project will help us shape future strategies for epigenetic modification of plant genomes. It will also allow epigenetic modification to be evaluated as a future strategy for crop improvement alongside gene editing, speed breeding and GM.