Determinants for deleterious epigenetic phenotypes

Current crop production needs to double to accommodate a growing population, alleviate the impact of climate change and ensure food security (Ray et al., 2013). Exploiting epigenetic variability in plants is an innovative way to improve crop traits which have agricultural importance. It also increases phenotypic plasticity in a way which is otherwise unobtainable from genetic engineering alone. Epigenetic variance exists naturally within plant varieties, with the absence of fruit ripening in tomatoes being attributed to an epiallele in the SBP-box transcription factor gene. Also, unlike in mammals, in plants a large proportion of epialleles can be transgenerationally inherited allowing the formation of stable plant lines. Despite its benefits, epigenetic studies in plants have been explored with difficulty. The main limitation in the use of epigenetic traits in agriculture, is the inability to induce sufficient epigenetic diversity without interfering with critical developmental pathways. The introduction of epigenetic variation in plants has been associated with strong developmental phenotypes and unviability. In rice, mutations in MET1 - coding for the methyltransferase involved in CG methylation- result in developmental arrest following germination. Moreover, in Arabidopsis met1 mutants there is a transgenerational decrease in fitness and fertility. The existence of a transgenerational developmental phenotype and the absence of knowledge regarding its determinants, is the largest barrier to the study of epigenetic trait development. It is therefore the aim of this project to identify the epialleles which are responsible for this transgenerational deleterious phenotype. In the hope that the regulation and repression of the causative epialleles will reduce the effect of the deleterious phenotypes; facilitating further study into the use of epigenetic variance to improve crop traits. Evidence in support of this approach was gained from Arabidopsis epigenetic recombinant inbred lines (epiRILs). In which a 2.5Mb region under negative selection was identified and will be the focus of this investigation.