Phenotypic variation in plants Roles for epigenetics

Besides genetics, also epigenetics can play a role in shaping the characteristics of a plant (phenotype). Epigenetics refers to chemical modifications of DNA and proteins associated with the DNA that can influence gene activity (the ‘epigenome’) and can be passed on through cell divisions and following generations.
This thesis aimed to explore relationships between epigenome and phenotype in plants. The focus is DNA methylation, an epigenetic modification that occurs on cytosine bases in the DNA sequence. We studied the role of the epigenome in a phenomenon termed heterosis, which refers to superior performance of hybrids as compared to their parents. Hybrids are usually derived from crossing parents, which differ in genome and epigenome but here we describe Arabidopsis thaliana hybrids created from parents with strong epigenetic but marginal genetic differences (epiHybrids). We demonstrate the occurrence of heterosis in particular phenotypic traits in epiHybrids (Chapter 3). Also, we implemented an approach to map epigenetic quantitative trait loci for heterosis (Chapters 2 and 3) and describe molecular insights from genome-wide analyses in four epiHybrids and their parents (Chapter 4).
In chapter 5, we studied paramutation, an epigenetic phenomenon where in trans communication between DNA regions with contrasting epigenetic profiles results in one region heritably acquiring the profile of the other. We monitored DNA methylation and small regulatory RNAs at two epialleles of the maize b1 locus (B’ and B-I) in the early steps of paramutation and gained insights into relevant features of the alleles involved and the early sequence of events.