A single-locus quantitative genetic model incorporating DNA methylation

We describe a single-locus quantitative genetic model that incorporates effects due to DNA methylation. Extending Fisher’s decomposition of the genotypic value, we distinguish two quantities to predict an individual’s phenotypic or genetic values: the “basic genetic value” and the “expressed genetic value”. We show how these quantities relate to the concept of breeding value and derive their corresponding formulas, along with those for phenotypic variance and covariance between relatives. The resulting parameters are influenced by several factors, including the population distribution of DNA methylation levels, the functional relationship between methylation and phenotype, the magnitudes of genetic and methylation effects, and allele frequencies. We show that under the conditions modeled, the presence of DNA methylation does not bias estimated breeding values.