Predicting heterosis in F1 hybrids from parental DNA methylomes.

Despite the importance and wide exploitation of heterosis in commercial crop breeding, the molecular mechanisms behind this phenomenon are not well understood. There is growing evidence that beside genetic also epigenetic factors contribute to heterosis. We recently used near-isogenic but epigenetically divergent parents to create so-called epigenetic F1 hybrids (epiHybrids) in Arabidopsis thaliana. Phenotypic analysis revealed many strong heterotic phenotypes in these epiHybrids, indicating that epigenetic divergence between the parental lines is sufficient to cause heterosis, independently of DNA sequence determinants. Moreover, we were able to associate some of the phenotypes with specific differentially methylated regions (DMRs) in the parental genomes, suggesting that the epigenetic state of the parents can be used to predict offspring phenotypic performance. Here we aim to confirm these predictions and to uncover the molecular mechanisms by which parental DNA methylation states produce heterosis.  To this end, we propose to construct and phenotype much larger and diverse epiHybrid populations and integrate these data with population-level, high-resolution methylome measurements.