Epigenetic Inheritance and Divergence within Apomictic Dandelion Lineage

Epigenetic mechanisms can be important contributors to trait variation. For instance, gene expression can be affected by DNA methylation via epigenetic silencing of nearby transposable elements. Because DNA methylation can be stably inherited in plants, stochastic and environment-induced DNA methylation modifications also have the potential to affect heritable traits. We use triploid apomictic dandelion as a model to explore the epigenetic contribution to heritable variation and adaptation. Asexual reproduction such as apomixis facilitates the study of epigenetic variants that are not confounded with genetic variants. I will show examples of heritable variation within individual apomictic lineages, both in gene expression and in phenotypes, that is associated with epigenetic mechanisms. This variation arises as a result of environmental experiences in previous generations and also as naturally evolved differences. To explore an underlying DNA methylation-based mechanism of epigenetic inheritance we developed a bisulfite sequencing extension to genotyping-by-sequencing to screen DNA methylation in a reduced subset of the genome. This revealed inherited methylation modifications mostly in CHG context, rather than CG context, after experimental exposure to a jasmonic acid treatment. Together, our results suggest a relevant role for epigenetic inheritance in heritable trait variation within apomictic lineages. Further exploration of the mechanism of epigenetic inheritance, and its possible association with transposable element activity, is enabled by a draft reference genome of a diploid sexual dandelion plant, which we recently assembled in a collaborative effort involving several research groups from the Netherlands.