PhD position on Exposing the Contribution of Epialleles to Heritable Variation

How much does epigenetic variation contribute to rapid adaptation? This PhD at Utrecht University uses CRISPR/Cas9 and SunTag-based epigenomic editing in apomictic dandelions to test whether epialleles drive heritable trait variation across generations by establishing causal links between DNA methylation, gene expression, and inherited traits. It pioneers transient epigenome editing in a wild, non-model plant species.

Your job
To face climate change and other environmental challenges, the capacity for rapid adaptation is crucial for both natural plant populations and crops. Heritable trait variation fuels such adaptation. While heritable trait variation can arise from genetic and epigenetic sources alike, the true contribution of epigenetics to plant adaptation remains uncertain. The primary challenge lies in distinguishing genetic from epigenetic effects and establishing a causal relationship between DNA methylation variants and gene expression.

In a collaborative project between Utrecht University (UU) and the Netherlands Institute of Ecology in Wageningen (NIOO-KNAW), we will tackle these challenges by using an apomictic dandelion lineage as a unique model system. Because apomictic plants reproduce through clonal seeds, they allow us to disentangle genetic from epigenetic effects with unprecedented clarity. The project combines high-resolution analysis of genetic, epigenetic, and gene expression variation between apomictic plants, which exposes putative natural epialleles (PhD project at NIOO-KNAW), with genomic and epigenomic editing that identifies genes regulated by DNA methylation and tests the causal effects of candidate epialleles on gene expression (this PhD project at UU).

In this PhD project you will:

• Develop and use state-of-the-art CRISPR/Cas9-based technologies to target DNA methylation maintenance machinery, inducing genome-wide hypomethylation to identify genes regulated by methylation.
• Deploy an advanced, inducible Suntag-TET1cd epigenomic editing system to target specific candidate epialleles, allowing you to prove the causal link between DNA methylation and gene expression.
• Investigate the transgenerational stability of these epigenetic marks over multiple generations.

This project represents a frontier in ecological epigenetics, marking the first application of epigenomic editing in a wild, non-model plant species. Beyond fundamental evolutionary questions, your work will contribute to the development of new transient (epi)genomic editing tools for asexual plants—technologies with significant potential applications in the improvement and breeding of clonally propagated crops