PhD position: Exposing the contribution of epialleles to heritable variation in plants

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 in plants can arise from genetic and epigenetic sources alike, the true contribution of epigenetics to plant adaptation remains uncertain. The primary challenge lies in distinguishing between genetic and epigenetic effects and establishing a causal relationship between DNA methylation variants and gene expression.

In a collaborative project between the Netherlands Institute of Ecology (NIOO-KNAW) and Utrecht University (UU), 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 (this 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 (PhD project at UU).

What you will be doing
In this PhD project at NIOO-KNAW you will study a panel of different accessions from a single, geographically widespread dandelion lineage, to (1) identify heritable differences in gene expression between accessions, (2) screen genomic evidence for the involvement of DNA methylation in observed gene expression differences, and (3) explore the role of environmental effects in the origin of putative epialleles. You will:

• Oversee DNA sequencing approaches for targeted analysis of DNA methylation, SNP and structural variation between accessions, including long read sequencing methods
• Perform differential gene expression analyses
• Perform bioinformatic and statistical analyses to identify and interpret gene-level genetic and DNA methylation variation between accessions
• Assist in greenhouse work as required for phenotypic analyses in the project
• Coordinate interaction with collaborating research groups and supervise BSc and MSc students
• Write and publish your research in leading scientific journals and communicate your findings through your PhD thesis, presentations at (inter)national conferences and via broader outreach.