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

How important is epigenetic variation for rapid adaptation in wild plant populations? This genomics-focused PhD project at the Netherlands Institute of Ecology in Wageningen investigates genetic, epigenetic and gene expression differences between apomictic dandelion plants, to uncover the role of natural epialleles in driving heritable trait differences.

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.

Your workplace

You will be based at the department of Terrestrial Ecology at NIOO-KNAW, consisting of a dynamic, interactive and collaborative group of researchers from diverse backgrounds. You will join an active community of researchers, postdocs, PhDs, research assistants and internship students.

The PhD project is embedded in the Plant ecological genetics research group of Prof. Koen Verhoeven. The project will be executed in interaction with the research group of Dr. Jason Gardiner (Translational plant biology, UU) who hosts a second PhD project in this research program; frequent interaction between the two PhD projects is envisioned.

What you will be contributing

We are looking for an enthusiastic, curious and proactive candidate who combines skills in genomic and bioinformatic analyses with an interest in epigenetics and adaptation in wild plant species. You are resilient, eager to learn, and enjoy finding creative solutions in a dynamic interdisciplinary and international research environment.

You also have:

• A successfully completed MSc degree in plant sciences, bioinformatics, plant genomics or a related field
• Excellent data analysis skills, both for bioinformatic and statistical aspects
• Experience in next-generation DNA sequence analysis, preferably including long-read ONT data
• An interest in linking molecular mechanisms to evolutionary and ecological concepts
• The capacity to thrive both independently and as a part of a collaborative team, taking ownership of your work while contributing effectively to shared goals
• The potential to guide and mentor students, coordinating tasks and fostering a positive and productive team environment
• A good command of both written and spoken English.

We consider it a plus if you have previous experience in sequencing-based DNA methylation and/or transposable element analysis.

For this position your command of the English language is expected to be at C1 level. Sometimes it is necessary to submit an internationally recognized Certificate of Proficiency in the English Language.

What do we offer?

We offer a dynamic and inspiring environment with excellent support for experimental work and analysis, and great opportunities for collaboration. The position is for 0.8-1.0 fte, initially for 1 year, and upon satisfactory performance to be prolonged to a maximum of 4 years total.

NIOO-KNAW provides an excellent training environment, including weekly seminars, science lunches, training opportunities and journal clubs to stimulate scientific development. You will also become a member of the graduate school Experimental plant sciences (https://graduateschool-eps.info/) through which you can follow courses on relevant scientific topics and transferrable skills.

More information

For more information please contact Prof. Koen Verhoeven, k.verhoeven@nioo.knaw.nl.

Application procedure

Please send us a motivation letter plus your complete and up-to-date curriculum vitae, including at least two references. The maximum length of the documents should not exceed 3 pages. Additional files such as grades and transcripts are not required during this stage and will not be considered.

You can apply up to and including 30 September 2026 and we will schedule the first job interviews soon after that date.

About NIOO

The Netherlands Institute of Ecology (NIOO) is a national research institute of the Royal Netherlands Academy of Arts and Sciences (KNAW). At NIOO we perform ecological research on biodiversity, climate change and sustainable use of land and water. We stimulate ecological research in the Netherlands and share our ecological knowledge with society. Everyone in our organisation is passionate about contributing to a sustainable world from their own area of expertise.

Terms of employment

Depending on education and experience the minimum salary is € 3.204 and the maximum salary is € 4.051 gross per month for a full-time appointment (scale P cao Nederlandse Universiteiten/KNAW). This is exclusive of 8% vacation allowance, 8.3% year-end bonus, travel allowance, internet allowance, home working allowance and pension accrual with ABP.

The KNAW offers its staff an excellent package of secondary benefits. A package that meets the different needs of employees depending on their stage of life, lifestyle or career ambitions. For example, by working an extra two hours a week, it is possible to increase the number of days off from 29 to 41 days a year (with full-time employment).

For a complete overview of the terms of employment, please refer to the web page: werken bij de KNAW.

Applying for a Certificate of Good Conduct can be part of the employment procedure.

Diversity & Inclusion

The KNAW considers a working environment in which everyone feels welcome and appreciated of great importance. A working environment in which attention is paid to individual quality and where development opportunities are paramount. Together we strive for an inclusive culture in which we embrace differences. We would therefore like to invite candidates who want to contribute to this through their background and experience. In the event of equal suitability, preference will be given to the candidate who thus enhances diversity within the Academy.

We will not respond to any supplier enquiries based on this job advertisement.