How significant is epigenetic variation for the rapid adaptation of wild plant populations? This PhD project at the Netherlands Institute of Ecology in Wageningen delves into genetic, epigenetic, and gene expression differences among apomictic dandelion plants, aiming to reveal the influence of natural epialleles on heritable trait differences. The ability to adapt quickly is vital for both natural plant populations and crops in the face of climate change and environmental challenges. Heritable trait variation is essential for such adaptation, yet the precise role of epigenetics in plant adaptation remains unclear. The main challenge is to differentiate between genetic and epigenetic effects and to establish a causal link between DNA methylation variants and gene expression.

About the Company

The Netherlands Institute of Ecology (NIOO-KNAW) is a national research institute under the Royal Netherlands Academy of Arts and Sciences (KNAW). We conduct ecological research on biodiversity, climate change, and sustainable land and water use, sharing our ecological knowledge with society.

The Role

In this PhD position at NIOO-KNAW, you will analyze a diverse panel of accessions from a single, widespread dandelion lineage. Your tasks will include:

• Identifying heritable differences in gene expression between accessions.
• Screening genomic data for DNA methylation involvement in gene expression variations.
• Investigating environmental factors contributing to potential epialleles.

Responsibilities

• Oversee DNA sequencing methods for targeted analysis of DNA methylation, SNP, and structural variation among accessions, including long-read sequencing techniques.
• Conduct differential gene expression analyses.
• Perform bioinformatic and statistical analyses to interpret gene-level genetic and DNA methylation variation.
• Assist with greenhouse work for phenotypic analyses.
• Coordinate interactions with collaborating research groups and supervise BSc and MSc students.
• Write and publish research findings in leading scientific journals and present at (inter)national conferences.

Requirements

We seek an enthusiastic, curious, and proactive candidate with a background in genomic and bioinformatic analyses, particularly interested in epigenetics and adaptation in wild plant species. You should possess:

• A completed MSc degree in plant sciences, bioinformatics, plant genomics, or a related field.
• Excellent data analysis skills for bioinformatics 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 ability to work independently and collaboratively, taking ownership of your work while contributing to shared goals.
• The potential to guide and mentor students, fostering a positive team environment.
• Proficiency in written and spoken English at C1 level.

Previous experience in sequencing-based DNA methylation and/or transposable element analysis is a plus.

What We Offer

We provide a dynamic and inspiring environment with excellent support for experimental work and analysis, along with opportunities for collaboration. The position is for 0.8-1.0 fte, initially for 1 year, with the possibility of extension up to a maximum of 4 years based on satisfactory performance. NIOO-KNAW offers a rich training environment, including weekly seminars, science lunches, training opportunities, and journal clubs to promote scientific development. You will also join the graduate school Experimental Plant Sciences, allowing you to take courses on relevant scientific topics and transferable skills.

Application Process

For more information, please contact Prof. Koen Verhoeven at k.verhoeven@nioo.knaw.nl. To apply, send a motivation letter and your complete CV, including at least two references, with a maximum length of 3 pages. Additional documents like grades and transcripts are not required at this stage. Applications are accepted until 30 September 2026, with interviews scheduled shortly after.

Terms of Employment

The minimum salary is €3,204 and the maximum is €4,051 gross per month for a full-time appointment, excluding additional benefits such as vacation allowance, year-end bonus, travel allowance, and pension accrual. The KNAW offers an excellent package of secondary benefits tailored to employees' needs.

Diversity & Inclusion

The KNAW values a welcoming and appreciative work environment. We strive for an inclusive culture that embraces differences and invites candidates who can contribute to this through their backgrounds and experiences. In case of equal suitability, preference will be given to candidates who enhance diversity within the Academy.