PhD Funded Position in Plant Epigenetics and Genomics at NIOO-KNAW, Netherlands

The Netherlands Institute of Ecology (NIOO-KNAW) in Wageningen, the Netherlands, is inviting applications for a PhD position in plant epigenetics, genomics, and evolutionary ecology. The doctoral project, titled “Exposing the contribution of epialleles to heritable variation in plants,” will investigate how epigenetic variation contributes to heritable differences in wild plant populations.

The genomics-focused PhD project addresses an important question in modern plant biology: how important is epigenetic variation for rapid adaptation in natural plant populations? The research will use apomictic dandelions as a unique model system to distinguish genetic effects from epigenetic effects and investigate how naturally occurring epialleles may contribute to differences in gene expression and plant traits.

The project is a collaboration between NIOO-KNAW and Utrecht University (UU). The NIOO-KNAW PhD project will focus on identifying genetic, epigenetic, and gene-expression differences between apomictic dandelion accessions, while a complementary PhD project at Utrecht University will use genomic and epigenomic editing to test the causal effects of candidate epialleles.

This position is particularly suitable for candidates with an MSc degree in Plant Sciences, Bioinformatics, Plant Genomics, or a related discipline, along with strong bioinformatic and statistical skills. Experience with next-generation sequencing, especially long-read Oxford Nanopore Technologies (ONT) data, is highly relevant.

The position is based in Wageningen, Netherlands, and is offered at 0.8–1.0 FTE. The appointment is initially for one year and can be extended, subject to satisfactory performance, to a maximum of four years. The salary ranges from €3,204 to €4,051 gross per month for a full-time appointment, depending on education and experience. The application deadline is September 30, 2026.

PhD Research Project: Epialleles, Gene Expression and Plant Adaptation

Plants need to adapt to changing environmental conditions if they are to survive and reproduce successfully. Climate change and other environmental pressures make rapid adaptation increasingly important for both wild plant populations and agricultural systems.

Heritable variation in plant traits provides the foundation for evolutionary adaptation. Such variation can originate from genetic differences in DNA sequence, but it can also arise from epigenetic mechanisms that influence how genes are regulated without changing the underlying DNA sequence.

One of the major challenges in studying epigenetic variation is determining whether an observed difference is genuinely epigenetic or instead caused by an underlying genetic difference. Establishing a causal connection between DNA methylation variants and gene expression is therefore an important challenge in plant evolutionary biology.

The PhD project at NIOO-KNAW will address this problem using an apomictic dandelion lineage as a model system. Apomictic plants produce clonal seeds, meaning that offspring can be genetically very similar to their parent. This unusual reproductive system makes apomictic dandelions particularly useful for investigating how epigenetic differences can contribute to heritable variation.

The project will compare different accessions from a geographically widespread dandelion lineage. By combining genomic, epigenomic, and gene-expression analyses, the researcher will identify potential natural epialleles and investigate their possible contribution to heritable differences in gene activity.

Key Details of the PhD Position

Details	Information
Position	PhD Position – Exposing the Contribution of Epialleles to Heritable Variation in Plants
Research field	Plant Epigenetics, Genomics, Bioinformatics, Evolutionary Ecology
Institution	Netherlands Institute of Ecology (NIOO-KNAW)
Research group	Plant Ecological Genetics
Department	Terrestrial Ecology
Collaborating institution	Utrecht University
Location	Wageningen, Netherlands
Application deadline	September 30, 2026
Start	Following the recruitment process
Employment	0.8–1.0 FTE
Initial contract	1 year
Maximum duration	Up to 4 years
Salary	€3,204–€4,051 gross/month at full-time appointment
Salary scale	Scale P, cao Nederlandse Universiteiten/KNAW
Maximum hours	40 hours/week
Required degree	MSc in Plant Sciences, Bioinformatics, Plant Genomics, or related field
English requirement	C1 level
Scientific institute	NIOO-KNAW

What Will the PhD Researcher Do?

The successful candidate will work with a panel of different accessions belonging to a single, geographically widespread apomictic dandelion lineage. The central goal will be to identify heritable differences in gene expression and determine whether genetic or DNA methylation variation may help explain these differences.

One major component of the project will involve overseeing DNA sequencing approaches for targeted analysis of DNA methylation, single-nucleotide polymorphisms (SNPs), and structural variation between accessions. The project will also make use of long-read sequencing methods, making experience with technologies such as Oxford Nanopore sequencing particularly valuable.

The researcher will perform differential gene-expression analyses to identify genes whose activity differs between dandelion accessions. These analyses will then be integrated with genomic and DNA methylation data to investigate potential relationships between molecular variation and gene regulation.

A substantial part of the work will involve bioinformatic and statistical analysis. The PhD researcher will analyze genetic and DNA methylation variation at the gene level and interpret the results in the context of plant adaptation, evolution, and epigenetic regulation.

The position may also involve greenhouse work when required for phenotypic analyses. This provides an opportunity to connect molecular findings with observable plant characteristics.

Beyond the individual research tasks, the candidate will coordinate interactions with collaborating research groups and supervise Bachelor’s and Master’s students. The researcher will communicate findings through peer-reviewed publications, a doctoral thesis, presentations at national and international conferences, and broader scientific outreach.

Understanding Epialleles and Their Role in Adaptation

An important concept behind this PhD project is the epiallele. In simple terms, an epiallele refers to an epigenetic state associated with a particular genomic region that can influence gene activity and, under some circumstances, be inherited.

DNA methylation is one of the key epigenetic mechanisms investigated in the project. Changes in DNA methylation can influence whether genes are more or less active without necessarily changing the DNA sequence itself.

The challenge is determining whether such epigenetic differences are stable and heritable enough to contribute meaningfully to evolutionary adaptation. The project therefore aims to combine DNA sequence information, methylation data, and gene-expression measurements to identify potential natural epialleles and understand their biological significance.

The use of apomictic dandelions provides an especially useful experimental framework because clonal reproduction can help reduce the genetic differences that would otherwise complicate the interpretation of epigenetic variation.

Eligibility and Candidate Profile

Applicants should have successfully completed an MSc degree in Plant Sciences, Bioinformatics, Plant Genomics, or a related field.

The ideal candidate will combine strong computational skills with a genuine interest in epigenetics, plant adaptation, genomics, and evolutionary biology. Excellent data-analysis abilities are important because the project involves substantial bioinformatic and statistical work.

Experience with next-generation DNA sequencing analysis is expected. Candidates with experience working with long-read sequencing, particularly Oxford Nanopore Technologies (ONT) data, are especially encouraged to apply.

The project requires someone who can connect molecular mechanisms with broader evolutionary and ecological concepts. Therefore, an interest in understanding how genomic and epigenomic processes influence plant adaptation will be highly valuable.

The successful candidate should also be resilient, proactive, curious, and eager to learn. Because the project involves several collaborating groups, the ability to work independently while contributing effectively to a team is essential.

Candidates should also be capable of guiding and mentoring students and coordinating research-related tasks in a constructive and collaborative manner.

Desirable Additional Experience

Previous experience with sequencing-based DNA methylation analysis would be an advantage. Experience with transposable element analysis is also considered a plus.

These additional skills are not presented as absolute requirements, but they could help candidates contribute more quickly to the genomic and epigenomic components of the research.

The position is therefore particularly attractive to researchers who already have experience with sequencing data and want to expand their expertise into plant epigenetics and evolutionary genomics.

English Language Requirement

A good command of both written and spoken English is required for the position.

The vacancy specifies an expected C1 level of English proficiency. In some circumstances, applicants may be asked to provide an internationally recognized certificate demonstrating English-language proficiency.

Because the research environment is international and the position involves scientific publications, conferences, collaboration, and student supervision, strong scientific communication skills will be important throughout the PhD.

Collaboration Between NIOO-KNAW and Utrecht University

The project forms part of a broader collaborative research programme involving the Netherlands Institute of Ecology and Utrecht University.

The NIOO-KNAW PhD will focus primarily on identifying putative natural epialleles by analyzing genetic, epigenetic, and gene-expression variation. A second PhD project at Utrecht University will complement this work through genomic and epigenomic editing.

The two doctoral projects are expected to interact frequently. This collaborative structure provides an opportunity for the successful candidate to work across research groups and gain exposure to complementary approaches for studying plant genome regulation.

Such collaboration can be particularly valuable for a doctoral researcher interested in building expertise that crosses the boundaries between molecular biology, genomics, epigenetics, ecology, and evolution.

Research Skills You Can Develop

This PhD position provides an opportunity to develop an advanced interdisciplinary skill set in modern plant research.

The successful candidate can gain experience with DNA sequencing, long-read genomics, DNA methylation analysis, SNP analysis, structural-variation analysis, differential gene-expression analysis, bioinformatics, and statistical modelling.

The project also offers experience in integrating multiple molecular datasets. Learning how to combine genetic variation, DNA methylation, and gene-expression information can be particularly valuable for researchers pursuing careers in plant genomics, computational biology, molecular ecology, or evolutionary research.

In addition, the candidate will develop transferable skills through scientific writing, conference presentations, research coordination, student supervision, interdisciplinary collaboration, and broader scientific outreach.

Workplace: Netherlands Institute of Ecology in Wageningen

The PhD researcher will be based in the Department of Terrestrial Ecology at NIOO-KNAW in Wageningen.

The department is described as a dynamic, interactive, and collaborative environment that brings together researchers from diverse scientific backgrounds. The successful candidate will join a community consisting of researchers, postdocs, PhD students, research assistants, and internship students.

The project is embedded in the Plant Ecological Genetics research group led by Prof. Koen Verhoeven. The candidate will also work in interaction with the research group of Dr. Jason Gardiner at Utrecht University, which hosts the complementary PhD project.

This setting provides a strong environment for researchers who enjoy interdisciplinary work and want to connect molecular approaches with ecological and evolutionary questions.

Training and Professional Development

NIOO-KNAW provides a research environment designed to support scientific development. Doctoral researchers can participate in weekly seminars, science lunches, training opportunities, and journal clubs.

The successful candidate will also become a member of the Graduate School Experimental Plant Sciences (EPS). Through the graduate school, researchers can take courses covering relevant scientific subjects as well as transferable professional skills.

This combination of institute-based activities and graduate-school training can help the PhD researcher develop both specialized scientific expertise and broader skills relevant to an academic or research career.

Salary and Employment Conditions

The position is offered at 0.8–1.0 FTE, with an initial appointment of one year. Subject to satisfactory performance, the contract can be extended to a maximum total duration of four years.

The salary ranges from €3,204 to €4,051 gross per month for a full-time appointment, depending on education and experience. The position follows scale P of the cao Nederlandse Universiteiten/KNAW.

In addition to the basic salary, the employment package includes an 8% vacation allowance and an 8.3% year-end bonus. Other benefits include travel allowance, internet allowance, home-working allowance, and pension accrual through ABP.

The KNAW also provides a range of secondary employment benefits intended to accommodate different stages of employees’ lives, lifestyles, and career ambitions.

For example, employees working an additional two hours per week can increase their annual leave from 29 to 41 days per year when employed full-time.

About NIOO-KNAW

The Netherlands Institute of Ecology (NIOO-KNAW) is a national research institute of the Royal Netherlands Academy of Arts and Sciences (KNAW).

NIOO conducts ecological research addressing major environmental challenges, including biodiversity, climate change, and the sustainable use of land and water.

The institute also contributes to the development of ecological research in the Netherlands and communicates ecological knowledge to wider society. Its research community brings together expertise from different areas of ecology and environmental science.

For a PhD focused on epigenetic variation and rapid adaptation in wild plants, this ecological research environment provides a highly relevant scientific setting.

Diversity and Inclusion

KNAW emphasizes the importance of creating a workplace where everyone feels welcome and appreciated. The organization states that individual quality and opportunities for professional development are important elements of its working environment.

The Academy aims to foster an inclusive culture that embraces differences and welcomes candidates who can contribute to this culture through their backgrounds and experiences.

In cases where candidates are considered equally suitable, preference may be given to a candidate who contributes to greater diversity within the Academy.

How to Apply for the PhD Position

Interested candidates should submit a motivation letter and a complete, up-to-date curriculum vitae, including at least two references. APPLY NOW

The combined application documents should not exceed three pages. Applicants do not need to submit grades or academic transcripts at this stage, as additional files such as these will not be considered during the initial application process. Applications can be submitted up to and including September 30, 2026. The first job interviews are expected to be scheduled shortly after the closing date. For further information about the position, applicants can contact Prof. Koen Verhoeven at k.verhoeven@nioo.knaw.nl.

Frequently Asked Questions

1. What is the topic of this PhD position?

The PhD investigates how epigenetic variation and natural epialleles contribute to heritable variation in plants, with a particular focus on gene expression and adaptation in apomictic dandelions.

2. Where is the PhD position located?

The position is based at the Netherlands Institute of Ecology (NIOO-KNAW) in Wageningen, Netherlands.

3. What degree is required?

Applicants should have an MSc degree in Plant Sciences, Bioinformatics, Plant Genomics, or a related field.

4. Is bioinformatics experience required?

Strong bioinformatic and statistical data-analysis skills are an important part of the desired candidate profile.

5. Is sequencing experience required?

Experience with next-generation DNA sequence analysis is expected. Experience with long-read ONT data is particularly desirable.

6. Is DNA methylation experience required?

Previous experience with sequencing-based DNA methylation analysis is considered a plus, rather than an absolute requirement.

7. What organism will be studied?

The research will use apomictic dandelion plants from a single geographically widespread lineage as the model system.

8. Why are apomictic dandelions useful for this research?

Because apomictic plants reproduce through clonal seeds, they provide an opportunity to better disentangle genetic differences from epigenetic differences when studying heritable variation.

9. What is the employment level?

The position is offered at 0.8–1.0 FTE.

10. How long is the PhD contract?

The initial appointment is for one year and can be extended, subject to satisfactory performance, to a maximum of four years in total.

11. What is the salary?

The salary is €3,204 to €4,051 gross per month for a full-time appointment, depending on education and experience.

12. What is the English-language requirement?

The position expects a C1 level of English in both written and spoken communication. An internationally recognized English certificate may sometimes be required.

13. What documents are required?

Applicants should submit a motivation letter and an up-to-date CV including at least two references. The combined documents should not exceed three pages.

14. Are transcripts required?

No. Grades and transcripts are not required during the initial application stage and will not be considered.

15. What is the application deadline?

The application deadline is September 30, 2026.