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.
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:
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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.
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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.
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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
We are looking for a candidate with a strong interest in epigenetics and genome editing, who is eager to collaborate in a multidisciplinary research environment and meets the following criteria:
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an MSc in molecular biology, genetics, biotechnology, plant sciences, or a related field;
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experience in molecular biology techniques;
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the ability to communicate and organize work effectively;
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a good command of both written and spoken English;
Experience with any of the following is welcome but not required: CRISPR/Cas9 or other genome-editing technologies, Agrobacterium-mediated transformation, bioinformatics, plant phenotyping or microscopy, DNA methylation analysis (e.g. bisulfite sequencing), or plant tissue culture.
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a position for 18 months, with an extension to a total of four years upon a positive assessment in the first 18 months;
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a gross monthly salary starting at € 3,204 in the first year and increasing annually up to €4,051 in the fourth year, based on full-time employment (salary scale P under the Collective Labour Agreement for Dutch Universities (CAO NU));
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8% holiday pay and 8.3% year-end bonus;
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a pension scheme, partially paid parental leave and flexible terms of employment based on the CAO NU.
In addition to the terms of employment laid down in the CAO NU, Utrecht University also offers a range of its own schemes for employees. This includes arrangements for professional development, various types of leave, and options for sports and cultural activities. You can also tailor your employment conditions through our Terms of Employment Options Model. In this way, we encourage you to keep investing in your personal and professional development. For more information, please visit Working at Utrecht University.
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You will be embedded in the Department of Biology. Research within this department is organized in two institutes: the Institute of Biodynamics and Biocomplexity (IBB) and the Institute of Environmental Biology (IEB). The Department of Biology coordinates the teaching of the Bachelor's programme in Biology, as well as Master's programmes and PhD courses that are offered through the Graduate School of Life Sciences.
You will be working within the Translational Plant Biology (TPB) group at Utrecht University, focused on applying molecular biology, genome editing, synthetic biology, and artificial intelligence to translate knowledge of plant biology into technologies for the climate adaptation of crops and sustainable food production. Here, you will have opportunities to collaborate closely with PhD candidates and postdoctoral researchers from the TPB group and other groups within the Faculty of Science at Utrecht University. The project will be executed in collaboration with the research group of Prof. Koen Verhoeven (Netherlands Institute of Ecology in Wageningen (NIOO-KNAW)), who coordinates the project and hosts a second PhD project in this research programme; frequent interaction between the two PhD projects is envisioned.
For more information about this position, please contact Dr. Jason Gardiner (Assistant Professor of Translational Plant Biology) via [email protected].
Do you have a question about the application procedure? Please send an email to [email protected].
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If you are enthusiastic about this position, just apply via the "Apply now" button! Please enclose:
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your letter of motivation, clearly outlining why this position interests you, your motivation for joining our team, and what makes you a suitable candidate;
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your curriculum vitae;
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the names, telephone numbers, and email addresses of at least two references;
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a copy of your Master's certificate or a letter from your university stating when your degree will be issued.
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