The immune system helps plants resist pathogen infections and has been well studied. However, it becomes increasingly clear that enhancing defense comes at a cost, as plants slow down growth even if the infection is successfully combatted. In this project, you will investigate how plants control their growth during and after an immune response. This research is embedded in the CropXR work package on growth-resilience trade-offs and combines digital phenotyping and molecular omics technologies.

Your job
Current projections show that the incidence of diseases on crops will increase in the coming decades, and thus, new strategies, beyond strengthening the immune system, are needed to ensure the resilience of future crops to diseases. It turns out that plants slow down their growth during and after an immune response regardless of the disease intensity. However, how these growth processes are regulated in plants is unclear. In this PhD project embedded in CropXR, you uncover the genetic and molecular basis of plant growth during and after an immune response. With this knowledge, we aim to develop solutions for resistance that do not compromise crop growth.

Your project is a part of the CropXR research programme. CropXR develops innovative breeding methods for making crops more resilient, sustainable, and climate-adapted. With a budget of 96 million euros for the next ten years, CropXR focuses on creating eXtra Resilient (XR), sustainable, and climate adaptive crops. By combining plant biology, simulation modelling, and artificial intelligence we aim to develop ‘smart breeding and cultivation’ methods. Thus, we try to speed up the breeding of complex resilience traits for several crops in different growing systems. This collaborative effort involves four universities and numerous companies. It encompasses scientific research, data collection and sharing, education, and practical applications in agriculture and plant breeding.

Your project is embedded in the CropXR work package C4 that brings together expertise on biotic and abiotic stress tolerance, proteomics, and molecular biology to decipher the molecular-genetic networks that plants use to regulate trade-offs between growth and stress resilience. You will work closely with other PhD candidates in this and other CropXR work packages.

The project comprises three phases:

• In the first phase of the project, you will perform high-throughput digital phenotyping of Arabidopsis thaliana mutant population grown with or without administered immunity-activating treatments in the Netherlands Plant Ecophenotyping Center (NPEC). You will utilise modelling, genetic mapping, and machine learning techniques to identify genes controlling the growth during and after an immune response.
• In the second phase of the project, validation of the genetic leads will be performed using CRISPR-Cas gene editing and alteration of gene expression.
• In the final phase, you will perform time-course experiments using quantitative proteomics (proximity labeling) and RNAseq methods for selected targets to gain insights into the protein complexes driving growth during and after an immune response. You will also have an option to explore possibilities to translate obtained knowledge into applications.

As a PhD candidate, you will be responsible for designing and conducting experiments behind the computer and in the laboratory. You will interact with other PhD candidates and researchers involved in experimental research, bioinformatics and/or modelling at Utrecht University, Wageningen University and Research, University of Amsterdam, and TU Delft, as well as with experts from breeding companies within CropXR. You will also be involved in supervising students and, occasionally, sharing your expertise in the classroom with Bachelor's students. This second part of the job will help you learn about teaching and open additional perspectives for the next career steps.

A supervision team of 2-3 people will support your professional development as a researcher. Our research group and the CropXR consortium provide all the needed expertise. You will have opportunities to discuss your professional development and future career steps with a mentor from an industry or other area of your choice.

We currently have another PhD position on growth-immunity tradeoffs available in Dmitry Lapin’s team. For more information about this position, check out our website.

We are looking for a collaborative, enthusiastic, and curious colleague who:

• has a completed MSc degree or is about to get an MSc degree in molecular and/or computational biology;
• has an affinity with experimental (plant) biology research;
• has demonstrated skills in either or both computational and molecular biology research;
• wants to learn, deploy, or even develop new methods of computational and molecular biology research.

We offer:

• a position for 4 years;
• a gross monthly salary between €2,770 and €3,539 in the case of full-time employment (salary scale P under the Collective Labour Agreement for Dutch Universities (CAO NU);
• 8% holiday pay and 8.3% year-end bonus;
• 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 has a number of schemes and facilities of its own for employees. This includes schemes facilitating professional development, leave schemes and schemes for sports and cultural activities, as well as discounts on software and other IT products. We also offer access to additional employee benefits through our Terms of Employment Options Model. In this way, we encourage our employees to continue to invest in their growth. For more information, please visit Working at Utrecht University.

Universiteit Utrecht

The department of Biology consists of an Education Institute and 12 chair groups with a total of 350 staff members. The chair groups are organised within the Institute of Environmental Biology and the Institute for Biodynamics and Biocomplexity. The department is responsible for the Bachelor's programme in Biology, where we annually welcome over 400 students. This means we educate over 30% of biology students in the Netherlands. Additionally, staff members of the department also teach in the Utrecht Bachelor's programme in Biomedical Sciences and the Bachelor's program of University College Utrecht. In addition to bachelor education, our staff also provide teaching in various master's programmes. The department of Biology is successful in attracting international and Dutch research funding (CropXR, GreenTE, grants from European Research Council, etc.).

You will join Dmitry Lapin’s team (5-10 team members) in the Translational Plant Biology (TPB) group. The TPB group includes four principal investigators with expertise in different aspects of plant-microbe interactions, plant development, and epigenetics. We exchange expertise to understand the principles of plant biology better and translate this knowledge into technologies that improve the sustainability of agriculture. To ensure that the researchers benefit from each other’s expertise in real-time the team and TPB have regular work-together sessions such as hackathons for data analysis, writing retreats, and thematic meetings.

In the Lapin team, we answer fundamental questions about plant immunity and growth in collaboration with industry partners. For that, we use cutting-edge technologies in high-throughput phenotyping (NPEC), machine learning, and omics analyses; the focus is not on technology development but on fascinating genetic and molecular principles of plant biology. The team is an active contributor to the research programmes LettuceKnow and CropXR. High-quality supervision and guidance are among the core values of the Lapin team, with a dedicated PhD supervision team of 2-3 members ensuring timely project guidance. You will also have opportunities to find a mentor in the plant breeding industry or public sector to enhance your career prospects after finishing the PhD research. The Graduate School of Life Sciences (GSLS) and the Graduate School of Experimental Plant Sciences (EPS), which you will be a part of, further guarantee the quality of supervision. The Lapin team, as a part of the TPB group, has monthly social events, annual retreats and goes for daily short walks in the University Botanical Gardens. We respect each other’s working hours and strive together to maintain a healthy working environment.

CropXR was launched in 2023 to contribute to improving agricultural production by making it less vulnerable to climate change. Furthermore, it aims to contribute to diminishing the dependency of agriculture on artificial fertilizers and chemical pesticides. The institute is a joint venture of the universities of Amsterdam, Delft, Wageningen and Utrecht in partnership with Plantum, the Dutch plant breeding sector association. CropXR brings together efforts from different academic disciplines (such as plant sciences, computational and data sciences, and social sciences) and private industry to catalyse sustainable change. It receives financial support from NWO, the Dutch National Growth Fund, and the Foundation for Food & Agricultural Research.