PhD Position on Evolution of Stress Response Networks across the Plant Kingdom

Do you want to be part of the development of resilient crops that require far fewer inputs that negatively impact our planet, and contribute to healthy life? Then you could be the ideal candidate to join our new, interdisciplinary research institute CropXR!

Your job

With a budget of 96 million Euro over the next decade, 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 to speed up breeding for complex resilience traits in different growing systems for several crops. This collaborative effort involves four universities, numerous companies, and encompasses scientific research, data collection and sharing, education, and practical applications in agriculture and plant breeding.

This PhD position is part of a project within the CropXRs core research programme. The project will study the evolution of the regulatory responses of plants to abiotic stresses such as temperature and drought. These networks will be investigated both in model plants and crop species, using bioinformatics and comparative genomics on genomic and transcriptomic datasets. This knowledge can be directly used in breeding for more resilient crops.

Research will help to answer question such as:

• How are the genes underlying the stress response network evolving?
• Is the expression of the genes underlying the stress response network conserved in important crop species?
• Can we predict which genes conserve their function in stress responses using machine learning?
• What is the role of duplicated genes in stress response networks?

The collected data and methods developed to answer these questions will be utilized by other researchers in CropXR to develop complex mechanistic models of stress response in crop species.

As a PhD candidate, you will co-execute the research project “Unravelling the evolution of stress response networks across the plant kingdom”. This involves:

• performing large scale orthology and detailed phylogenetics of stress response genes;
• integrating transcriptomic data with comparative genomics data;
• collecting genomic and proteomic features to train machine learning models to predict expression of key genes in crop organisms;
• interacting with academic and company colleagues working in related CropXR projects.

Next to that, you will support in teaching BSc and MSc students who participate in the project. You will also 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 and green genomics companies who are partners to CropXR.

You receive co-supervision from Wageningen University & Research (WUR) (Professor Dick de Ridder) andGenetwister (Dr Lidija Berke).We highly encourage candidates from diverse backgrounds and nationalities to apply. We strive to create an open, diverse, and inclusive work environment for everyone. People of any gender identity, ethnicity and sexual orientation are welcome.

Your qualities

We are looking for a highly motivated and creative PhD candidate to join us in CropXR.

You are:

• a team player motivated to help CropXR in working towards its mission;
• skilled in bioinformatics work in the areas of comparative genomics and/or transcriptomics;
• interested in collaborating with colleagues in academia and industry.

You have:

• a strong interest in regulatory networks, genome evolution, and bioinformatics;
• a MSc in Bioinformatics, Computational Biology, or another relevant field;
• demonstrable experience with comparative genomics and ideally transcriptomics;
• experience with the Unix command line and Python;
• demonstrable communication and organisation skills and the ability to contribute to a friendly and collaborative working environment in an international and cross-disciplinary scientific research team;
• an excellent command of written and spoken English.

Our offer

We offer:

• a position for four years (1.0 FTE);
• a gross monthly salary ranging between €2,770 in the first year to €3,539 in the fourth year 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.