PhD Candidate: Structural variation in cucumber genomes

Job Description
Plant traits are defined by their genes, which can have different alleles encoding proteins with activities that determine the expression of a trait. In addition, genes have differences in promoters that are responsible for differences in gene expression. However, new long-read sequencing technologies and genome comparisons show that larger structural variations in the genome are also important for breeding traits. Some of these variants are gene copy number variations (CNVs) that influence a related trait.

This research will focus on the effect of structural variations in the cucumber genome on plant traits. Several examples of structural genomic variation in cucumber show that gene CNVs lead to differences in trait expression. We aim to better understand the origin of the structural variations, how they are inherited, and how they influence plant traits.

As a PhD Candidate you will:

• carry out independent research, supported by your supervisors from Plant Functional Genomics and the Maastricht Centre for Systems Biology
• write publications based on your scientific work, culminating in a PhD thesis.

Specifically, you will work at the interface of plant physiology, molecular biology and bioinformatics. You will phenotype plants, compare genomes, identify structural variants in genomes and study their origin and the function of the affected genes in relation to the traits that are relevant for breeding.

Were are you going to work?
The research is embedded in the Plant Functional Genomics group led by Prof Dr Wim Vriezen, and you will work with specialists in bioinformatics and systems biology. The research group is part of the Brightlands Future Farming Institute (BFFI) of the Faculty of Science and Engineering from the University of Maastricht (UM)(https://www.maastrichtuniversity.nl/research/brightlands-future-farming-institute) located at the Campus Greenport Venlo. For clarity, the location where the study is being conducted is at the BFFI in Venlo.

This project is a research collaboration between the BFFI, and BASF|Nunhems. At the BFFI, University of Maastricht scientists and students work on genetics, growth recipes and crop management related to vegetable production. Together they strive for the optimal phenotype by integrating plant genetics, plant environment and crop management.

Requirements
You are a scientifically curious person who wants to understand how differences in plants are regulated by the genome.

• you may already be in a PhD program, but you cannot be a PhD holder;
• you must have less than 4 years of research experience, i.e., you should be an early-stage researcher;
• you should have a high-level knowledge of the English language;

Furthermore, the position-related requirements are:

• an MSc degree in bioinformatics, or a plant science related discipline with demonstrable experience in bioinformatics (computational work).
• enrolment as a doctoral student at UM within four months
• experience or willingness to learn programming in R or other relevant programming language.
• affinity or experience with molecular analyses (wet lab work)
• a hands-on attitude for phenotyping plants for own research and help with maintenance (greenhouse work)

What we offer
As a PhD at Faculty of Science & Engineering, you will be employed by the most international university in the Netherlands, located in the beautiful city of Maastricht. In addition, we offer you:

• Good employment conditions. The position is graded in scale P according to UFO profile PhD, with corresponding salary based on experience ranging from €2770,00 and €3539,00 gross per month (based on a full-time employment of 38 hours per week). In addition to the monthly salary, an 8.0% holiday allowance and an 8.3% year-end bonus apply.
• An employment contract for a period of 12 months with a scope of 1,0 FTE. Upon a positive evaluation, an extension of 3 years will follow.
• At Maastricht University, the well-being of our employees is of utmost importance, we offer flexible working hours and the possibility to work partly from home if the nature of your position allows it. You will receive a monthly commuting and internet allowance for this. If you work full-time, you will be entitled to 29 vacation days and 4 additional public holidays per year, namely carnival Monday, carnival Tuesday, Good Friday, and Liberation Day. If you choose to accumulate compensation hours, an additional 12 days will be added. Furthermore, you can personalize your employment conditions through a collective labor agreement (CAO) choice model.
• As Maastricht University, we offer various other excellent secondary employment conditions. These include a good pension scheme with the ABP and the opportunity for UM employees to participate in company fitness and make use of the extensive sports facilities that we also offer to our students.
• Last but certainly not least, we provide the space and facilities for your personal and professional development. We facilitate this by offering a wide range of training programs and supporting various well-established initiatives such as 'acknowledge and appreciate'.

The terms of employment at Maastricht University are largely set out in the collective labor agreement of Dutch Universities. In addition, local provisions specific to UM apply. For more information, click here.

Maastricht University
Why work at Maastricht University?

At Maastricht University (UM), everything revolves around the future. The future of our students, as we work to equip them with a solid, broad-based foundation for the rest of their lives. And the future of society, as we seek solutions through our research to issues from all around the world. Our six faculties combined provide a comprehensive package of study programmes and research.

In our teaching, we use the Problem-Based Learning (PBL) method. Students work in small groups, looking for solutions to problems themselves. By discussing issues and working together to draw conclusions, formulate answers and present them to their peers, students develop essential skills for their future careers.

With over 22,300 students and more than 5,000 employees from all over the world, UM is home to a vibrant and inspiring international community.

Are you drawn to an international setting focused on education, science and scholarship? Are you keen to contribute however your skills and qualities allow? Our door is open to you! As a young European university, we value your talent and look forward to creating the future together.

Click here for more information about UM.

Faculty of Science and Engineering
At the Faculty of Science and Engineering (FSE), we focus on themes such as circularity and sustainability, future farming, digitisation and (scientific) instrument development. FSE's leading projects, like the Einstein Telescope Pathfinder, are sure to grab anyone's attention. The faculty is a vibrant hub of education and research in Science, Technology, Engineering, and Mathematics (STEM) and Liberal Arts and Sciences (LAS). At FSE, over 450 staff members and 3700 students gather to explore e exciting interdisciplinary research and educational programmes. Feel welcome, be part of our team and put your brilliant mind to work!

FSE at the Brightlands Campuses
Maastricht, Sittard-Geleen, Heerlen, and Venlo, the home of four creative Brightlands campuses, are bustling with 30,000 entrepreneurs, researchers, and students working diligently to solve global challenges. The Faculty of Science and Engineering is active on all four Brightlands campuses, and this is where our impact reaches its peak. To give you an idea of what is happening at each campus: Sittard-Geleen is home to the largest chemical site in the Euregion, while Venlo is a large hub for agri-food innovation. Maastricht is the site of the Health Campus, and Heerlen is the place to be for Smart Services.

Curious?
Are you interested in this exciting position but still have questions? Feel free to contact Wim Vriezen, Professor Plant Functional Genomics at wim.vriezen@maastrichtuniversity.nl for more information.

Applying?
Or are you already convinced and ready to become our new PhD? Apply now, no later than 08/04/2024, for this position.

Please upload your CV and motivation letter.

The vacancy is open for internal and external candidates. In case of equal qualifications, internal candidates will be prioritized.

Maastricht University is committed to promoting and nurturing a diverse and inclusive community. We believe that diversity in our staff and student population contributes to the quality of research and education at UM, and strive to enable this through inclusive policies and innovative projects led by teams of staff and students. We encourage you to apply for this position.

38 hours per week

Nassaustraat 36