PhD position exploring genome dominance and genetic networks as drivers for polyploidy breeding

For the Van de Peer Lab (Bioinformatics and Evolutionary Genomics) in collaboration with the Flemish Research Institute for Agriculture Fisheries and Food (ILVO) Plant Sciences Unit we are looking for a m/f/x doctoral fellow.

About the project

Global climate change will challenge the productivity of major agricultural crops. Therefore more resilient crops are required to secure sufficient food production worldwide. To create plants with desired productivity and better environmental stress tolerance strategies such as genome doubling of agriculturally important crops and generating hybrids hold great promise. Yet just how a plant manages to maintain a double set of chromosomes and how all alleles interact in dynamic genetic networks to create more phenotypic plasticity remains poorly understood.

This fully funded PhD project is part of the Methusalem project granted to Prof. Yves Van de Peer and aims to gain a deeper understanding of polyploidy through genomics experimental evolution modeling and artificial intelligence. Partner institute ILVO explores the benefits of polyploidization in crop breeding by studying genome doubling and interspecific hybrids.

More specifically this PhD project focuses on species of the nutritious Lolium ryegrass the droughttolerant Festuca fescue the interspecific Lolium hybrids and the intergeneric hybrid Festulolium that combines the parental agronomical traits. Bringing the divergent genomes together widens the range of possible responses to environmental stresses and thus increases the adaptability to new extreme conditions. However it also leads to plants with unstable genomes and subsequent elimination of chromosomal fragments over generations hampering the breeding of superior cultivars. This project aims to unravel the underlying molecular mechanisms driving genome dominance and chromosome elimination in hybrids at different ploidy levels using genomics and transcriptomics together with specialized phenotyping.

About your job

In this project you will investigate the phenotypic physiological and molecular response of interspecific tetraploid hybrids and their diploid parents in drought experiments and yield trials. Experiments will span the range from single cells to plant populations at the field level with both fundamental research questions and direct practical applications in plant breeding through an interdisciplinary approach. You will collect genomic data with high throughput sequencing (HTS) methods and combine it with phenotypic field observations. Additionally you will apply molecular markers to study genome constitution and perform singlecell RNASeq experiments to study differential gene expression networks. You will apply innovative data analysis workflows to integrate singlecell genotyping with shifts in gene regulatory networks and understand how genome constitution drives phenotypic diversity at the cell organ plant and population levels. You will report the scientific findings through academic publications as well as presentations on (inter)national events.

This project offers the applicant flexibility according to their own interests and a diverse set of learning opportunities within wet lab procedures and bioinformatics. The goal is to obtain a doctoral degree at the end of the research period. The work is performed at ILVO in Melle a unique and transdisciplinary research institute with an open atmosphere where you will be embedded in a team of fellow PhD students technicians and field workers. Finally the close collaboration with the researchers and plant breeders at ILVO and the interaction with the Van de Peer research group at UGent/VIB offers the applicant the opportunity to develop a broad scientific network.

Profile

• You have a keen interest in applied plant research and in combining wetlab experiments with bioinformatics.
• Practical experience in a molecular lab and/or HTS data analysis/bioinformatics expertise is strongly recommended.
• You have programming skills in Python or another scripting language or you are willing to learn it.
• You have good communication and writing skills and have an excellent knowledge of written and spoken English.
• You are highly motivated enthusiastic and selfcritical. You work with attention to detail and you have an open mindset to learn new skills.
• You combine being a team player with a strong sense of autonomy and responsibility.
• You are willing to apply for additional funding when eligible.
• You are willing to participate in the training and supervision of graduate students.

We offer

• A fulltime PhD scholarship of 4 years (starting with 1 year that can be extended with another three years after positive evaluation).
• Your appointment will start by 01/10/2024 at the earliest.
• You will receive a PhD scholarship according to the general conditions at Ghent University. The taxfree scholarship includes full social security coverage. More information on the PhD scholarship can be found on the Ghent University website.
• A multitude of training opportunities organized at Ghent University VIB and ILVO to broaden your expertise and skillset.
• You will work in a dynamic research group in a multidisciplinary research institute. All Ghent University staff members enjoy several benefits such as 36 days of paid leave bicycle commuting reimbursement etc.

How to apply

Please complete the online application procedure and include a detailed CV a letter of motivation and the contact details of two referees no later than August 21st 2024.

For more information about this vacancy please contact Prof. dr. Tom Ruttink or dr. Marlies Peeters (; ). Selected candidates will be informed no later than August 28th. Interviews will be held in the second week of September.