PhD proposal on epigenetic mechanisms

The proposal was written for the call ‘Graduate Schools Green Topsectors’ which provides excellent conditions for private co-funding. The call establishes lucrative conditions to join these proposals, as only 15% private funding is necessary, of which half can be in-kind. Furthermore, this 15% concerns the total private funding needed, so if more partners join the proposal, the individual contribution will be less.

Abstract of the proposalEpigenetic variation can result in trait variation and contribute to the diversity we observe. Various interesting plant phenotypes are shown to be unstable, meaning they do not seem to follow the laws of genetics. This obviously poses problems (and frustration) in the selection and improvement process for breeders. In such cases of phenotypic instability, the expression of genes underlying the phenotypes is likely downregulated, which can have various epigenetic-related causes. One such cause is paramutation, also called “trans-chromosomal methylation”.

Up until recently there were no real tools to deal with epigenetic variants and the processes that underly unstable phenotypes. Based on our recent data in maize, we have leads about the mechanism underlying silencing through paramutation and why this happens with some DNA sequences and not with others. We selected two cases for exploring this further: we will study the best understood case, that of the BOOSTER1 locus in maize, as well as the recently better characterised paramutation event of the SULFUREA locus in tomato. Importantly, our current data point to similar mechanisms in the monocot maize and dicot tomato, indicating that the knowledge obtained can be broadly applicable.

Understanding the epigenetic mechanisms that cause unstable phenotypes in crop plants, and identification of allele variants affected are the first steps towards harnessing these aspects of regulation and stabilisation of desired traits.
For our project we are currently looking for private partners to collaborate and fund part of this PhD project. In return we will provide insights in the spontaneous silencing of phenotypes of interest of the plant breeding industry and investigate approaches to stabilize traits. The funding would encompass a total of 25K in cash and 37.5 K euro in-kind divided over all private partners and four years. The in-kind contribution would mostly be growing of plant materials and help on large-scale phenotyping. Two private partners are already on board of this exciting project and we hope you will be in for the challenge as well!

If you are interested and want to know more, you can reach us via email! Due to the deadline for the call, please contact us preferably no later than September 1^st 2021.

Contact by email: 
M.E.Stam  or Kevin Peek