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Fully-funded White Rose BBSRC DTP iCASE project: Elucidating conserved gene regulatory networks driving plant immunity

   White Rose Doctoral Training Partnership in Mechanistic Biology

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  Prof K Denby, Dr Jamie Claxton  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

Lead supervisor: Prof Katherine Denby (Department of Biology)

Co-supervisor: Dr Jamie Claxton (Tozer Seeds) and Dr Frances Gawthrop (Tozer Seeds)

The student will be registered with the Department of Biology

This research project will identify transcriptional regulators of the plant immune response, determine whether these regulators and their molecular function are conserved across multiple crop plants, and assess the potential of these regulators to enhance disease resistance and reduce crop loss.

The fungal pathogens Botrytis cinerea and Sclerotinia sclerotiorum can cause substantial losses of field-grown and protected lettuce crops and strike late in the growing season after significant cost (and associated C emissions) of inputs required for production. Chemical control is problematic, with development of enhanced crop resistance a more sustainable solution to prevent waste. This project builds on a successful collaboration between Prof. Denby and Tozer Seeds Ltd. combining systems biology, molecular biology and plant pathology.

We have built a high-confidence gene regulatory network of the lettuce transcriptional response to Botrytis/Sclerotinia infection which predicts hub transcription factor (TF)-encoding genes that have a major influence on immunity-related gene expression. We have validated three of these novel hub TFs and shown that their role is conserved in lettuce and the model plant Arabidopsis, opening up faster methods of functional testing and raising the potential that key immune regulators could be conserved in other crops.

This project will test new hub TFs predicted to impact defence against these fungal pathogens and investigate their gene regulatory function in plant immunity using transient/stable transformation in lettuce/Arabidopsis. Importantly, this project will determine to what extent our immunity gene network is conserved in other crops (targeting celery and cucurbits). Genome editing will be used to assess the ability of key TFs to enhance disease resistance and determine the role of these new regulators of plant immunity. The research will not only identify new components of immunity against these fungal pathogens but will improve our understanding of how transcriptome network analysis can enhance breeding and the types of genes for which the network is able to predict function.

The project combines state-of-the-art molecular skills (including genome editing, genomics, transcriptomics) with bioinformatics, plant-pathogen interaction and research in both crop and model plants. The research project will include a placement at Tozer Seeds where you will gain skills in genome editing, learn about trait selection and the design of breeding programmes for different crops, as well as develop an understanding of the plant breeding business and the process of taking a new variety to market.

The Department of Biology holds an Athena SWAN Gold Award. We are committed to supporting equality and diversity and strive to provide a positive working environment for all staff and students. 

The WR DTP and the University of York are committed to recruiting future scientists regardless of age, ethnicity, gender, gender identity, disability, sexual orientation or career pathway to date. We understand that commitment and excellence can be shown in many ways and we have built our recruitment process to reflect this. We welcome applicants from all backgrounds, particularly those underrepresented in science, who have curiosity, creativity and a drive to learn new skills.

Entry Requirements: Students with, or expecting to gain, at least an upper second class honours degree, or equivalent, are invited to apply. The interdisciplinary nature of this programme means that we welcome applications from students with any biological, chemical, and/or physical science backgrounds, or students with mathematical background who are interested in using their skills in addressing biological questions. 

Programme: PhD in Mechanistic Biology (4 years)

Start Date: 1st October 2023

Interviews: February/March 2023 (date tbc)

Funding Notes

This 4-year fully-funded White Rose DTP industrial CASE PhD project in collaboration with Tozer Seeds. This studentship covers: (i) a tax-free stipend at the standard Research Council rate (£17,668 for 2022/23, (ii) research costs, and (iii) tuition fees at the UK rate. The industrial partner will enhance the stipend with an additional £800 a year.
International students will need to have sufficient funds to cover the costs of their student visa, NHS health surcharge, travel insurance and transport to the UK as these are excluded from UKRI funding.

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