ACCE+ DLA programme - EpiPlasticity: exploring the ecological and evolutionary significance of epigenetic defence plasticity

The ACCE+ DLA is committed to recruiting extraordinary future scientists regardless of age, disability, ethnicity, gender, gender identity, sexual orientation, faith or religious belief, pregnancy or maternity, parental or caring responsibilities or career pathway to date. We understand that a student’s potential can be shown in many ways and we strive to recruit students from all backgrounds, and support them on their scientific journey.

We have designed our application systems to identify candidates who are likely to be successful in research regardless of what opportunities may have been available to them prior to their application.

Project Overview:

Have you ever wondered how plants without a brain or cellular immune system successfully cope with simultaneous and recurrent episodes stress from diseases, poor nutrition and drought? This PhD will give you the opportunity to address this fundamental question in an exciting and multidisciplinary PhD project. 

BACKGROUND: 

After recovery from stress, plants acquire defence traits that can be transmitted to their offspring. This heritable defence plasticity is controlled by epigenetic mechanisms and enables plants to prime their offspring against persistent environmental stresses. However, the evolutionary relevance of this response remains controversial as it is yet unclear whether it benefits plants under the multivariate and variable stress conditions of natural environments. Furthermore, while stress-inducible changes in DNA methylation have been implicated in its regulation, whether the epigenetic defence phenotypes are sufficiently stable and functional to be selected for/against by the environment remains unknown. 

RESEARCH QUESTIONS: 

1. What are the costs and benefits of stress-induced epigenetic variation? You will quantify reproductive fitness of epigenetically native/primed Arabidopsis populations, which are genetically tagged with different fluorescent proteins (FPs). These common garden experiments will impose variable environmental stresses, including disease (downy mildew), poor soil nutrition, and drought. 
2. Is epigenetic variation shaped by environmental selection? You will identify the impacts of multiple generations of environmental stress on reproductive fitness and epigenetic variation (DNA methylation).
3. What is the evolutionary significance of stress-induced epigenetic plasticity and how does it relate to genetic variation? To address this question, you will exploit publicly available (epi)genomic and bioclimatic data from >1000 wild Arabidopsis accessions.  

KEY METHODS AND SKILLS: 

1. Experimental Design and Execution of Experiments: You will learn to execute common garden experiments, which impose epigenetically diverse Arabidopsis populations to multifactorial stress conditions, including diseases, soil quality and water availability. 
2. Molecular Biology: You will be trained in DNA extraction and long-read ONT sequencing to quantify epigenetic variation.
3. Microscopy and Imaging: You will use epi-fluorescence microscopy to quantify reproductive fitness of naïve/primed populations in F1 progeny and use light microscopy to visualise root interactions with beneficial soil fungi.
4. Computational skills: You will be trained in statistical analysis of data from common garden experiments and ONT sequencing data, as well as multivariate statistics and machine learning algorithms to integrate epigenomic data from wild accessions with bio-climatic data.
5. Effective communication: This interdisciplinary character of the project requires effective written and oral communication skills to collaborate across diverse disciplines and translate research findings.

RESEARCH ENVIRONMENT:

You will become part of a multidisciplinary cluster of research labs studying the epigenetic drivers of plant immunity (Ton), plant adaptation to novel environments (Dunning), the role small RNAs in interspecies communication and epigenetic memory (Shahid), and the ecological/evolutionary consequences of plant-soil-fungus interactions (Field). The project also involves supervision from ENZA Zaden (Posthuma), who are the industry partner on a closely aligned UKRI/BSBRC-IPA project to lead supervisor Ton, which investigates the potential of epigenetic defence memory in crop protection. Thus, you will become part of a diverse team that translates basic scientific discoveries into sustainable crop protection solutions. Accordingly, this PhD position will optimally equip you for a range of career directions in academia, industry, conservation and/or policy development. We welcome applications from students with diverse backgrounds.

How to Apply

Please see the ACCE website for all details of how to apply to the programme at each ACCE+ institution: https://accedtp.ac.uk/how-to-apply/.

All applicants to ACCE+ must complete the ACCE+ personal statement proforma. This is instead of a personal/supporting statement or cover letter. The proforma is designed to standardise this part of the application to minimise the difference between those who are given support and those who are not. Candidates should also submit a CV and the contact details of two referees.

The proforma is available here. 

Part-Time Study Options

All ACCE+ PhDs are available as part time or full time, with part time being a minimum of 50% of full time. Please discuss potential part time arrangements with the primary supervisor before applying to the programme.

Project CASE Status

This project is not a CASE project. 

Candidate webinar

A candidate webinar has taken place to provide information to candidates about this project, this takes the place of traditional candidate:supervisor contact. The webinar can be viewed here.

A live FAQs document is also available, collating key information about the project. You can access the FAQ document for this project here

Funding Information

NERC ACCE+ DLA programme starts from October 2025.

UKRI provide the following funding for 3.5 years:

• Stipend (2024/25 UKRI rate £19,237)

• Tuition Fees at UK fee rate (2024/25 rate £4,786)

• Research support and training grant (RTSG)

Note - UKRI funding only covers UK (Home) fees. The DLA partners have various schemes which allow international students to join the DLA but only be required to pay home fees. Home fees are already covered in the UKRI funding, meaning that successful international candidates do not need to find any additional funding for fees.

International candidates should ensure that they have sufficient funds to pay for a UK student visa, NHS health surcharge fees and travel expenses to the UK, if they are successfully offered a studentship following a formal interview. These costs are not covered by ACCE+

Closing date for all applications is Wednesday 8th January 2025