Project No.2442

STANDARD PROJECT

Primary Supervisor

Dr Sara Lopez-Gomollon – University of Kent

Co-Supervisor(s)

Dr Mark A. Chapman University of Southampton

Dr Alessia Buscaino – University of Kent

Dr Helen Bate – University of Kent

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Summary

Hybridisation: from new traits to viral disease

Why is this Opportunity Special?
Hybrids are widely used in agriculture because of their unique traits, but how these traits appear is not well understood. Our research has uncovered a key mechanism: Plants have dormant viruses, called EPRV, that get activated in hybrids. The activation of these “sleeping agents” can cause viral disease. Therefore, plants activate an immune response, RNA silencing, to cleave the viral RNA into small RNAs. This process not only stops the potential disease, but it is also going to affect the phenotypes of plants, so we think it can be behind interesting traits in hybrids and therefore have implications from food security to crop breeding.

How We Are Going to Study This:
We will use cutting edge technology like Oxford Nanopore and Next Generation Sequencing to understand how EPRVs get activated, by using it for genome sequencing, DNA methylation analysis and other genomic techniques. To characterise the molecular mechanism, we will create an on-demand system to activate EPRV that mimic a “hybrid” status.

What We Want to Achieve:
1. Characterize the genome and epigenome of plant hybrids.
2. Identify active EPRV molecules and their association to epigenetic marks
3. Investigate the mechanisms that activate EPRV looking at genetic and epigenetic features.
4. Pioneer transformative technology: Develop a transgenic system for on-demand EPRV activation. This will bypass the complexities of hybrid genomes, allowing real-time monitoring of EPRV effects on crops. The proof-of-concept approach can be applied to other crops to combat viral diseases or induce phenotypes.

Who can achieve this?
We are looking for a dedicated student interested in molecular biology, genetics, epigenetics, genomics and bioinformatics. The project then includes both computational and experimental components, supervised by experts in these fields, and adapted to the interests of the student. A background/interest in bioinformatics is required, and additional training will be provided. The project, using an exciting variety of specialized tools and knowledge from several fields, will provide a challenge to understand the activation of EPRV and the effect on the plant phenotype and fitness.
More info in references: PMID: 35597968; PMID: 35710830.