Exploring the epigenetic response of Larix kaempferi to Phytophthora ramorum infection

Abstract

The detection of microbes by plants induces considerable changes in the plant’s physical and biochemical state, referred to as the phenotype. Phenotypic changes are internally coordinated through a combination of phytohormones and dynamic alterations to gene expression, which in turn are partly regulated by epigenetic mechanisms. Epigenetics encompasses modifications to DNA and its expression that occur without altering the underlying nucleotide composition. The best studied of these mechanisms is cytosine methylation. Plants have a sophisticated system for epigenetic regulation of gene expression through transient and dynamic methylation of specific cytosine residues. Given the emergent role for epigenetic regulation in plant-microbe interactions, this project aimed to identify genomic loci that undergo differential methylation upon infection. Methylation at these loci could potentially function as epi-marks of infection, serving as early indicators. The process of epi-mark discovery has two parts; mark identification and mark retrieval, both addressed through a novel pipeline. This pipeline comprised the inoculation design, genome subsampling, high throughput sequencing and bioinformatic analysis, and a further step for validating and retrieving epi-marks. While here applied to forestry diagnostics, this pipeline could also be used for identifying differential methylation in response to various abiotic or biotic factors. Here, we explored changes in cytosine methylation in Larix kaempferi (Larch) seedlings infected with the invasive Oomycete pathogen Phytophthora ramorum. This forest pathogen has caused the death of millions of trees worldwide, and significantly disrupted the UK forestry industry. Several loci showing methylation variability upon infection were identified. However, further work is needed to optimise the bioinformatic analysis before epi-marks identified through this pipeline can be reliably used for diagnosis.

Date of Award	2023
Original language	English
Awarding Institution	Aberystwyth University
Sponsors	Knowledge Economy Skills Scholarships
Supervisor	Michael Wilkinson (Supervisor) & Gareth Griffith (Supervisor)