PhD defence: Small changes fuel a rapidly evolving threat - The genomic basis of resistance breaking in spinach downy mildew

PLEASE NOTE: The candidate gives a layman's talk, therefore the livestream will start fifteen minutes earlier.

Peronospora effusa is a microscopic water mold (an oomycete) that causes spinach downy mildew, the most economically damaging spinach disease worldwide. It infects leaves, creates yellow patches and fuzzy growth, and can ruin crop quality quickly, especially in cool, humid conditions. Resistant spinach varieties are used to manage this disease, but they are often planted in large, dense monocultures. As a result, P. effusa is strongly pressured to adapt, and new resistance-breaking isolates spread quickly.

My thesis explains how P. effusa keeps overcoming resistant spinach varieties so quickly. I studied the genomes of 19 pathogen strains, including strains that can break known plant resistances. Using high-resolution genome sequencing and new comparison methods, I showed that the pathogen evolves through a mix of sexual and clonal reproduction. In simple terms, it can reshuffle its genes to create new combinations and rapidly spread by copying successful versions.

I also found that overall chromosome structure is surprisingly stable, but smaller genomic changes are very common. Many of these changes occur in effector genes, molecules the pathogen uses to manipulate plant defences. These genes often change through duplication, deletion, mutation, and recombination, often multiple times independently in the population. This helps explain how new resistance-breaking strains can appear within a single growing season.

Overall, this work provides the complete genomic view so far of P. effusa and identifies candidate genetic changes linked to spinach resistance breakdown. The findings give breeders and researchers better targets for longer-lasting resistance and show why field monitoring is essential.