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Bourquin, Finlay (2025) Understanding Botrytis cinerea infection in strawberries. PhD thesis, University of Nottingham.

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Abstract

Botrytis cinerea is a ubiquitous necrotrophic plant pathogen. It has a wide array of virulence mechanisms, enabling it to evade host immune responses, initiate infection and proliferate in the host and neighbouring plants. In strawberries, B. cinerea can infect all the above ground organs and is responsible for both pre- and post-harvest infection. Currently, fungicides are the most effective control method; however, B. cinerea can become recurrently resistant to fungicides and there is growing public concern over fungicide residues on fruit. Therefore, novel control methods need to be investigated to mitigate B. cinerea infection, whilst also appealing to consumers in a sustainable manner. In order to further understand the strawberry-B. cinerea pathosystem, the molecular mechanisms influencing plant pathogen interactions need to be examined.

Pathogenicity assays for strawberry leaves, fruits and flowers were developed to gain a comprehensive overview of how different isolates of B. cinerea infect strawberry plants. Aggressiveness rankings, from high, medium and low, were determined for the isolates, with isolates varying in their ability to infect leaves and flowers, whereas all isolates exhibited high aggressiveness on fruit. Additionally, one isolate with moderate aggressiveness on strawberry exhibited high aggressiveness on Nicotiana benthamiana, indicating isolates can have adaptations for infection on certain hosts.

Resistance to B. cinerea in strawberry is understood to be under polygenic control. To target as many genes as possible, the chemical mutagen ethyl methanesulfonate was utilised to induce random single nucleotide polymorphisms into the genome. The leaf pathogenicity assay was then conducted on the mutant plants, with thirteen exhibiting a change in susceptibility to B. cinerea infection. These more susceptible plants were sequenced and through variant analysis, 774 variants were identified for further investigation. A pipeline consisting of BLASTP searches, determining whether variants were in protein domains, induced amino acid substitutions and were predicted to alter protein structure, along with RNA-seq analysis, was carried out to narrow down which variants could have caused the changes in susceptibility. The candidate resistance genes identified were found to function in established defence pathways, including those involving the plant hormones jasmonic acid, ethylene, salicylic acid and abscisic acid, as well as reactive oxygen species. A list of 26 candidate resistance genes was generated and can now be functionally validated.

Since there was variation in aggressiveness in the B. cinerea isolates, comparative genomics, particularly presence of secreted effectors and phylogenetic analysis, was conducted on 10 B cinerea isolates to deduce if these factors could explain the variation observed. Aggressiveness could not be attributed to the presence of retrotransposons, which contradicts previous evidence in the literature.

Nor was aggressiveness associated with phylogenetic relationships, since the most and least aggressive isolates were grouped in the same clade. Aggressiveness could perhaps be explained, not by predicted secreted effector count, but by the presence of unique secreted effectors, although this requires functional validation. The predicted virulence factors possessed roles regarding competitive fitness between fungi and secretory pathway regulation.

Overall, pathogenicity assays capable of determining quantitative differences in B. cinerea aggressiveness and strawberry resistance were developed. Identifying candidate resistance factors and candidate virulence factors lays the foundation for future work. Should validation confirm that these genes have roles in resistance and virulence, they can inform future breeding strategies by ensuring their presence in new varieties, and aid in the development of targeted, sustainable control methods, ultimately reducing crop losses and improving strawberry production efficiency.

Item Type:	Thesis (University of Nottingham only) (PhD)
Supervisors:	Nellist, Charlotte Cockerton, Helen Price, Jordan Robbins, Tim Dickinson, Matt Clarke, Andrew
Keywords:	strawberries, Botrytis cinerea, plant pathogens
Subjects:	S Agriculture > SB Plant culture
Faculties/Schools:	UK Campuses > Faculty of Science > School of Biosciences
Item ID:	82880
Depositing User:	Bourquin, Finlay
Date Deposited:	12 Dec 2025 04:40
Last Modified:	12 Dec 2025 04:40
URI:	https://eprints.nottingham.ac.uk/id/eprint/82880

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