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Title: Elucidating key components of the Lactuca sativa and Sclerotinia plant-pathogen interaction
Author: Ransom, Elspeth M.
ISNI:       0000 0004 8498 0201
Awarding Body: University of Warwick
Current Institution: University of Warwick
Date of Award: 2018
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Globally, plant-pathogens pose a large threat to crop yield and subsequent food security. Pre-harvest, 15% of crops worldwide are lost to disease. Sclerotinia species necrotrophic fungi are particularly devastating, possessing broad host and geographical ranges. In the UK, lettuce losses of up to 50% have been reported as a result of Sclerotinia sclerotiorum infection, stressing the need for the development of new varieties with resistance to Sclerotinia. However, identification of durable sources of disease resistance requires in depth understanding of both the plant defence mechanisms and Sclerotinia pathogenicity factors, as well as the interaction of these to determine disease outcome. This work presents novel dual-species time series RNA sequencing of the Lactuca sativa (lettuce)-Sclerotinia sclerotiorum pathosystem, using a detached leaf infection approach. Over 42 hours post infection, 6446 lettuce genes and 2788 S. sclerotiorum genes were identified as being differentially expressed. Functional analysis elucidated the chronology of the lettuce defence response from initial perception to defence gene activation, including identification of groups of known defence related-proteins. Changes in transcript abundance of S. sclerotiorum pathogenesis genes and effector candidates were identified. This has allowed examination of potential host-pathogen interaction points during infection. Relationships between differentially expressed lettuce transcription factors during S. sclerotiorum were inferred using the causal structural inference algorithm. This identified core 'hub' regulators of the defence response, whose roles were tested using transgenic Arabidopsis and lettuce lines. Over-expression in Arabidopsis of two lettuce hub genes led to enhanced resistance to S. sclerotiorum. Furthermore, a CRISPR-Cas9 pipeline for generation of hub gene knockout lettuce lines was developed. MinION genome sequencing of Sclerotinia sclerotiorum, Sclerotinia subarctica and Sclerotinia minor ) produced highly contiguous genomes. Comparative analysis revealed high levels of synteny, with evidence for similar mechanisms of pathogenicity. The transcriptomic and genomic resources generated during this work, in combination with detailed analyses, provide a wealth of information on the pathogenicity mechanisms of Sclerotinia species and defence responses of lettuce. This information will drive future development of Sclerotinia resistant lettuce (and other crop) varieties, as well as enhanced crop protection strategies.
Supervisor: Not available Sponsor: Midlands Integrative Biosciences Training Partnership
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: QK Botany ; QR Microbiology ; SB Plant culture