Windram, Oliver P. (2010) Using a systems biology approach to elucidate transcriptional networks regulating plant defence. PhD thesis, University of Warwick.

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Abstract

The phytopathogen Botrytis cinerea is responsible for the devastating grey mould
disease that affects hundreds of economically important crop species. B. cinerea
represents a necrotrophic pathogen that must kill host tissue before if can consume the
nutrients, this distinguishes it from other biotrophic pathogens that exist parasitically.
Importantly, B. cinerea is capable of infecting the model plant organism Arabidopsis
thaliana. Together with the availability of the sequenced B. cinerea genome and the
available molecular tools that now allow fungal genome manipulation makes the
pathosystem ideal for studying necrotrophic pathogen life style from a systems biology
perspective.
This thesis focuses on the transcriptional responses of the A. thaliana host to B. cinerea
infection. A high resolution transcriptome time series experiment was conducted to
compare transcriptional variation between infected and mock infected A. thaliana leaves
over 48 hours. This identified 9838 unique host genes differentially expressed over the
course of infection.
High resolution temporal expression profiles of genes were used to build transcriptional
gene regulatory networks using a Variational Bayesian State Space Modeling technique.
Approximately 56% of principle network components identified by this method and
tested using a reverse genetics approaches showed an effect on defence against B.
cinerea. This represents a significant increase in the predictive power (of gene
essentiality) when using this method compared to classical forward genetics approaches
and simple reverse genetic approaches following on from expression profiling studies.
Attempts were made to resolve the local networks surrounding two of these previously
uncharacterised principle network components involved in defence against B. cinerea
using further transcriptome expression profiling and Yeast-1-Hybrid analysis.
Subsequent re-modeling and experimental studies identified a number of high
probability targets and several potential regulators of these principle network
components. Overall the A. thaliana-B. cinerea interaction presents a experimentally
tractable pathosystem for studying necrotrophic plant defence from a systems biology
perspective.

Item Type:	Thesis or Dissertation (PhD)
Subjects:	S Agriculture > SB Plant culture
Library of Congress Subject Headings (LCSH):	Botrytis cinerea, Arabidopsis thaliana -- Genetics, Genetic transcription
Official Date:	September 2010
Dates:	Date Event September 2010 Submitted
Institution:	University of Warwick
Theses Department:	Warwick HRI
Thesis Type:	PhD
Publication Status:	Unpublished
Supervisor(s)/Advisor:	Denby, Katherine
Extent:	xxii, 304, lxxii p. : ill., charts
Language:	eng

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