Date of Award

5-1-2016

Degree Name

Doctor of Philosophy

Department

Plant Biology

First Advisor

Geisler, Matt

Second Advisor

Fakhoury, Ahmad

Abstract

The relationship between a pathogen and its host is a complex series of events that occurs at the molecular level and is controlled by transcriptional and protein interactions. To facilitate the understanding of these mechanisms in Aspergillus flavus and Zea mays, three approaches were taken: 1) the development of a predicted interactome for Z. mays (PiZeaM), 2) the development of co-expression networks for Z. mays and A. flavus from RNA-seq data, and 3) the development of causal inference networks depicting interactions between the host and the pathogen. PiZeaM is the genome-wide roadmap of protein-protein interactions that occur within Z. mays. PiZeaM helps create a novel map of the interactions in Z. mays in response to biotic and abiotic stresses. To further support the predicted interactions, an analysis of microarray-based gene expression was used to produce a gene co-expression network. PiZeaM was able to capture conserved resistance pathways involved involved in the response to pathogens, abiotic stress and development. Gene Co-expression networks were developed by the simultaneous use of correlations to develop networks for differentially expressed genes, resistance marker genes, pathogenicity genes, and genes involved is secondary metabolism in Z. mays and A. flavus. From these networks, correlation and anti-correlation of host and pathogen gene expression was detected, revealing genes that potentially interact at different stages of pathogenesis. Finally, causal gene regulatory relationships were inferred using partial correlation analysis of Z. mays infected with A. flavus over a 3 day period. The gene regulatory network (GRN) sheds light on the specifics of the mechanisms of pathogenesis and resistance that govern the Z. mays-A. flavus interaction. The direct product of this research is the understanding of key transcription factors and signaling genes involved in resistance. This body of research highlights how PPIs and GRNs can be utilized to identify biomarkers and gene functions in both Z. mays and A. flavus.

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