Date Available


Year of Publication


Degree Name

Doctor of Philosophy (PhD)

Document Type

Doctoral Dissertation


Agriculture, Food and Environment


Plant Pathology

First Advisor

Dr. Mark Farman


Rice blast disease, caused by the ascomycete fungus Magnaporthe oryzae, occurs in over 85 countries and results in an annual crop loss of 10-30%, a corresponding nutrient value of meals for 60 million people. As a result, it is listed as a critical plant disease by the United Nations. Understanding factors affecting disease severity is of critical concern for food security. M. oryzae has been used as a model system for studying effector-triggered immunity (ETI) by understanding that ETI is primarily a plant response. M. oryzae has been used as a model to study fungal pathogenicity, host specificity, genome evolution, and population biology. This dissertation explores the environmental impacts on the disease progression of rice blast with a primary goal of understanding unexpected variation in infection phenotypes from one experiment to another.

Fungal strain 2539 was studied to characterize possible AVR genes. Using growth rate studies, artificial inoculation assays, and southern blots, 2539 was shown to have undergone massive, seemingly spontaneous, genome rearrangement, resulting in an unpredicted infection phenotype. This genomic rearrangement resulted in a newly observed virulence of 2539 on rice cultivar 51583 and higher disease ratings on rice cultivar Yt16. Resistance of CO39 to 2539 indicated that AVR1-CO39 remained intact after the genomic rearrangement. Additional resistance of M2O2 to 2539 indicated a possible unidentified AVR gene in 2539 or broad resistance conveyed through AVR1-CO39.

Based on the irreproducibility of inoculation assay results, factors such as plant age, light, and time of day at inoculation were studied as influencers of the infection phenotype of M. oryzae strains. Plant age at inoculation displayed a high susceptibility of plants between 14-18 d, which correlated to the early tillering stage of rice plants. The light inoculations displayed a cultivar and strain-specific influence where one strain/cultivar experienced increased disease severity while another experienced decreased severity. The time of day inoculations displayed a slight trend of increased disease severity for inoculations performed later in the day but were dependent on the stock. Irreproducibility between inoculation was observed in the control groups of these experiments, indicating a confounding factor not yet identified.

Uncontrolled temperature exposures were also studied as a possible factor contributing to the irreproducibility between experiments. Temperature treatments were performed pre and post-inoculation at 4℃ and 37℃. The results of these experiments indicated that the influence of temperature exposures pre and post-inoculation were strain and cultivar-specific. There was not an overall trend with any of the temperature treatments for all of the strains. However, post-inoculation heat treatment of 37℃ for 24 h did present an increased degree of infection for two 2539 stocks. This indicated a possible suppression of host resistance early in infection. Due to this result, post-inoculation 37℃ exposure was further studied with different fungal strains, multiple rice cultivars, and varying exposure times. The results supported the influence of brief exposure to higher temperature post-inoculation acting at the level of recognition.

The last topic covered in this dissertation was a final exploration into the confounding factor introducing irreproducibility between experiments. Fungal paper stocks had been used during plant inoculations to activate fungal stocks in the creation of inoculum. Since these were the only differences between experimental replicates, it was proposed that the fungal stocks were introducing variability in inoculum. The results supported the presence of clonal variation in fungal paper stocks. Although rare, one stock out of multiple taken from a single plate could be phenotypically different from the other stocks. This could cause a stark difference in disease incidence and severity on rice plants.

Digital Object Identifier (DOI)