Fungal Genomics and Biosecurity

NON-TECHNICAL SUMMARY: Fungi represent the largest group of plant pathogens and throughout history have significantly limited the production of a safe and sustainable food supply. For example, late blight of potato, caused by Phytophthora infestans, resulted in the death of thousands of people and the emigration of millions from Ireland. The majority of serious plant epidemics in the US have been caused by non-indigenous pathogens. This threat of introduced pathogens is increasing due to a global trade, a highly mobile world population, and potential acts of bioterrorism. Rapid response to new pathogens requires accurate and reliable diagnostic procedures. This research is directed toward identifying regions of DNA diagnostic for pathogenicity, survival, and toxin production in fungi. Completion of the outlined research is necessary to locate specific DNA regions that can be used to identify individuals within a population and to distinguish between endemic and introduced fungal pathogens.

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APPROACH: We propose extensive survey sequencing and detailed sequencing of defined loci and genomic regions of representative isolates from several lineages/VCGs to reconstruct the evolution of pathogenesis at the whole genome level. We will infer gene genealogies from nuclear loci (linked and unlinked) across isolates from major VCGs and diverse Magnaporthe oryzae repeat (MGR) lineages in M. oryzae. Bottom-up approaches will be used to test whether differences in pathogenicity are associated with the presence of certain repetitive elements in populations or with the proximity of pathogenicity factors to telomeres. We also will use bottom-up approaches to examine the evolutionary processes that have given rise to the specific organization and function of genes in the aflatoxin gene pathway. To do this, we will identify nucleotide sequence variation within coding and noncoding portions of the aflatoxin gene cluster in population samples of A. flavus or A. parasiticus. The ancestral history of populations will be reconstructed using all available sequence information. Studies also are planned to characterize the role of hypE, a newly describe gene in the aflatoxin cluster, in aflatoxin biosynthesis. Research in this proposal will focus on characterizing a putative pathway intermediate that accumulates in the hypE deletion mutant. To gain a better understanding of the factors necessary for the pathogenicity of A. flavus we will carefully follow the infection of maize kernels with wild type and mutant strains of A. flavus impaired in pathogenicity. To examine the genetic relationship of fungi in the Rhizoctonia species complex we will develop an expanded DNA-sequence database framework for rapid detection of dominant fungal groups from different soils and phylogenetic-based probes will be designed and tested for their ability to detect these fungi. We will also develop methods that will complement previously funded research to target genes in the quinic acid cluster.