Virulence of the stem rust fungus and non-host resistance against stem rust

Abstract

Wheat stem rust is a destructive disease caused by the fungal pathogen Puccinia graminis f. sp. tritici (Pgt), which poses a significant threat to global wheat production. A highly virulent Pgt strain known as Ug99 emerged in Uganda in 1998 overcame an important disease resistance gene Sr31. Ug99 can infect 90% of wheat cultivars worldwide. Part of the Ph.D. research included in this dissertation focuses on creating genomic resources to study Pgt and understanding the underlying genetic differences that explains virulence evolution. The research also aims to discover novel genes in mediating resistance or susceptibility against Pgt in the grass species, Brachypodium distachyon. In Chapter 1, I present a comprehensive literature review of our current state of knowledge of cereal rust fungi, particularly Pgt in light of the recent evolution of new broadly virulent races. I also discuss current genomic resources and approaches to study virulence evolution of rust fungi. Finally, I present an overview of genetic disease resistance and its mechanisms, as the main strategy to mitigate the effect of Pgt in wheat production. Chapter 2 describes the construction of the first de novo haplotype-phased genome assemblies of Pgt, including Ug99 and an Australian Pgt isolate 21-0. Importantly, a systematic comparison of both genomes shows that the Ug99 lineage emerged through a somatic hybridization event. This study also provides the first molecular demonstration that whole nuclear exchange at the vegetative stage contributes to the evolution of rust virulence in the field. One important goal within our scientific community is to develop novel and durable stem rust disease management strategies. Thus, another objective of my dissertation was to investigate non-host resistance against rust fungi to identify genes that may enable the development of these approaches. Using a reverse genetics approach, Chapter 3 describes a pipeline that merges phenotypic and genotypic screenings to identify rust defense-associated genes in Brachypodium distachyon, which serves as a non-host to several cereal rust fungi. Here, I utilized a collection of T-DNA insertional lines of B. distachyon to characterize genes of interest in Brachypodium-rust interactions. Two candidate genes, a WRKY transcription factor and a sugar transporter, were identified to play a role in non-host resistance. Finally, I also attach appendices that refer to my contributions to four other independent publications, including a research manuscript that defines the non-host status of B. distachyon to Puccinia coronate, the causal agent of oat crown rust; a research publication of the cloning of the first effector gene in Pgt; a review and perspectives on B. distachyon as a donor of resistance against cereal rusts and finally one pathogen profile of P. coronata. Overall, research presented in this dissertation has important implications for crop protection and advances the field of biology and genomics in rust fungi. By creating suitable genomic resources to study Pgt and enabling effector discovery, this dissertation is deemed to contribute to rust resistance gene stewardship and minimize wheat losses due to stem rust epidemics.