Feng Li Doctoral Dissertation Defense October 2019
Wheat stem rust, a destructive fungal disease threatening wheat production, is caused by Puccinia graminis f. sp. tritici (Pgt). A highly virulent Pgt strain known as Ug99 emerged in Uganda in 1998 and overcame an important disease resistance gene Sr31. Ug99 can infect 90% of wheat cultivars worldwide. Part of my Ph.D. research included in this dissertation focuses on creating genomic resources to study genome biology of Pgt and understanding the underlying genetic diﬀerences that explains virulence evolution. The ﬁrst research chapter 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 the whole nuclear exchange at vegetative stage contributes to the evolution of rust virulence in the ﬁeld. In addition, my work also aims to discover novel genes in mediating resistance or susceptibility against Pgt. Here, I utilized a small grass and model species Brachypodium distachyon as a system to study non-host resistance mechanisms against Pgt. Because of the close phylogenetic relationship of B. distachyon to wheat and barley, this species has potential applications for translational research to deliver durable and broad-spectrum resistance. In the second research chapter, a comparative RNA-seq transcriptome analysis and a functional genomics approach assisted with the identiﬁcation of rust defense-associated genes in B. distachyon. I developed a pipeline that merges phenotypic and genotypic screenings using a collection of T-DNA insertional lines of B. distachyon to identify and characterize these candidate genes. Two genes, a WRKY transcription factor and a sugar transporter, were identiﬁed and further validated to play a role in non-host resistance. 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 gene stewardship to minimize wheat losses due to stem rust epidemics and proposes novel ways to engineer resistance in wheat.