Genetic analysis of the oat crown rust pathogen Puccinia coronata f. sp. avenae and identification of candidate avirulence genes

Abstract

The oat crown rust pathogen, Puccinia coronata f. sp. avenae (Pca), causes significant disease in oat production globally. Pca is an obligate biotrophic pathogen requiring two hosts to complete its life cycle: the telial host (oat) and the alternate host (Rhamnus sp.). Despite breeding efforts, including the Australian Cereal Rust Control Program (ACRCP), resistance to Pca is often short-lived, with new pathotypes overcoming resistance in 3-5 years. In Australia, where Rhamnus sp. is absent, Pca reproduces asexually, limiting genetic variation but still evolving through the introduction of exotic isolates, mutation, and somatic hybridization.

Advances in next-generation sequencing (NGS) technologies have enabled the rapid and cost-effective generation of reference genomes, critical for studying pathogen evolution. My research addresses these challenges by focusing on genome assembly and genetic variability in Pca. In Chapter 2, I generated two highly contiguous haplotype genome assemblies for an Australian Pca isolate using PacBio and Illumina sequencing, providing a valuable resource to study virulence mechanisms. I identified 651,163 single-nucleotide polymorphisms (SNPs), and predicted 28,618 proteins, 1,862 of which are potential small secreted effector proteins.

In Chapter 3, I identified nearly 1 million SNPs across 73 Australian Pca isolates collected since the 1950s. Principal component analysis (PCA), fastSTRUCTURE and phylogenetic tree construction combined with pathogenicity data provided clear evidence of four incursions of exotic isolates of Pca over a 70-year time period, and local evolution through single-step acquisition of virulence for specific resistance genes in oat via mutation, and of somatic hybridisation between two endemic pathotypes.