E. Henningsen: eva.henningsen@anu.edu.au

M. Figueroa: Melania.figueroa@csiro.au

Wheat stem rust, caused by the fungal pathogen Puccinia graminis f. sp. tritici (Pgt), ranks highly as a threat to global food security. After the emergence of Ug99 (race TTKSK), which represented the first major international outbreak of stem rust since the widespread deployment of Sr31, other unrelated Pgt strains have also emerged and caused epidemics in east Africa and Europe.

The combination of Hi-C chromatin contact sequencing and long-read DNA sequencing led to the first nuclear haplotype phased genome assemblies for rust fungi, (wheat stem rust isolates Pgt21-0 and Ug99). Following these advances, we have generated haplotype-phased genome references for two important Pgt races TKTTF (ETH2013-1) and TTRTF (ITA2018-1) which have spread through east Africa and Europe. These isolates contain novel nuclear haplotypes designated G, H (ETH2013-1), I and J (ITA2018-1) which are highly divergent.

A comparative analysis showed that ETH2013-1 is one of two distinct lineages that emerged in Ethiopia in 2012 and share the same pathotype (TKTTF) but are highly divergent in genome sequence. Importantly, a potential nuclear exchange of the H nuclear haplotype involving the ETH2013-1 lineage and another lineage represented an isolate (IR-06) collected in Iran in 2015, was detected.

This observation suggests that, as observed for Ug99, nuclear exchange events may be behind other global stem rust outbreaks. The ETH2013-1 and ITA2018-1 reference genomes were mined for alleles of known avirulence (Avr) genes and their virulence genotypes at these Avr loci defined based on functional analysis of recognition of the encoded effector proteins by the corresponding wheat Sr genes.

We propose a genomics-driven approach to global rust surveillance with a focus on Avr genotypes to better anticipate the emergence of isolates that overcome widely used resistance genes.