An Avr gene atlas for wheat stem rust to support resistance gene deployment

Rust fungi are important pathogens of many crops, especially wheat and other cereals where they cause substantial economic losses worldwide. While progress in resistance (R) gene cloning and stacking has accelerated in recent years, crop breeding for durable disease resistance is challenging due to the rapid evolution of virulence in these pathogens. Known Avr genes in Melampsora lini (flax rust) and Puccinia graminis f. sp. tritici (Pgt) (wheat stem rust) encode secreted proteins that are co-ordinately expressed in haustoria structures during infection. However, broader Avr gene identification in rusts has been hindered due to the complex genomes of these dikaryotic fungi (containing two divergent haploid nuclei), their obligate biotrophic nature and the large number of potential effector genes they encode. To address these limitations, we developed a platform for pooled library screening in plant protoplasts to allow rapid identification of interacting R-Avr pairs. Using this platform we have screened libraries of candidate effectors from wheat stem rust and isolated several new Avr genes recognised by known stem rust resistance (Sr) genes. We have generated haplotype-phased reference genomes for important lineages of stem rust that have caused major epidemics in Africa and Europe and minded these genomes for novel Avr gene variants. Virulence genotypes at these Avr loci are defined based on functional analysis of recognition of the encoded effector proteins by the corresponding wheat Sr genes. Defining Avr genotypes in important lineages of Pgt is beginning to populate an Avr gene atlas to underpin rational deployment of Sr genes in breeding and in multigene cassettes.