Diversity-informed R gene deployment strategies enabled by rapid avirulence gene identification

Breeding for resistance against fungal pathogens in crops such as wheat relies heavily on resistance (R) genes, which, upon recognizing of specific avirulence (AVR) effectors, trigger an immune response. The evolutionary dynamics within pathogen populations, particularly the standing genetic variation in AVR effectors, significantly influence the durability of these R genes. Due to the delayed identification of AVR effectors in fungal pathogens, evaluating new resistance sources often remains challenging. We therefore established a new method called the “avirulence depletion assay”. This method combines directed selection of pathogen populations on resistant wheat lines with bulk sequencing, allowing for the rapid and cost efficient identification of fungal avirulence genes. Using this approach, we identified several avirulence genes of the Pm60 and Pm3 allelic series that are active against the wheat powdery mildew pathogen (Blumeria graminis f.sp. tritici, Bgt). We created a regional map of the activity of these two promising R genes by combining diversity data from re-sequencing of several hundred Bgt isolates paired with functional analysis of the identified sequence AVR variants. Our work demonstrates the usefulness of rapid AVR identification combined with diversity analysis in enhancing pathogen-informed breeding strategies, thereby facilitating the targeted incorporation of novel resistance sources into the wheat breeding pool.