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The globally distributed causal agent of powdery mildew on wheat, Blumeria graminis f. sp. tritici (Bgt), is one of the most rapidly adapting plant pathogens and requires monitoring for shifts in virulence to wheat resistance (Pm) genes. Virulence frequencies were assessed in a total of 346 Bgt isolates from several countries that had either lately recorded increasing powdery mildew epidemics (Brazil, South Africa, and Australia) or not recently been surveyed (Turkey and Russia). The results were compared to previously published surveys of United States and Egyptian Bgt (390 isolates). Many of the Pm genes that have potentially been employed longer (Pm1a–Pm17) were shown to have lost effectiveness, and the complexity of virulence to those genes was higher among Brazilian isolates than those from any other country. Some cases of high virulence frequency could be linked to specific Pm gene deployments, such as the widespread planting of cultivar Wyalkatchem (Pm1a) in Australia. Virulence was also assessed to a set of Pm genes recently introgressed from diploid and tetraploid wheat relatives into a hexaploid winter wheat background and not yet commercially deployed. The isolate collections from Fertile Crescent countries (Egypt and Turkey) stood out for their generally moderate frequencies of virulence to both the older and newer Pm genes, consistent with that region’s status as the center of origin for both host and pathogen. It appeared that the recently introgressed Pm genes could be the useful sources of resistance in wheat breeding for other surveyed regions.

Abstract Background Effective disease management depends on timely and accurate diagnosis to guide control measures. The capacity to distinguish between individuals in a pathogen population with specific properties such as fungicide resistance, toxin production and virulence profiles is often essential to inform disease management approaches. The genomics revolution has led to technologies that can rapidly produce high-resolution genotypic information to define individual variants of a pathogen species. However, their application to complex fungal pathogens has remained limited due to the frequent inability to culture these pathogens in the absence of their host and their large genome sizes. Results Here, we describe the development of Mobile And Real-time PLant disEase (MARPLE) diagnostics, a portable, genomics-based, point-of-care approach specifically tailored to identify individual strains of complex fungal plant pathogens. We used targeted sequencing to overcome limitations associated with the size of fungal genomes and their often obligately biotrophic nature. Focusing on the wheat yellow rust pathogen, Puccinia striiformis f.sp. tritici (Pst), we demonstrate that our approach can be used to rapidly define individual strains, assign strains to distinct genetic lineages that have been shown to correlate tightly with their virulence profiles and monitor genes of importance. Conclusions MARPLE diagnostics enables rapid identification of individual pathogen strains and has the potential to monitor those with specific properties such as fungicide resistance directly from field-collected infected plant tissue in situ. Generating results within 48 h of field sampling, this new strategy has far-reaching implications for tracking plant health threats.