Genetic Diversity of Pyrenophora tritici-repentis Based on Virulence Phenotyping, Effector Gene Profiling, and SSR Markers

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Tan spot is an economically important disease that occurs wherever wheat is grown in Russia. The variability of Pyrenophora tritici-repentis isolates collected in 2025 from common and durum wheat in the Volga region of the Russian Federation—namely Tatarstan, Penza, and Saratov—was characterised for virulence phenotypes, effector genes ToxA, ToxB, and ToxC, and SSR loci. A total of 74 isolates were studied. The ToxA gene was identified in 83.8% of the isolates, while ToxB was not detected; conversely, the ToxC1 allele, one of the genetic determinants of PtrToxC, was present in all isolates. A discordance between phenotypic and molecular assays was noted for PtrToxA detection. Genetic diversity was examined using ten microsatellite (SSR) markers. After clone correction, 55 multilocus haplotypes were resolved. Isolates from common wheat in Tatarstan and Penza showed high similarity, in contrast to the Saratov isolates from durum wheat, which were significantly differentiated. The observed differentiation may be associated with host specialisation to durum wheat, but this hypothesis requires further validation with multi-year and genomic data.