Fungus Puccinia graminis f. sp. tritici (Pgt) is important pathogen of spring bread wheat in different agricultural areas of Russia. Pgt urediniospores cause stem rust disease of wheat crops and spread easily throughout the country. High genetic plasticity of Pgt genome serves to increase the disease pressure and overcome the resistant genes of the host plant. Genotyping of Pgt isolates can facilitate and speed analyses of larger samples comparing with virulence surveys of the pathogen.

Objectives of this study were to determine SSR (simple sequence repeats) genotypes of Pgt isolates, and to study differentiation among and variability within regional Pgt populations based on the multilocus genotypes. Sixteen SSR markers were screened against Pgt samples from four different agricultural areas within the temperate climate zone of Russia: Central and Volga regions in the European part of Russia, and Omsk and Novosibirsk provinces in Western Siberia.

Results. The amplicons were polymorphic, with 1–7 alleles for each marker. Analyses were performed assuming two models of SSR evolution: Infinite Alleles Model (IAM) and Stepwise Mutation Model with variable mutation rate (SMMv). Variability within the regional samples (Kosman’s KW index) was higher among the Western Siberia samples: 0.556/0.292 in Omsk and 0.36/0.21 in Novosibirsk (assuming IAM/SMMv models, respectively) against 0.09/0.057 and 0.131/0.075 in the Central and Volga regions, respectively. SSR loci were indicating due to the different number of alleles and unequal distribution of homo- and heterozygotes in the samples. Six SSR loci (Pgestssr024, Pgestssr059, Pgestssr318, PgtCAA80, PgtCAA93, PgtCAA98) were useful to track the origin of Pgt isolates.

The study was funded by the budgetary project of ICG SB RAS № 0259-2019-0001 and RFBR grant № 18-016-00170a.