Diversity of Northwestern and North Caucasian Populations of Puccinia striiformis f. sp. tritici by Virulence and Microsatellite Loci in 2022

Yellow rust (Puccinia striiformis f. sp. tritici (Pst)) is a potentially dangerous disease of wheat. Genetic protection of wheat is an environmentally safe method to control the disease, but its successful application requires information on the structure of regional populations of the pathogen. Virulence and molecular polymorphism were characterized in two Russian Pst populations in 2022. Wheat leaves with Pst urediniopustules were collected from the North Caucasus (Krasnodar Krai, Dagestan, and Kalmykia) and Northwestern Russia (Leningrad Oblast). Virulence was tested on 14 isogenic lines (AvocetNIL) and 15 differentiator cultivars. Polymorphism at 20 microsatellite loci was evaluated in molecular analyses. The SSR markers were as recommended by the Global Rust Reference Center. Virulence was assessed in 74 monopustular isolates, including 29 Dagestan, 10 Krasnodar, 5 Kalmyk, and 30 Northwestern ones. Resistance to all isolates was observed in lines with the genes Yr5, Yr10, Yr15, Yr24, and Yr26 and the cultivars Moro (Yr10, YrMor) and Nord Desprez (Yr3, YrND, Yr+). Isolates virulent to the AvYr17 line were detected for the first time in the Dagestan and Krasnodar populations. Their occurrence was moderate (13%) in the Northwestern population. A significant variation was observed in lines and cultivars with the Yr1 and Yr3 genes. Virulence to Yr7 and YrSp was found to be lower than in 2019 to 2021. In total, 28 phenotypes (races) were determined in the virulence analysis (15 in Dagestan, 11 in the Northwestern region, 3 in Krasnodar, and 2 in Kalmykia). A common phenotype was detected in three North Caucasian Pst samples. Genetic distances between the phenotypes were estimated. Most phenotypes grouped together in a multidimensional diagram, with the exception of three Dagestan phenotypes with the fewest virulence alleles. Based on the Fst index, the Dagestan and Kalmyk Pst collections were high similar to each other and differed moderately from the other collections. Long-term trends in virulence (from 2019 to 2022) were assessed in the Pst populations. A high similarity was observed between all regional population samples in 2019 and 2020. The Northwestern and Dagestan populations slightly differed from the other populations in 2021 and 2022. In 2022, the Krasnodar and Kalmyk populations formed separate groups, which differed from each other and from the main group. The long-term virulence analysis indicated that the structure of Pst populations is highly dynamic in Russia. All North Caucasian isolates and 23 Northwestern isolates were used in the SSR analysis. Six loci (RYN3, RYN9, RYN12, WU6, RJO21, and RJO24) were monomorphic. Three polymorphic alleles were identified in each of the RYN13 and RJO27 loci; two alleles, in each of the remaining loci examined. Significant deviations from Hardy-Weinberg equilibrium were observed for most loci. The observed heterozygosity exceeded the expected one, suggesting a clonal origin of the Pst population. Twenty multilocus genotypes (MGs) were found in the total isolate collection (11 in Dagestan, 11 in the Northwestern region, 3 in Krasnodar, and 1 in Kalmykia). Common MGs were detected in the Dagestan, Krasnodar, and Northwestern populations (MG_1); Dagestan, Kalmyk, and Northwestern populations (MG_2); and Dagestan and Krasnodar populations (MG_3 and MG_4). Genetic distances between MGs were estimated. MGs formed four groups in a multidimensional diagram. A major group included 80% of MGs. One Dagestan MG, two Northwestern MGs, and MG_3 common for the Dagestan and Krasnodar collections were significantly differentiated from the major group and differed from each other. Based on Fst, most regional Pst collections were moderately differentiated from each other, with the exception of the Dagestan and Kalmyk collections. The finding was consistent with the virulence analysis results. The Mantel test detected a moderate correlation between the virulence and SSR data (r = 0.6). This indicates that both analyses can be used to assess genetic polymorphism in Pst. The high variability of the virulence and microsatellite loci warrants annual monitoring of regional Pst populations in Russia.