Virulence Profiles and Fungicide-Target-Gene Variability in Puccinia graminis f. sp. tritici Populations from Russian Regions

Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), threatens food security owing to the pathogen’s high virulence and evolutionary variability, as well as the risk of selecting fungicide-resistant forms. For the first time in Russia, we performed a comparative analysis of virulence and genetic diversity in fungicide-target genes (SdhA–SdhD, Cyp51) in 35 monopustular Pgt isolates collected from regions with contrasting fungicide pressure (Saratov, n = 12; Chelyabinsk, n = 12; Moscow, n = 11). Phenotyping on an extended set of nearly isogenic lines carrying different Sr genes revealed regional specificity in effective resistance genes (Sr13, Sr26, Sr31, Sr32, Sr35), underscoring the vulnerability of genetic protection in Russian commercial cultivars. Targeted amplicon sequencing using the Oxford Nanopore Technologies platform produced 175 amplicons (~38,290 long reads, N50 = 1.06 kb), identifying 87% synonymous SNPs, 12% non-synonymous substitutions, and a single nonsense mutation in SdhA (position 580). The Cyp51 and SdhA genes were the most polymorphic. Recurrent non-synonymous mutations in these genes were detected in Pgt clones from regions with intensive agriculture and high use of chemical plant protection products. These results support the need for predictive breeding of resistant cultivars and adaptation of chemical control within integrated Pgt management in the European part of Russia.