The analysis of Puccinia triticina field populations in Canada between 2018 and 2020 using restriction site-associated DNA genotyping-by-sequencing

Puccinia triticina, the causal agent of wheat leaf rust, is a dynamic pathogen causing significant yield losses worldwide. In this study, we analysed the virulence and genetic structure of 98 P. triticina isolates collected in Canada between 2018 and 2020. Isolates from Manitoba and Saskatchewan were found to be highly related for virulence, as were isolates from Quebec and Ontario. Isolates from Alberta had a virulence profile more similar to those from Manitoba and Saskatchewan than to Ontario and Quebec. To study the genetic structure of P. triticina populations, we used the restriction site-associated DNA (RAD) genotyping-by-sequencing method to identify single-nucleotide polymorphisms (SNPs). The Puccinia DNA sequences were aligned against the reference genome of P. triticina race BBBD and 1898 SNPs were identified. The phylogenetic analysis using SNP markers grouped these P. triticina into three genetic clades. The separation of P. triticina into three genetic clades was also supported by principal component analysis. Isolates from Clade 1 and Clade 2 were found throughout Canada, whereas Clade 3 isolates were only found in Ontario and Quebec. There were differences in virulence profiles among P. triticina isolates from the three genetic clades and a general correlation between virulence phenotypes and SNP genotypes was observed. These results indicate that the SNPs derived from RAD genotyping-by-sequencing could be useful in tracking the genetic and virulence dynamics of this pathogen in Canadian wheat.