Construction and Application of a Rapid Method for Population Genetic of Plant Pathogens: A Case Study of Puccinia striiformis f. sp. tritici

Population genetic studies of plant pathogens by traditional molecular markers often rely on the purification and multiplication of pathogens, which is time-consuming, labor-intensive and costly. To address these limitations, we developed a rapid method for monitoring pathogen population diversity using the obligate biotrophic fungus Puccinia striiformis f. sp. tritici ( Pst ) as a case study. A set of specific and high-efficiency housekeeping gene SNP (HG-SNP) markers was developed using genome and transcriptome sequencing data (GRSD) to generate genotype data directly from field-collected Pst -infected wheat leaves for population genetic analysis. These markers showed high consistency in the results of population genetic diversity with GRSD. Furthermore, population genetic analysis of 2,101 field samples from China using HG-SNP markers revealed low exchange among Xinjiang, Xizang, and Inland regions and major dispersal routes from the Northwest Oversummering Region and Yunnan-Guizhou to Sichuan and eastern China. This framework supports rapid and accurate monitoring of population genetics and can be readily applied to other plant pathogens. The method facilitates the distribution of host resistance and the development of plant disease management strategies at a regional and national scale.