Development of KASP Markers in Association with Avirulence Genes of <i>Puccinia striiformis</i> f. sp. <i>tritici</i> , the Wheat Stripe Rust Pathogen

<i>Puccinia striiformis</i> f. sp. <i>tritici</i>, causing stripe rust, is one of the most prominent pathogens of wheat worldwide. The biotrophic and obligate fungus is capable of rapidly developing new virulent races that can overcome race-specific resistance in host plants. The traditional virulence characterization of the pathogen requires strict conditions for testing isolates on wheat differentials with specific resistance genes, which is time-consuming. Developing molecular markers for avirulence genes could provide an efficient method for monitoring virulence changes in the pathogen population. In this study, secreted protein gene-based single-nucleotide polymorphism markers previously identified to be associated with avirulence genes of the pathogen were converted to kompetitive allele-specific PCR (KASP) markers. The KASP markers were screened with a diverse panel of 192 isolates selected from various countries based on their virulent races and molecular genotypes. The markers significantly correlated with the avirulence/virulence phenotypic data of the 192 isolates were further validated with 845 isolates collected from the United States in 2019 to 2021. Based on the results of both the screening and validation data, 21 KASP markers significantly associated with different avirulence genes were developed. Seventeen of the 21 markers were significantly associated with two or more avirulence genes, and except <i>AvrYr10</i>, and the remaining 15 avirulence genes had two or more markers. Different combinations of up to three markers could be used for specific detection of 16 avirulence genes in monitoring the pathogen population.