IGS1 Haplotype Genotyping Enables Efficient Dissection of Population Diversity of the Wheat Stripe Rust Fungus ( Puccinia striiformis f. sp. tritici )

Wheat stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is a destructive disease affecting wheat production because of its capacity for long-distance dispersal. This pathogen exhibits high genetic diversity, yet the low resolving power of currently used molecular markers has restricted in-depth understanding of its migration routes. We previously detected variations among isolates in the ribosomal intergenic spacer 1 (IGS1) region of Pst. In the current study, Pst IGS1 fragments were amplified directly from DNA extracted from wheat rust lesions each bearing a single uredinium, and the intraspecific variation pattern of IGS1 was comprehensively analyzed. Thirty polymorphic loci characterized by variations in repeat units and subunits were detected, with up to 12 polymorphic loci identified within single isolates. Among the 3,050 field samples examined, 506 distinct haplotypes were identified based on combinations of these polymorphic loci, demonstrating that the IGS1 haplotypes can be effective markers for revealing genetic diversity of Pst. Furthermore, IGS1 haplotypes allowed dissection of genetic structure and gene flow among different Pst populations. The IGS1 haplotype genotyping system features several advantages: it requires no fungal isolation or culturing, relies on only one pair of specific primers, and supports high-throughput sample processing. It therefore represents a powerful tool for elucidating the gene flow and genotype flow among populations, as well as for tracking long-distance dispersal of Pst both on regional and continental scales.