Genotyping Puccinia striiformis f. sp. tritici Isolates with SSR and SP-SNP Markers Reveals Dynamics of the Wheat Stripe Rust Pathogen in the United States from 1968 to 2009 and Identifies Avirulence Associated Markers.

Abstract

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating disease of wheat in the United States. The fungal pathogen can rapidly evolve, producing new virulent races infecting previously resistant cultivars and genotypes adapting to different environments. The objective of this study was to investigate the long-term population dynamics of Pst in the US. Through genotyping 1,083 isolates of 1968 to 2009 using 14 simple sequence repeat (SSR) markers and 92 secreted protein single nucleotide polymorphism (SP-SNP) markers, 614 and 945 genotypes were detected, respectively. In general, the two types of markers produced consistent genetic relationships among the Pst populations over the 40 years. The prior 2000 and 2000-2009 populations were significantly different, and the latter showed higher genotypic diversity and higher heterozygosity than the former populations. Clustering analyses using genotypes of either SSR and SP-SNP markers revealed three molecular groups (MGs), of which MG1 and MG2 existed in both the prior 2000 and 2000-2009 populations while MG3 mainly emerged in 2000 to 2009. Some of the isolates in the period of 2000-2009 formed individual clusters, suggesting exotic incursions; whereas other isolates of the same period were clustered together with prior-2000 isolates, indicating that they were developed from the previously established populations. The data suggest the co-existence of newly introduced populations with established populations in the United States. Twenty SP-SNP markers were significantly associated to individual avirulence genes. The results are useful for developing more accurate monitoring systems and provides guidance for the disease management.