Indications of genetic recombination, international migration and local survival of Puccinia horiana based on new SNP markers

Puccinia horiana, causal agent of chrysanthemum white rust, is of major economic concern for chrysanthemum production worldwide due to its highly pathogenic nature and its quarantine status. In the 1960s P. horiana spread to most of the chrysanthemum producing areas in the world, but migration pathways have not been elucidated. In some countries, findings of P. horiana are rare and are considered to be only exotic introductions. Control of this pathogen via breeding is complicated by the presence of pathotypes, which are geographically clustered in some cases. The objective of this research was to determine the genetic variability of a worldwide collection of isolates based on neutral markers and use the data to address questions about migration, survival, clonality and virulence. Using a limited number of isolates and the CRoPS technology, based on sequencing of AFLP fragments, we developed 32 single nucleotide polymorphism (SNP) markers. These were used to genotype a total of 45 isolates originating from North and South America, Asia and Europe. Migration and local survival events were determined by combining the data on the phylogenetic placement of the isolates with the data on geographical origin and collection year. The level of genotypic diversity was large and in most cases, the phylogenetic clustering was related to the geographic origin. The European isolates and a Colombian isolate represented two major clades. This indicates that at least two historic introductions took place in Europe and that P. horiana migrated between Europe and Colombia. A third major clade consisted of isolates from Malaysia and isolates found in Europe by a national plant protection organization, which again illustrates intercontinental migration events. Some of the USA isolates were clonal. These isolates originated in different states and different years, which suggests local survival and therefore indicates that not all of the USA findings were of exotic origin. Presumed clonal propagation of this microcyclic rust was verified by analyzing the marker data for recombination events. At least four isolates showed clear indications of recombination, likely as a result of anastomosis. Finally, the genotype information was combined with the pathotype data of 24 isolates to determine if certain markers are linked to specific pathotypes or avirulence genes. In general, there was no link, except for the virulent isolates from the “Malaysian” clade. In conclusion, the genotyping technique allowed us to address specific questions of the epidemiology and biology of this pathogen. In combination with a fast SNP detection system, this technique would allow rapid characterization of intercepted or local isolates and would help address the need for quarantine measures.