New SNP markers for the genetic characterization of the quarantine pathogen Puccinia horiana and their application in pathogen migration analysis

The quarantine pathogen Puccinia horiana, causal agent of chrysanthemum white rust, is one of the most important diseases in chrysanthemum-producing regions worldwide. During this study we determined the genetic variability of forty five isolates originating from North and South America, Asia, and Europe based on neutral SNP-markers. Together with information on collection year and geographical origin this allowed us to address questions of migration, survival, and recombination. A high level of genotypic diversity was observed and in most cases phylogenetic clustering was related to the geographic origin. Local survival was demonstrated based on multi-year findings of specific clones in a given geographic area. Recent long distance migration events were demonstrated but were limited in number. Exclusive clonal propagation of this microcyclic rust was disproved given clear indications of recombination between specific genotypes. The genotype data were also combined with the pathotype data of specific isolates but pathotype-specific markers were only observed in one of the clades. In combination with a fast SNP detection system, this technique could allow rapid characterization of intercepted or local isolates, which may help in questions relating to the need for quarantine action.