Genetic relationships in an international collection of Puccinia horiana isolates based on newly identified molecular markers and demonstration of recombination

The obligate biotrophic pathogen Puccinia horiana is the causal agent
of chrysanthemum white rust. Although P. horiana is a quarantine
organism, it has been able to spread to most chrysanthemum-producing
regions in the world since the 1960s; however, the transfer routes are
largely obscure. An extremely low level of allelic diversity was observed
in a geographically diverse set of eight isolates using complexity reduction
of polymorphic sequences (CRoPS) technology. Only 184 of the
16,196 contigs (1.1%) showed one or more single-nucleotide polymorphisms
(SNPs). Thirty-two SNPs and one simple-sequence repeat
were translated into molecular markers and used to genotype 45 isolates
originating from North and South America, Asia, and Europe. In most
cases, phylogenetic clustering was related to geographic origin, indicating
local establishment. The European isolates mostly grouped in two major
populations that may relate to the two historic introductions previously
reported. However, evidence of recent geographic transfer was also
observed, including transfer events between Europe and South America
and between Southeast Asia and Europe. In contrast with the presumed
clonal propagation of this microcyclic rust, strong indications of marker
recombination were observed, presumably as a result of anastomosis,
karyogamy, and somatic meiosis. Recombination and transfer also explain
the geographic dispersal of specific markers. A near-to-significant
correlation between the genotypic data and previously obtained pathotype
data was observed and one marker was associated with the most virulent
pathotype group. In combination with a fast SNP detection method, the
markers presented here will be helpful tools to further elucidate the
transfer pathways and local survival of this pathogen.