New microsatellite markers for the population studies of Racodium therryanum, a causal agent of snow blight in Japan

Snow mold fungi cause serious damage to the seedlings of some coniferous species in the boreal region where deep snow covers the seedlings in winter. Racodium therryanum is one of the fungi causing such damage in Japan. Neither sexual nor asexual spores of R. therryanum have been found in the field, and thus, the taxonomy and life cycle of this fungus is unclear. In this study, we developed seven microsatellite markers for population studies such as population structure, recombination and genetic diversity of R. therryanum through de novo genome assembly. Seven microsatellite markers were developed and applied for 133 R. therryanum isolates from Picea glehnii, P. jezoensis and Abies sachalinensis in a nursery and two planted sites in forests (forest sites) situating 10–20 km apart. Little genetic differentiation between the two forest sites suggests that gene flow had occurred between the forest sites. The nursery population was characterized by low genetic diversity compared to the two forest sites. Discriminant analysis of principal components (DAPC) indicated three genetically differentiated clusters of R. therryanum which occurred sympatrically in each site. No dominant clusters were observed in the three host species, and no genetic differentiation was observed among the host species. The observed not significant linkage disequilibrium suggested the genetic recombination of R. therryanum. Microsatellite markers developed in this study can be useful for the further population studies of R. therryanum.