New simple sequence repeat markers reveal undetected diversity in Spanish and Californian Diplodia sapinea populations

Diplodia sapinea is the causal agent of Diplodia shoot blight, an emerging disease affecting pine forests worldwide. The range expansion of this pathogen in northern Europe has been suggested to be partially facilitated by recent warmer conditions. Although D. sapinea has been studied extensively, critical aspects of its infection biology and population structure remain unexplored. In this study, we developed nine simple sequence repeat (SSR) markers mined from D. sapinea genomes to assess the genetic diversity at higher resolution. Isolates from northern Spain, an area formerly regarded as having low genetic diversity and samples from a Californian population that was formerly regarded as clonal, were analysed in the study. In Spain, the nine SSR markers identified 56 genotypes in 285 samples. Isolates from symptomatic shoots, cones and asymptomatic tissues collected from different stands, suggested admixture between local populations. The same genotype tended to dominate within a single cone, and the same genotypes were usually found in both symptomatic and asymptomatic shoot tissues. The nine new SSR markers developed in this study revealed a high level of genetic diversity in both the northern Spanish and northern Californian populations than previously anticipated. Analyses using these nine SSR markers should contribute to a better understanding of the epidemiology, evolution and origin of D. sapinea, a pathogen that is gaining prominence in many parts of the world.