Differences in population structure and zygosity between heteroecious and autoecious forms of Cronartium pini suggest selfing in the autoecious form

Cronartium pini causes Scots pine blister rust. This rust fungus has two different forms without differentiation in morphology and internal transcribed spacer: the heteroecious form has a macrocyclic life cycle and infects pine and an alternate host; the autoecious form only infects pine. Epidemics caused by these two forms impose severe risk on the pine forest in Sweden, therefore knowledge of their distribution and diversity is needed for strategic disease management. We designed microsatellite markers with improved resolution based on the C. pini genome, developed a multiplex amplification system, and analyzed the C. pini population diversity and structure in Sweden using 396 isolates. The heteroecious and autoecious populations showed clear differences in diversity, linkage disequilibrium, and structure. The heteroecious isolates had unique multilocus genotypes. Autoecious isolates shared the same genotypes more frequently, especially three autoecious multilocus genotypes that were commonly found over a in northern Sweden. The genetic distances among autoecious isolates are closer than those among the heteroecious isolates. The results confirmed that heteroecious C. pini populations were sexual and autoecious C. pini populations were clonal. We further discussed the hypothesis that autoecious C. pini originated from self-fertilization, and frequent self-fertilization and infrequent mutation generate homozygous but diverse genotypes.