Hemileia vastatrix is the most important fungal pathogen affecting Coffea arabica and has invaded nearly every coffee-growing region in the world and the causal agent of recurrent disease epidemics. The development of resistant varieties of coffee against H. vastatrix requires fundamental understanding of the biology of the fungus. However, the complete life cycle of H. vastatrix remains unknown and conflicting studies exist as to whether the fungus is capable of sexual reproduction or not. Here we used population genetics of H. vastatrix to determine the reproductive mode of the fungus across most of its current geographic range. The genetic relationships among H. vastatrix isolates were determined using eight simple sequence repeat markers (SSRs) developed for this study. The analyses of the standardized index of association (rbarD = 0.114 - 0.557, p = 0.001), Hardy Weinberg equilibrium (p ≤ 0.05), and clonal richness (0 - 0.19) all strongly support asexual reproduction of H. vastatrix in all sampled areas. Similarly, the Minimum Spanning Network reinforces the interpretation of clonal reproduction in the global H. vastatrix population. These findings may have profound implications for resistance breeding and other programs against H. vastatrix.

Screening of potential microsatellite loci was performed using a modified M13-tailed primer method (Schuelke, 2000), as previously described (Díaz-Valderrama & Aime, 2016; Koch & Aime, 2018). We accomplished an initial screening of ~100 microsatellite markers (Table S2) located on separate scaffolds on a set of six H. vastatrix specimens collected from three geographical regions (Puerto Rico, Jamaica, and Cameroon). 

This is the file from SSR screening analysis.