Global Analysis of <i>Hemileia vastatrix</i> Populations Shows Clonal Reproduction for the Coffee Leaf Rust Pathogen Throughout Most of Its Range

Abstract

<i>Hemileia vastatrix</i> is the most important fungal pathogen of coffee and the causal agent of recurrent disease epidemics that have invaded nearly every coffee growing region in the world. The development of coffee varieties resistant to <i>H. vastatrix</i> requires fundamental understanding of the biology of the fungus. However, the complete life cycle of <i>H. vastatrix</i> remains unknown, and conflicting studies and interpretations exist as to whether the fungus is undergoing sexual reproduction. Here we used population genetics of <i>H. vastatrix</i> to infer the reproductive mode of the fungus across most of its geographic range, including Central Africa, Southeast Asia, the Caribbean, and South and Central America. The population structure of <i>H. vastatrix</i> was determined via eight simple sequence repeat markers developed for this study. The analyses of the standardized index of association, Hardy-Weinberg equilibrium, and clonal richness all strongly support asexual reproduction of <i>H. vastatrix</i> in all sampled areas. Similarly, a minimum spanning network tree reinforces the interpretation of clonal reproduction in the sampled <i>H. vastatrix</i> populations. These findings may have profound implications for resistance breeding and management programs against <i>H. vastatrix</i>.