Cacao is a commodity crop from the tropics cultivated by about 6 million smallholder farmers. The tree, Theobroma cacao, originated in the Upper Amazon where it was domesticated ca. 5450 to 5300 B.P. From this center of origin, cacao was dispersed and cultivated in Mesoamerica as early as 3800 to 3000 B.P. After the European conquest of the Americas (the 1500s), cacao cultivation intensified in several loci, primarily Mesoamerica, Trinidad, Venezuela, and Ecuador. It was during the colonial period that cacao diseases began emerging as threats to production. One early example is the collapse of the cacao industry in Trinidad in the 1720s, attributed to an unknown disease referred to as the “blast”. Trinidad would resurface as a production center due to the discovery of the Trinitario genetic group, which is still widely used in breeding programs around the world. However, a resurgence of diseases like frosty pod rot during the republican period (the late 1800s and early 1900s) had profound impacts on other centers of Latin American production, especially in Venezuela and Ecuador, shifting the focus of cacao production southward, to Bahia, Brazil. Production in Bahia was, in turn, dramatically curtailed by the introduction of witches’ broom disease in the late 1980s. Today, most of the world’s cacao production occurs in West Africa and parts of Asia, where the primary Latin American diseases have not yet spread. In this review, we discuss the history of cacao cultivation in the Americas and how that history has been shaped by the emergence of diseases.

Frosty pod rot disease of cacao (FPR), caused by the fungus Moniliophthora roreri , has severely impacted the production of cocoa in Latin America since its discovery. Prior to the 1950s, FPR was known only from Colombia and Ecuador. However, beginning in the 1970s, its geographical range has dramatically expanded throughout most of the cacao‐producing regions of the Americas. The origin of the pathogen remains unknown. In this study, we evaluated the genetic diversity of M . roreri from areas spanning, as much as possible, its current geographical range using simple‐sequence repeat markers and a publicly available single‐nucleotide polymorphism data set. Two hotspots of genetic diversity were found: coastal Ecuador and the inter‐Andean Magdalena Valley of Colombia, neither of which correspond to the Amazonian origin of the host. However, both areas were early centres of intense cultivation of cacao. Our results indicate that M . roreri was introduced into both areas from its centre of origin, where intensive cacao cultivation probably led to the increase of inoculum and further dissemination of the disease. Current invasions can be traced to two genotypes responsible for all known instances of the pathogen in Central America, the Caribbean, Peru and Bolivia. We also report for the first time M . roreri in Maynas (Peruvian Amazon), which is probably the result of a recent introduction from Colombia.

Hemileia vastatrix 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 H. vastatrix requires fundamental understanding of the biology of the fungus. However, the complete life cycle of H. vastatrix remains unknown, and conflicting studies and interpretations exist as to whether the fungus is undergoing sexual reproduction. Here we used population genetics of H. vastatrix 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 H. vastatrix 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 H. vastatrix in all sampled areas. Similarly, a minimum spanning network tree reinforces the interpretation of clonal reproduction in the sampled H. vastatrix populations. These findings may have profound implications for resistance breeding and management programs against H. vastatrix.