POPULATION GENETICS AND GENOMICS TO UNDERSTAND THE INVASIVE HISTORY OF THE CACAO PATHOGEN MONILIOPHTHORA RORERI

Cacao (Theobroma cacao L.) is an ancestrally cultivated crop that has been the source of one of the most beloved commodities, chocolate. Its worldwide demand has shaped the history of its cultivation. In Chapter 1, the center of origin of cacao, its center of domestication, the most outstanding movements of germplasm from the Pre-Columbian to the Republican era, the appearance and discovery of major diseases, among other important economic, agricultural and social aspects regarding cacao cultivation are reviewed. The following chapters focus on one of the major pathogens of cacao in the Americas, Moniliophthora roreri causing frosty pod rot disease. Chapter 2 presents evidence that the center of origin of M. roreri is not limited to the Magdalena Valley in Colombia, as other studies have suggested, but extends to Ecuador and the Peruvian Upper Amazon. Chapter 3 focuses on the A and B mating type loci diversity of M. roreri and reports a new A mating allele in Colombia and new mating types in Colombia, Ecuador and infers the presence of even more mating types in Ecuador and the Peruvian Upper Amazon. Additionally, Chapter 3 introduces rapid approaches to collect M. roreri and to diagnose mating types. Finally, Chapter 4 touches the genomic aspect of M. roreri and its close relatives within the Marasmiineae suborder. It presents the most complete genome of a Moniliophthora species generated so far and describes the evolution of predicted effectors and other proteins that might be involved in pathogenicity in this suborder. It also releases a custom program called SyLOCAL that evaluates synteny of a cluster of genes between two genomes.