Population genomic analyses of the chocolate tree, Theobroma cacao L., provide insights into its domestication process

Domestication has had a strong impact on the development of modern societies. Wesequenced 200 genomes of the chocolate plant Theobroma cacao L. to show for the first timeto our knowledge that a single population, the Criollo population, underwent strongdomestication ~3600 years ago (95% CI: 2481–13,806 years ago). We also show that duringthe process of domestication, there was strong selection for genes involved in the metabolismof the colored protectants anthocyanins and the stimulant theobromine, as well asdisease resistance genes. Our analyses show that domesticated populations of T. cacao(Criollo) maintain a higher proportion of high-frequency deleterious mutations. We also showfor the first time the negative consequences of the increased accumulation of deleteriousmutations during domestication on the fitness of individuals (significant reduction in kilogramsof beans per hectare per year as Criollo ancestry increases, as estimated from a GLM,P = 0.000425).