Geographic and Genetic Population Differentiation of the Amazonian Chocolate Tree (Theobroma cacao L)

Abstract

Numerous collecting expeditions of Theobroma cacao L. germplasm have been undertaken in Latin-America. However, most of this germplasm has not contributed to cacao improvement because its relationship to cultivated selections was poorly understood. Germplasm labeling errors have impeded breeding and confounded the interpretation of diversity analyses. To improve the understanding of the origin, classification, and population differentiation within the species, 1241 accessions covering a large geographic sampling were genotyped with 106 microsatellite markers. After discarding mislabeled samples, 10 genetic clusters, as opposed to the two genetic groups traditionally recognized within T. cacao, were found by applying Bayesian statistics. This leads us to propose a new classification of the cacao germplasm that will enhance its management. The results also provide new insights into the diversification of Amazon species in general, with the pattern of differentiation of the populations studied supporting the palaeoarches hypothesis of species diversification. The origin of the traditional cacao cultivars is also enlightened in this study.

Understanding the genetic diversity, spatial genetic structure and mating system at the hierarchical levels of fruits and individuals of a continuous Theobroma cacao population from the Brazilian Amazon

“…Genetic diversity Cacao populations in the upper Amazon region have been suggested to possess a greater genetic diversity in comparison to those in the lower Amazon (Sereno et al, 2006;Motamayor et al, 2008). The genetic diversity observed for the present plot comprising a continuous stand of cacao trees under natural conditions in the lower Amazon region supports this hypothesis.…”

“…One possible explanation for the lower expected heterozygosity observed herein could be related to the origin of the population, which was typically the lower Amazon Amelonado (Motamayor et al, 2008). However, the results obtained with less precise method of allele detection using silver-stained polyacrylamide gels cannot be discounted, as the other studies have utilised fluorescence capillary electrophoresis (Zhang et al, 2008;Efombagn et al, 2009b).…”

“…The putative centre of T. cacao diversity was originally hypothesised to be located in the region between Ecuador, Colombia and Peru (Cheesman, 1944) and was later confirmed by a microsatellite marker analysis (Motamayor et al, 2002(Motamayor et al, , 2008. Despite the importance of this plant, little is known about the natural genetic structure of the T. cacao population because most studies have utilised accessions that were originally collected in the wild, but maintained in ex situ germplasm repositories.…”

“…Despite the importance of this plant, little is known about the natural genetic structure of the T. cacao population because most studies have utilised accessions that were originally collected in the wild, but maintained in ex situ germplasm repositories. The accessions have been analysed as a group according to the approximate collection location, the river basin (Sereno et al, 2006;Motamayor et al, 2008;Zhang et al, 2008). Moreover, to our knowledge, no report has estimated the clonality, intrapopulation spatial genetic structure (SGS), effective population size, mating system at the hierarchical level of fruits and individuals, and pollen flow in natural cacao populations, which are fundamental parameters that are required to establish long-term ex situ or in situ conservation strategies.…”

Origin and Domestication of Native Amazonian Crops

“…One of the major implications of this study is that Cuatrecasas' [43] classification of two subspecies is incorrect [44], which also raises questions about the usefulness of the Criollo-Forastero dichotomy, even though numerous molecular genetic analyses have identified clear differences between these types (references in [44,46]). These conclusions led to a search for a new intraspecific classification that would be useful for plant breeders [46].…”