Genetic Diversity and Natural Population Structure of Cacao (Theobroma cacao L.) from the Brazilian Amazon Evaluated by Microsatellite Markers

Abstract

A sample of 94 accessions of Theobroma cacao L. (cacao), representing four populations from the Brazilian Amazon (Acre, Rondoˆnia, lower Amazon and upper Amazon) were analyzed using microsatellite markers to assess the genetic diversity and the natural population structure. From the 19 microsatellite loci tested, 11 amplified scorable products, revealing a total of 49 alleles, including two monomorphic loci. The Brazilian upper Amazon population contained the largest genetic diversity, with the most polymorphic loci, the highest observed heterozygosity; and the majority of rare alleles, thereby this region might be considered part of the center of diversity of the species. The observed heterozygosity for all the Brazilian populations (H o =0.347) was comparable with values reported for other similar upper Amazon Forastero cacao populations, with the Acre and Rondoˆnia displaying the lowest values. The lower Amazon population, traditionally defined as highly homozygous, presented an unexpectedly high observed heterozygosity (H o =0.372), disclosing rare and distinct alleles, with large identity with the upper Amazon population. It was hypothesized that part of the lower Amazon population might derive from successive natural or intentional introduction of planting material from other provenances, mainly upper Amazon. Most of the loci exhibited a lower observed heterozygosity than expected, suggesting that self-pollination might be more common than usually assumed in cacao, but excess of homozygotes might also derive from sub-grouping (Wahlund effect) or from sampling related individuals. Most of the gene diversity was found to occur within groups, with small differentiation between the four Brazilian Amazon populations, typical of species with high gene flow.

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.…”

“…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. The expected heterozygosity observed in the adults (H e ¼ 0.477) was less than that previously detected in other lower Amazon populations (for example, H e ¼ 0.553; Sereno et al, 2006), whereas both populations demonstrated lower values than that detected in populations in the upper Amazon region, such as the Huallaga (H e ¼ 0.610) and Ucayali (H e ¼ 0.740) valleys in the Peru or the coastal valley of Ecuador (H e ¼ 0.561, Zhang et al, 2008). In comparison, other studies investigated more diverse cacao germplasm from the upper Amazon region n is the sample size of each family and of the fruits within families; t m is the multilocus outcrossing rate; t m Àt s is the outcrossing rate among relatives; r p(m) is the multilocus outcrossing rate; N ep is the effective number of pollen donors; Y is the coancestry coefficient within a family; N e is the effective population size within a family.…”

“…Young healthy leaves were collected from the trees at the site, stored in paper bags, transferred to the laboratory within two days and stored at À80 1C until extraction. DNA was extracted using a protocol adapted from Doyle and Doyle (1990), as described by Sereno et al (2006). The DNA was quantified using a spectrophotometer (Biomate 3; Thermo Electron Co., Madison, WI, USA), and the DNA quality was evaluated by gel electrophoresis.…”

“…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.…”

“…The high rate of deforestation in Amazonia threatens the conservation of the untapped genetic diversity of natural cacao. In Brazil, a systematic collection project designed to obtain a representation of the genetic diversity of natural or cultivated cacao in the whole Brazilian Amazon region was conducted by the Brazilian government from 1976 to 1991 (Almeida et al, 1995), but only a small fraction of the Brazilian Amazon river basins have been sampled and maintained in ex situ collections (Sereno et al, 2006). Therefore, we examined the genetic diversity, inbreeding, SGS and mating system at hierarchical levels of individuals and fruits within individuals and pollen dispersal patterns and distance in a continuous T. cacao population in the Brazilian Amazon.…”