Abstract
Beans of the species Theobroma cacao L., also known as cacao, are the raw material to produce chocolate. Colombian cacao has been classified as a fine flavor cacao that represents the 5% of cacao world’s production. Colombian genetic resources from this species are conserved in ex situ and in-field germplasm banks, since T. cacao has recalcitrant seeds to desication and long-term storage. Currently, the collection of T. cacao of the Colombian Corporation of Agricultural Research (CORPOICA) has approximately 700 germplasm accessions. We conducted a molecular analysis of Corpoica’s cacao collection and a morphological characterization of some accessions with the goal to study its genetic diversity and population structure and, to select interesting accessions for the cacao’s breeding program. Phenotypic evaluation was performed based on 18 morphological traits and 4 biochemical traits. PCA analysis of morphological traits explained 60.6% of the total variation in seven components and 100% of the total variation of biochemical traits in four components, grouping the collection in 4 clusters for both variables. We explored 565 accessions from Corpoica’s germplasm and 252 accessions from reference populations using 96 single nucleotide polymorphism (SNP) molecular markers. Molecular patterns of cacao Corpoica’s collection were obtained amplifying specific alleles in a Fluidigm platform that used integrated circuits of fluids. Corpoica’s collection showed highest genetic diversity [Expected Heterozygosity (HE = 0.314), Observed Heterozygosity (HO = 0.353)] that is reduced when reference populations were included in the dataset (HE = 0.294, HO = 0.261). The collection was divided into four clusters based on population structure analysis. Cacao accessions from distinct groups showed some taxonomic concordance and reflected their geographic origins. For instance, accessions classified as Criollo were clearly differentiated in one group and we identified two new Colombian genetic groups. Using a number of allelic variations based on 87 SNP markers and 22 different morphological/biochemical traits, a core collection with a total of 232 accessions was selected as a primary genetic resource for cacao breeders.
Highlights
Theobroma cacao L. referred as cacao, is a native plant of tropical forests of South America (Motamayor et al, 2002) that belongs to the family Malvaceae
The Amazonian regions of Peru, Colombia, and Ecuador have been considered the geographical origin of the species, because there are the regions with the highest genetic diversity of cacao (Thomas et al, 2012)
The present study showed that 450 cacao accessions conserved in the National Germplasm Bank and 115 accessions from Corpoica’s breeding collection conformed a rich and diverse collection supported by molecular and phenotypic data
Summary
Theobroma cacao L. referred as cacao, is a native plant of tropical forests of South America (Motamayor et al, 2002) that belongs to the family Malvaceae. Cacao is grown with other fruit and commodity crops throughout the world in the humid tropics. Cocoa is the world’s third most important agricultural export commodity, after coffee and sugar. It provides economic benefits to some of the poorest areas of the world and it is the major foreign income for countries that dominate production such as Ivory Coast (Guiltinan et al, 2008). Besides the seeds producing the chocolate, cacao’s fruits are used to produce sweets, jellies, ice cream, liqueurs, cosmetic and medicinal products (Donald, 2004; Othman et al, 2007)
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