Colombia a Source of Cacao Genetic Diversity As Revealed by the Population Structure Analysis of Germplasm Bank of Theobroma cacao L.

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.

Ancestry informative alleles captured with reduced representation library sequencing in Theobroma cacao

“…The mean expected heterozygosity value was higher than the observed heterozygosity, indicating a deficit of heterozygotes. Compared with recent published genetic diversity studies in cacao [ 16 , 17 , 51 ], our results present slightly lower values of He, Ho and PIC, probably due to the high presence of homozygous genotypes of the Criollo and Amelonado populations and the impact of a well-known effect of allelic dropout in GBS datasets [ 30 , 52 ].…”

“…Estimates of genetic variability are comparable with those estimated in previous studies of cacao [ 18 ]. Enhanced SNP discovery, SNP quality, production steps, and optimization of parameters improved the SNP detection when compared to those obtained from 96 SNPs from small Fluidigm arrays or the 6K SNP array previously reported [ 15 – 17 ]; or even from the 15K SNP arrays considering the fact that a large proportion of SNPs cannot be identified with array systems. According to Romay et al 2013 [ 50 ], one important advantage of GBS over the SNP array systems, is the MAF distribution.…”

“…Recently, approaches to infer genetic diversity in T . cacao have been completed using a small panel of single nucleotide polymorphisms (SNPs, ranging from 87 to 6,000) developed with a Fluidigm array system [ 15 – 17 ]. Also, using the information generated from a subset of the 200 cultivars project, an Ilumina Infinity II genotyping array of 13,530 markers was recently developed [ 18 ].…”

Chemical and sensory profiles of Peruvian native cocoas and chocolates from the Bagua and Quillabamba regions

“…The ratio of theobromine to caffeine (T/C) is considered to be associated with the quality of cacao and with the genotype. T/C values <2 correspond to the criollo type, values between 2 and 6 correspond to the trinitario type, values of 6 to 8 are considered miscellaneous, and from values 8 upward correspond to the forastero type (Davrieux et al, 2005;Osorio-Guarín et al, 2017). Cocoa from Bagua, with a T/C ratio of 4.5, would be labeled as a trinitario type, while cocoa from Quillabamba showed a T/C ratio of 1.2, typical of a criollo type.…”

Opportunities and challenges for improving a Colombian public research program in plant breeding and plant genetic resources lead by Agrosavia

“…Second, as part of the same project, new approaches such as genomics for a robust characterization of collections are beginning to be used [38]. Currently, results for two critical crop collections, such as potato [39]and cacao [40], are available for the public. Soon, we expected to publish similar results for avocado and other native crops.…”