What DNA studies have shown about where cacao came from, how many kinds there are, and how far genetics can yet be used to breed a better tree.
14 studies2002 to 2024Each checked against its published abstract
What these studies add up to
The three-way division into Criollo, Forastero and Trinitario does not survive genetic analysis. The study that replaced it found ten clusters, and later work has added to them rather than confirmed a final number.
Cacao was used in the upper Amazon about 5,300 years ago, and its dispersal and mixing by people is older and wider than the Mesoamerican story suggests.
Genomic prediction works in trials. No study read here reports a cultivar that was actually bred that way.
The link between a tree's genetics and the flavour of chocolate has been shown within one variety. It has not been quantified between the genetic clusters.
Ancient Criollo came from a few South American trees
Where did the cacao cultivated by the Maya originate?
How
RFLP and microsatellite analysis of ancient Criollo and other cacao samples.
Finding
Ancient Criollo showed high homozygosity and significantly low genetic diversity, consistent with descent from a few individuals in South America rather than an independent Central American origin.
Does not establish: When or by whom cacao was carried north, or which wild population it came from.
Limits: The abstract does not give the number of trees studied. The marker technology predates genome sequencing.
What are the parents of the Trinitario cacao grown around the world?
How
Molecular marker analysis of Trinitario samples from 17 countries.
Finding
Trinitario results from natural hybridisation between Criollo and Amelonado Forastero, and the cultivated Trinitario traces to a small number of parental genotypes.
Does not establish: That anything sold as Trinitario today has that ancestry. The name is applied loosely.
Limits: Sample numbers are not given in the abstract. 'Trinitario' is a trade category, and the study covers the samples so labelled.
How should the world's cacao germplasm be classified, and how do its populations differ?
How
1,241 accessions from a wide geographic sample were genotyped at 106 microsatellite markers and grouped by Bayesian clustering, after mislabelled samples were discarded.
Finding
Ten genetic clusters, where tradition recognised two groups. The authors proposed a new classification of cacao germplasm on that basis.
Does not establish: That there are exactly ten groups, or that any cluster has a particular flavour, yield or disease resistance. The study measured relatedness, not traits.
Limits: The markers are neutral ones chosen to show ancestry. Wild Amazonian cacao was sampled as far as collections allowed, and a meaningful share of the accessions had to be dropped as mislabelled before analysis.
An assembly covering 76% of the estimated genome, with 82% of genes anchored on the ten chromosomes, and expansion of some gene families including flavonoid-related ones.
Does not establish: What any of those genes do in a living tree. A genome is a parts list.
Limits: A draft assembly of one highly homozygous tree, chosen partly because that made it easier to assemble.
80 microsatellite markers were used to compare a small set of non-introgressed Nacional trees with 169 wild and cultivated accessions from South and Central America, followed by a parentage analysis.
Finding
The closest relatives of Nacional were wild trees sampled along the Yacuambi, Nangaritza and Zamora rivers in Zamora Chinchipe, pointing to that area as its possible centre of origin.
Does not establish: That Nacional's flavour comes from that ancestry, or that modern Nacional plantings are genetically Nacional.
Limits: The pool of 'pure' Nacional trees available for comparison was very small.
Fine mapping in a selfed progeny and a genome-wide association study, with gene expression and tissue localisation.
Finding
Two loci, on chromosomes 1 and 4, act by different processes; only the chromosome 4 locus is involved in the main fruit drop. Diagnostic markers were designed that predict self-compatibility.
Does not establish: The molecular mechanism itself.
Limits: The candidate genes are identified by position and expression, not by a demonstration of function.
What do whole genomes say about the domestication of cacao?
How
200 cacao genomes were sequenced and analysed with population-genomic methods.
Finding
One population, Criollo, shows the signature of strong domestication, dated to roughly 3,600 years ago.
Does not establish: A precise date or place of domestication, or any genetic basis for Criollo's flavour.
Limits: The date is a model estimate that depends on an assumed mutation rate, and its uncertainty is wide. The authors themselves call for it to be validated.
Which works better for predicting disease resistance in cacao: individual markers or genomic selection?
How
Three related populations in Ecuador genotyped on a 15,000-marker array, for witches' broom, frosty pod and productivity traits.
Finding
Markers associated with resistance in one population were not significantly associated with the same trait in the others. Genomic selection, trained on one population and tested on the rest, varied by trait.
Does not establish: That marker-assisted selection is useless, only that these markers did not generalise.
What is the genetic and biochemical basis of the floral aroma of Ecuador's Nacional cocoa?
How
A genome-wide association study on 152 trees of modern Nacional, combining genotyping with biochemical assays of roasted and unroasted beans and sensory evaluation.
Finding
Regions of the genome were associated with floral notes and with the compounds behind them, and two biosynthesis pathways appear mainly related to the floral note.
Does not establish: That genetics outweighs fermentation in determining flavour, or that the result holds outside Nacional.
Limits: One variety, in one country. Associations are statistical, and beans were fermented in small batches for the study.
How does cocoa swollen shoot virus disease affect yield across a wide range of clones?
How
210 clones planted in 2010 in a randomised block design in Ghana and observed under natural infection.
Finding
180 of the clones had fewer than half their trees showing symptoms, and trees without symptoms out-yielded symptomatic trees of the same clone by 21% on average.
Does not establish: Resistance. The authors describe tolerance, and attempts to breed resistance since 1936 are described as having had little success.
Limits: Natural infection at one station, so disease pressure was not controlled. Absence of symptoms is not absence of virus.
Ancient DNA recovered from residues on archaeological ceramics from several countries, compared with modern reference trees.
Finding
Widespread use of cacao outside its native Amazonian range extending back 5,000 years, and strong genetic mixing between geographically distant cacao populations as early as the middle Holocene.
Does not establish: Cultivation as opposed to use or trade, at any particular site.
Limits: Ancient DNA from pottery residue survives in very short fragments, so each ancestry assignment rests on few genetic markers. No physical cacao remains were found.
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