USDA Lab: Cacao Leaf DNA Results

We want to shout out and Thank Matt Kempf for asking the question in a recent e-mail to the TREE center. Also a big THANK YOU goes to Dapeng Zhang from the USDA for providing us with the research results. So what were the USDA test results of our Cacao leaf? (sample sent in late 2012).
We've been curious as to what type of cacao tree we had at our San Francisco Conservatory of Flowers greenhouse. This particular cacao tree had been donated to the conservatory and planted in ground inside one of the back greenhouses over 15 years ago. It had a sign that said Criollo Theobroma cacao, but we were all doubtful and curious. Today this tree produces two to three full harvests every year and the very pods we use to keep our collection growing. It also provides visitors with plenty of sample pods to experience during their tours of the conservatory.
In general there are three major groups of cacao. First there is the well known and widely produced Forastero cacao. This cacao type is often used as a filler, in combination with different quality cacao seeds for chocolate making. Its pod is rounder in shape, can vary in color from green, yellow, orange to red and have anywhere between 12 - 75 seeds in their pods. The taste of chocolate made from Forastero dominant cacao is said to be more fruity and the seeds are usually purple in color. I say "usually purple" because just as with the human race there are many different genes some dominant and some recessive that can become apparent at any time. Our particular tree produced pods with mostly purple seeds, but on average 3 out of 10 were white as are most of  the Criollo pod seeds. The Criollo cacao pod is said to be used for making some of the tastier/earthier more expensive chocolates, rarely mixed with other chocolates and its pods are more likely to be pointier, longer and with deeper grooves resembling a flattened American Football. The Criollo pods also range in color from green to red. The Forastero cacao would likely resemble more of the Rugby style ball as well as a smoother outer surface almost devoid of grooves. Then there is the Trinitario cacao, which is a hybrid of the two major groups mentioned above. The most sought after "Criollo" meaning Native cacao pods are rare abroad, but they are usually easily found in their native countries where they grow best such as Colombia, Ecuador, Panama or the Caribbean. The Forastero can be more readily found being grown in South Africa under intense sunny heat vs the shadier environment of the typical Criollo cacao. Ultimately, the climate, soil, water, elevation, original seed genes and cooking procedures will determine the taste of your derived chocolate just as with Coffee. Coffee arabica is usually used to make some of the more expensive cups of Joe so it can be compared to the typical Criollo cacao and the Forastero cacao would be more like the Coffee robusta used for making more of the value brand coffee.

 As the data demonstrates our first cacao leaf was derived from a cultivar that is most closely related to the Lower Amazonian Forastero cacao or "LAF Hybrid". The analysis was based on 54 SNP markers. These are gene markers that differentiate the sample (cacao/human/animal, etc). 28 known international clones were used as reference points. Both results of Bayesian clustering analysis and the PCOA respectively show that our tree is a Lower Amazon Forastero, but with a small proportion of gene introgression from the Trinitario. Below are two pictures also sent from our contact at the USDA showing a typical Lower Amazon Forastero "Matina" and "Criollo" showing the significant difference in pod morphology.