Cracking the code – Part 1

Boccarra, M. 2015.

Edited by Dr. Marissa Moses and Dr. Lambert Motilal (Cocoa Research Centre, The UWI St. Augustine Campus) of a Paper presented at the International Fine Cocoa Innovation Centre Conference & Symposium, Trinidad and Tobago, March 23-24, 2015

At the Cocoa Research Centre laboratories in Trinidad, new genetic tools and procedures are being developed and optimised for use in cocoa breeding.

Every age seems to be characterised by some form of technology. Back in our parents’ day it was nuclear power, in our time it was the internet and mobile communication but today, in our children’s generation, genetics will play a large part in the decisions of the future.

Is manipulating genes a new technology per se?

Technically no, but the ease which we can perform analyses, the reduced time and expense, the precision which we now take for granted, and the wide array of investigations for which gene analysis can now be applied, takes us into a wholly new dimension. Indeed, the technology which had its start in the medical sciences, has now moved on to influence all spheres of biological science. In the plant sciences for instance, the use of genetics has all but led to a complete rethink of breeding programmes.

However, the tricky thing that we have discovered about the gene code is that even though we all have them, from the smallest mouse to the giant blue whale, methods for effectively analysing DNA needs to be developed on a case by case basis. As such, new genetic tools and procedures are constantly being optimised for use in different species, and cacao is no exception. In the last decade, several genetic protocols have been developed at the Cocoa Research Centre to investigate the cacao material in their International Genebank collection.

What then can these genetic protocols help us to accomplish?

To the general public, the use of genetics as a tool for identification is perhaps its most recognised function. For instance, Dr. Michel Boccara, liaison scientist from CIRAD , has been using some of these genetic protocols to identify mislabelled accessions in the massive cacao collection located in Trinidad. Likened to a CSI detective, but perhaps without the cool shades and Miami accent, Dr. Boccara together with other researchers have been doggedly unravelling and verifying the identity of trees in the collection, utilising 840 data points called SNPs. (Think of a barcode on the side of a can of vegetables, where each line is like a SNP data point, the pattern of which is used to unambiguously identify the product). Proper identification is the first and most crucial step in implementing an effective and reproducible research programmes. The efforts of Dr. Boccara has saved years of research time, and in the process, will help bring improved varieties to farmers.

Our mastery of the genetic code however allows us to accomplish so much more, and identification is only the tip of the iceberg. Consider for instance the breeder.

A plant breeder selects and then crosses plants with desirable characteristics (high yielding, short tree, disease resistance), to produce superior types. Depending on the characteristic, a breeder might need the parents of his cross to be either very similar or as different as possible. Unfortunately, unless pods are present and even when they are there, trees can be difficult to distinguish from each other. The selection of ideal parents for breeding is now made more efficient through the generation of molecular or genetic profiles. In Figure 1. for instance, a simplified representation of the genetic profile of three variants has been generated to visualise the similarity or dissimilarity of potential parent plants, (where each colour represents a different genetic group). Examination of the profiles indicates that Parent A and Parent B are more similar to each other than they are to Parent C.

Fig 1. A simplified representation of the genetic profile of three cocoa varieties A-C. (Yellow, pink and blue representing the Forastero, Criollo and Iquitos genetic groups respectively)

Fig 1. A simplified representation of the genetic profile of three cocoa varieties A-C. (Yellow, pink and blue representing the Forastero, Criollo and Iquitos genetic groups respectively)

Let us consider another tricky problem that frequently plagues breeders: unravelling the family tree of commercially important varieties. In true Sherlock Holmes fashion, Dr. Boccarra has used existing written records, genetic profiling and deductive reasoning to narrow down the likely parental suspects. To illustrate let us examine the profile of TSH 1188 (Figure 3) an important hybrid in Trinidad and Tobago. The known parent of this clone belongs to the blue and green genetic groups (Iquitos and Contamana respectively) which means through a process of elimination that the unknown parent must have genetic material from the pink, yellow and red groups (Criollo, Amelonado and Maraňon). This analysis greatly reduces the number of prospective parents to be evaluated.

Figure 2. A simplified representation of a genetic profile of TSH1188 and important Trinitario hybrid (Yellow, blue, green, red and pink representing the Amelonado, Iquitos, Contamana, Maraňon and Criollo genetic groups respectively)

Figure 2. A simplified representation of a genetic profile of TSH1188 and important Trinitario hybrid (Yellow, blue, green, red and pink representing the Amelonado, Iquitos, Contamana, Maraňon and Criollo genetic groups respectively)

If you are interested in having any of your trees genetically profiled, please contact the Centre for more information.


To read more about such studies we recommend:

  1. Fang, Wanping, Lyndel W. Meinhardt, Sue Mischke, Cláudia M. Bellato, Lambert Motilal, and Dapeng Zhang (2013). “Accurate determination of genetic identity for a single cacao bean, using molecular markers with a nanofluidic system, ensures cocoa authentication.” Journal of agricultural and food chemistry 62, no. 2: 481-487.
  2. Solorzano, Rey Gaston Loor, Olivier Fouet, Arnaud Lemainque, Sylvana Pavek, Michel Boccara, Xavier Argout, Freddy Amores, Brigitte Courtois, Ange Marie Risterucci, and Claire Lanaud (2012). “Insight into the wild origin, migration and domestication history of the fine flavour Nacional Theobroma cacao L. variety from Ecuador.” PLoS One 7, no. 11: e48438.