Genetic Markers Identified Along the Cocoa Genome

When we – along with our partners from the US Department of Agriculture – Agriculture Research Service, Indiana University, Hudson-Alpha Institute and IBM – mapped the cocoa genome in 2010, we knew that was the first step to using cocoa science research to create higher producing cocoa plants that did not sacrifice quality or flavor.  Mars has always had an interest in the scientific study of cocoa as a crop, and the work we are pursuing in cocoa science is an important element in our Sustainable Cocoa Initiative.  The more we understand the cacao plant, the better able we are to grow more productive trees and planting material for cocoa farmers around the world.

So we are very excited to talk about the latest findings in our research into the cocoa genome, which is being published this week by Genome Biology, an open access academic journal that publishes articles on the full spectrum of genomics.  With our research partners, we were able to show in the Genome Biology paper is that the quality of our latest genome sequence assembly  is such that it can lead to the identification of genes that can facilitate the selection of higher yielding cocoa plants that still produce better tasting cocoa.  And that is good news for the entire cocoa sector, especially those of us focusing on cocoa science.

So how did we do it?  Using our latest genome sequence (version 1.1), genetic analyses and comparisons with other varieties, we highlighted a gene involved in the color variation of cocoa pods, which are either red or green.  Focusing even more intently on the gene sequence, we then identified a single DNA letter change that affected levels of the gene’s expression, and thus the color of the pod.

Now, the color of the cocoa pod – red or green – does not mean much to either cocoa farmers or consumers, though it is similar to a gene found in peaches or plums, which could mean quite a lot to growers of those crops.  However, it has immediate applications in countries such as Ecuador, where red pod varieties show high yields but poor taste, while the rich taste varieties have green pods but are low yielding. Indeed mixing between the red and green variety occurs causing the deterioration of the Ecuadorian flavor. With the new marker, breeders will be able to select for green podded trees that could also show rich taste and rich flavor while easily differentiable from the red podded varieties in order to avoid the adulteration issue. The quality of our latest assembly and the methods we published – could also lead to the discovery of genes regulating taste and productivity that will mean much to everyone within the sector in the long term.  Why is this important?  Because it would save breeders the expense and labor of growing potential duds, allowing them to focus on plants that they know are highly productive and can produce tasty cocoa, which will ultimately improve the quality of the chocolate made from them.

As an orphan crop, cocoa has not had the attention from the agricultural scientific community as other crops.  Mars Chocolate is working on perhaps the most extensive traditional breeding program in the sector in part because we strongly believe that cocoa plants that are higher yielding – and therefore more productive for the farmers who grow them – can also produce great tasting cocoa.  We are pleased to have this first evidence and we are looking forward to discovering even more interesting insights into the genome.

Read the press release on the Genome Biology paper here and if you are a researcher interested in learning more about the genome, please visit

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