An international consortium of genetic researchers has sequenced the genome of the Costa Rican Matina cacao variety, the most widely cultivated cacao type in the world.

Cacao trees are grown throughout the humid tropics in more than 50 countries, and cacao beans, harvested from the plants’ pods, are used to produce chocolate as well as in the confectionary and cosmetic industries. Cacao production is essential to the livelihoods of around 45 million people worldwide.

There are many varieties of the cacao tree, but the green podded Costa Rican Matina variety (Theobroma cacao L. cultivar Matina) is the most popular because of its high yield and pleasant flavor.

The scientists have described the sequencing and assembly of the genome of the Matina cacao in a paper published in the journal Genome Biology.

They used genetic analyses and comparisons with other cacao varieties, to highlight a gene involved in pod color variation. Zooming further in on the gene sequence, they identified a single DNA letter change that affected levels of the gene’s expression, and so the color of the pod.

Cacao plant breeders trying to produce a delicious high-yield strain through cross breeding have met with limited success. So the genetic marker could, in theory, be used to screen young seedlings, and highlight desirable plants long before they reach maturity. This would avoid the expense and labor of growing up potential duds, ultimately improving the quality of cacao plants and the chocolate made from them.

Although the genome sequence of the Criollo cacao variety was reported in 2010, it’s genetically quite distinct and so a poor representative of the cacao types cultivated worldwide.

Since the publication of the Criollo genome sequence, researchers have been working to identify genetic markers that can produce more productive cocoa plants for farmers while still providing consumers with high quality and superior taste.

The genome sequence research is a part of an overall effort to use traditional breeding techniques to develop planting materials that farmers can use to be more productive.

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Bibliographic information: Juan C Motamayor et al. 2013. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biology, 14:R53; doi: 10.1186/gb-2013-14-6-r53