New genome sequence could make finest chocolate better

Chocolate: the finer the better. Fortunately, the recent sequencing and assembly of the chocolate tree genome is likely to benefit chocolate lovers and producers all over the world.

An international team led by Claire Lanaud of CIRAD, France, with Mark Guiltinan of Penn State, and including scientists from 18 other institutions has recently conducted research that led to the sequencing of the chocolate genome.


According to a Penn State press release, the team sequenced the DNA of a variety of Theobroma cacao, which experts say produces the world’s finest chocolate. The Maya cultivated this variety of Theobroma cacao, Criollo, about 3,000 years ago in Central America, as it is one of the oldest domesticated trees.


Today, many farmers choose to grow hybrid cacao trees that yield chocolate of lower quality but are more resistant to disease.

“Fine cocoa production is estimated to be less than 5 percent of the world cocoa production because of low productivity and disease susceptibility,” said Guiltinan, professor of plant molecular biology.

The researchers have reported in the current issue of Nature Genetics “consumers have shown an increased interest for high-quality chocolate made with cocoa of good quality and for dark chocolate, containing a higher percentage of cocoa, while also taking into account environmental and ethical criteria for cocoa production.”


Currently, most farmers earn around $2 per day, but the producers of the fine cacao earn more. Improving the productivity involved in growing cacao can help to bring about a sustainable cacao economy. The trees are viewed as an environmentally useful crop because they grow best in shaded areas allowing land rehabilitation and enhanced biodiversity.


The team’s work has identified a collection of gene families that may have impact in the future on improving cacao trees and fruit either by enhancing their attributes or giving protection from fungal diseases and insects that damage cacao trees.


“Our analysis of the Criollo genome has uncovered the genetic basis of pathways leading to the most important quality traits of chocolate — oil, flavonoid and terpene biosynthesis,” said Siela Maximova, who is an associate professor of horticulture at Penn State, and a member of the research team. “It has also led to the discovery of hundreds of genes potentially involved in pathogen resistance, all of which can be used to accelerate the development of elite varieties of cacao in the future.”


Because the Criollo trees have been found to be self-pollinating, they are usually highly homozygous, meaning that they possess two identical forms of each gene, making this variety a good choice for conducting accurate genome assembly.


The researchers put together 84 percent of the genome that identifies 28,798 genes that code proteins. They assigned 88 percent or 23,529 of these protein genes to one of the 10 chromosomes in the Criollo cacao tree. They also took a look at microRNAs, short noncoding RNAs that regulate genes, and discovered that microRNAs in Criollo are most likely major regulators of gene expression.


“Interestingly, only 20 percent of the genome was made up of transposable elements, one of the natural pathways through which genetic sequences change,” said Guiltinan “They do this by moving around the chromosomes, changing the order of the genetic material. Smaller amounts of transposons than found in other plant species could lead to slower evolution of the chocolate plant, which was shown to have a relatively simple evolutionary history in terms of genome structure.”


Hidden deep within the genome researchers also found the genes that account for the production of cocoa butter, which is a substance that is highly prized in chocolate making, pharmaceuticals and cosmetics. The majority of cocoa beans are already around 50 percent fat, but these 84 genes determine not only the amounts but also the quality of the cocoa butter.


Some of the other genes that were found control the production of flavonoids, natural antioxidants and terpenoids, hormones, pigments and aromas. Changing around the genes for these chemicals might be able to produce chocolate with better flavors, smells and even (gasp) healthier chocolate.