Cacao flowers on tree. Credit: Mark Guiltinan, Penn State
The production of high quality
chocolate, and the farmers who grow it, will benefit from the recent sequencing
and assembly of the chocolate tree genome, according to an international team
led by Claire Lanaud of CIRAD, France, with Mark Guiltinan of Penn State,
and including scientists from 18 other institutions.
The team sequenced the DNA of a
variety of Theobroma cacao, considered to produce the world’s finest chocolate.
The Maya domesticated this variety of Theobroma cacao, Criollo, about 3,000
years ago in Central America, and it is one of
the oldest domesticated tree crops. Today, many growers prefer to grow hybrid
cacao trees that produce chocolate of lower quality but are more resistant to
“Fine cocoa production is
estimated to be less than 5% of the world cocoa production because of low
productivity and disease susceptibility,” said Guiltinan, professor of
plant molecular biology.
The researchers report in 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
Currently, most cacao farmers
earn about $2 per day, but producers of fine cacao earn more. Increasing the
productivity and ease of growing cacao can help to develop a sustainable cacao
economy. The trees are now also seen as an environmentally beneficial crop
because they grow best under forest shade, allowing for land rehabilitation and
The team’s work identified a
variety of gene families that may have future impact on improving cacao trees
and fruit either by enhancing their attributes or providing protection from
fungal diseases and insects that effect 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, associate professor of horticulture, 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
Because the Criollo trees are
self-pollinating, they are generally highly homozygous, possessing two
identical forms of each gene, making this particular variety a good choice for
accurate genome assembly.
The researchers assembled 84% of
the genome identifying 28,798 genes that code for proteins. They assigned 88%
or 23,529 of these protein-coding genes to one of the 10 chromosomes in the
Criollo cacao tree. They also looked at microRNAs, short noncoding RNAs that
regulate genes, and found that microRNAs in Criollo are probably major
regulators of gene expression.
“Interestingly, only 20% 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.”
Guiltinan and his colleagues are
interested in specific gene families that could link to specific cocoa
qualities or disease resistance. They hope that mapping these gene families
will lead to a source of genes directly involved in variations in the plant
that are useful for acceleration of plant breeding programs.
The researchers identified two
types of disease resistance genes in the Criollo genome. They compared these to
previously identified regions on the chromosomes that correlate with disease
resistance—QTLs—and found that there was a correlation between many the
resistance genes’ QTL locations. The team suggests that a functional genomics
approach, one that looks at what the genes do, is needed to confirm potential
disease resistant genes in the Criollo genome.
Hidden in the genome the
researchers also found genes that code for the production of cocoa butter, a
substance highly prized in chocolate making, confectionary, pharmaceuticals and
cosmetics. Most cocoa beans are already about 50% fat, but these 84 genes
control not only the amounts but also quality of the cocoa butter.
Other genes were found that
influence the production of flavonoids, natural antioxidants and terpenoids,
hormones, pigments and aromas. Altering the genes for these chemicals might
produce chocolate with better flavors, aromas and even healthier chocolate.