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International Team Sequences Criollo Cacao Genome

Chocolate cake (Mikage Takasugi/ from 18 institutions in five countries reported sequencing the genome of Theobroma cacao, commonly called the Criollo cacao tree. The findings are published in the current online issue of Nature Genetics.

The tree is known for its high quality, but also for low productivity and weak resistance to disease. Most commercial chocolate today comes from lower-quality hybrid cacao trees with greater disease resistance. The researchers hope that identification of the tree’s genetic families will lead to an improved strain that can overcome these properties.

The team reports assembling 84 percent of the genome identifying 28,798 genes that code for proteins. They assigned 88 percent or 23,529 of these protein-coding genes to one of the 10 chromosomes in the Criollo cacao tree. They also looked at microRNAs — noncoding RNAs that regulate genes — and found that microRNAs in Criollo are probably major regulators of gene expression.

Among the scientists on the team were researchers from Pennsylvania State University in University Park, who identified two types of disease resistance genes in the Criollo genome. They compared these genetic types to previously identified regions on the chromosomes that correlate with disease resistance, called QTLs. The Penn State team found a correlation between many the resistance genes’ QTL locations. The findings suggest that further investigations take a functional genomics approach, one that looks at what the genes do, 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 key substance in chocolate making, confectionary, pharmaceuticals and cosmetics. Most cocoa beans are already about 50 percent fat, but these 84 genes control both the amounts and quality of the cocoa butter.

Photo: Mikage Takasugi/

Related: Government-Industry-Academic Team Sequences Cacao Genome

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