To many people, chocolate is a divine food that brings happiness to their everyday lives. However, little is known about the mechanisms that control the flavor qualities of cacao beans, from which chocolate is derived. In an article published in the Genome Biology special issue on plant genomics, David Kuhn from the Agricultural Research Service (US Department of Agriculture) and colleagues, describe a genomics-based approach to solving the genetic basis of important cacao traits, such as cacao pod color and flavor, by sequencing the genome of a popular variety of cacao plant that has been widely cultivated .
Theobroma cacao tree with seed pods. Image source: Wellcome Images
The cacao tree, Theobroma cacao, is an economically important plant species grown across the tropics, whose beans, which are derived from the pods of the tree, are used to make chocolate. Although there are several varieties of cacao available to breeders, the Matina cultivar is the most extensively cultivated variety because it has favorable traits such as high yield and disease resistance. Unfortunately, Matina beans have an unpleasant aroma and flavor, caused by high acidity and astringency, which is associated with red pod coloration. Matina cacao beans are often blended with other beans, derived from green pods, that have more desirable flavors, however, this blending of cacao often reduces the overall quality of the chocolate. A breeding program will therefore be crucial to select for cacao trees that have high yields and disease resistance, coupled with green pods and good quality flavors.
To improve the speed and accuracy of cacao breeding, the authors generated a high quality sequence and assembly of the genome of Theobroma cacao cultivar Matina. By utilizing the genome sequence, in conjunction with mapping populations, they were able to fine map a genetically small region that is associated with the red/green pod color trait. This revealed that a gene encoding a MYB transcription factor (TcMYB113) is likely to regulate pod color. They further showed that transcript levels for the MYB transcription factor are regulated by a tasi-RNA (TAS4-siR81), and that accumulation of the TcMYB113 transcript positively correlated with color intensity: higher expression being associated with red pod coloration.
It is hoped that the results of this study will allow the successful breeding of Matina cultivars with high quality beans at a much more rapid pace. Given the time it takes for a cacao seedling to mature and produce pods, knowing the sequence of the gene regulating pod color should enable genetic screening of seedlings to determine their pod-color phenotype years, if not decades, before pods could actually be phenotyped. The bar for chocolate quality is therefore set to rise higher and higher in the coming years, bringing great comfort to chocolate-lovers across the globe.