Cocoa Tree Genome Sequenced - Science News - redOrbit

"While sweets maker Mars Inc. isn’t necessarily known for producing the world’s finest chocolate, scientists at the company may have opened the door to better tasting cocoa and a more productive plant. According to a report in the open access journal Genome Biology, researchers from the candy bar maker in collaboration with several other research institutions have just sequenced the genome of the most commonly cultivated cacao plant in the world. Previous research had shown that one species of the cocoa tree has more than 28,000 protein-coding genes. By comparison, humans have around 23,000. The new study describes the sequence of a more common variety known as CCN 51, and will likely lead to real changes in the industry. Grown in Latin America, CCN 51 accounts for massive parts of the Brazilian, Peruvian and Colombian economies. Cocoa beans are harvested from red, purple, orange, yellow, and green colored pods. The Costa Rican Matina variety produces one of the world’s finest chocolates from its mature green pods. While CCN 51 is known for its high yields and is robust disease resistance, its red pods create chocolate with a more acidic, less desirable flavor than other varieties. The discrepancy is a problem for farmers who grow the variety, especially for the small farms that provide over 90 percent of the world’s supply. Some have tried to cross-breed CCN 51 with Matina trees, however, the quality of those hybrids remains inferior to the pure Matina, and crossbreeding often produces 'duds' that don’t yield any cocoa pods at all. 'Because of its high yield and disease resistance, the most ubiquitous clone in large cacao plantations in Latin America is CCN 51,' the researchers wrote in the study. 'Unfortunately, it has a rather undesirable flavor profile because of its high acidity and astringency, and also because it lacks desirable floral aromas.' In the study, the researchers sequenced the genome of the Matina variety and then performed a genetic analysis to identify a gene on the fourth chromosome that is involved in pod color variation. They also found that a single DNA letter change in the gene can affect levels of the gene’s expression, resulting in the pod’s color change. The scientists said they will continue to work on identifying genes responsible for color and taste, and noted that sequencing a tree’s DNA before deciding which ones to breed could lead to a more efficient process for farmers. 'Identification of genes that regulate pod color therefore constitutes a crucial first step toward the development of a platform for marker-assisted selection (MAS) aimed at the development of high-yielding alternatives to CCN 51,' they wrote. 'The ability to screen young cacao seedlings with molecular markers and to select only those carrying alleles that result in green pods would greatly reduce the population sizes required for the laborious and expensive phenotypic evaluations of unlinked flavor and yield traits.' The study could have a massive impact on the $100 billion that is spent on chocolate each year, according to World Cocoa Foundation statistics."