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Cacao Plants Show Unexpected Genetic Diversity

NEW YORK (GenomeWeb News) – Cacao plants are far more genetically diverse than anticipated, new research suggests.
Researchers from Mars, Inc., the US Department of Agriculture’s Agricultural Research Service, and agricultural institutions in France, Brazil, and Ecuador genotyped roughly a thousand wild and cultivated cocoa plants, Theobroma l. cacao. Their results, appearing online this week in PLoS ONE, suggest that the current T. cacao classification scheme is genetically inaccurate.
To date, the plants have been classified into two main cacao sub-species. But researchers say there are actually ten genetically distinct T. cacao groups. By mapping the geographic distribution of these groups, the team also began exploring T. cacao’s origin and diversification. Overall, they say, such genetic insights may eventually help boost the productivity of cacao crops.
“Beyond the major effort to properly categorize and understand cacao’s proper genetic history, this new classification of cacao genotypes and the localization of their geographic origins will facilitate the collection of new germplasm with resistance to the devastating cacao disease,” lead author Juan Carlos Motamayor, a researcher affiliated with USDA-ARS and Mars, said in a statement.
Cacao beans are a major crop in West African countries, including Cote d’Ivoire and Ghana, and in some South American and Asian countries, and cacao crops fuel a chocolate industry worth billions of dollars.
Even so, diseases can cause devastating losses in these crops. Consequently, researchers are keen to understand the genetics of this plant in order to find clues to increasing yield and decreasing disease resistance. For instance, earlier this year, researchers from the USDA-ARS, Mars, and IBM announced that they were launching a project to sequence the cacao genome.
To date, cacao plants have been classified into two main sub-species groups called cacao, commonly known as “Criollo,” and sphaeorocarpum, known as Forastero. Other cultivars have also been described, including Trinitario, a Criollo-Forastero hybrid first grown in Trinidad.
But these groups do not accurately reflect the genetic differences and diversity in cacao plants, Motamayor and his colleagues found. They genotyped 106 microsatellites markers in 1241 plant samples, including wild T. cacao samples collected in Peru, Brazil, Colombia, Ecuador, French Guiana, and Central America over nearly 70 years as well as cultivated clones from these and other locations.
After weeding out about 300 mislabeled plant samples and inconsistent data from ten markers, the researchers used a clustering algorithm to group the individual plants based on the frequencies of specific alleles in their genome.
Instead of identifying two main genetic groups, the researchers found ten genetic clusters, which they classified as Marañon, Curaray, Criollo, Iquitos, Nanay, Contamana, Amelonado, Purús, Nacional, and Guiana.
They then began teasing apart the geographic origins and distribution of these genetically distinct groups, mapping the genetic clusters onto Central and South America and coming up with hypotheses to explain some of the genetic diversity in Amazonian T. cacao plants.
Based on their results, the authors urged those studying T. cacao genetics and/or curating cacao collections to adopt a new classification scheme that reflects the genetic clusters identified in the paper in order to manage the crop more effectively.
And, Motamayor noted, clarifying the genetic differences between T. cacao plants will ultimately help those interested in mining the cacao genome for clues to better yield and disease resistance.
“The new findings, together with our recently announced program to sequence the cacao genome ... should considerably help to speed up the genetic improvement of this species and the selection of new cultivars capable of withstanding the diseases that threaten the existence of our beloved chocolate,” he said.

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