The seeds are the main ingredient of chocolate, while the pulp is used in some countries to prepare juice, smoothies, jelly, and cream.

These groups are: Amelonado, Criollo, Nacional, Contamana, Curaray, Cacao guiana, Iquitos, Marañon, Nanay, and Purús.

[13] This study also identified areas, for example around Iquitos in modern Peru and Ecuador, where representatives of several genetic clusters originated more than 5000 years ago, leading to development of the variety, Nacional cocoa bean.

[14] This result suggests that this is where T. cacao was originally domesticated, probably for the pulp that surrounds the beans, which is eaten as a snack and fermented into a mildly alcoholic beverage.

[15] Using the DNA sequences and comparing them with data derived from climate models and the known conditions suitable for cacao, one study refined the view of domestication, linking the area of greatest cacao genetic diversity to a bean-shaped area that encompasses Ecuador, the border between Brazil and Peru and the southern part of the Colombian–Brazilian border.

[23] Roasting T. cacao by using superheated steam was found to be better than conventional oven-roasting because it resulted in the same quality of cocoa beans in a shorter time.

The pests and diseases to which cacao is subject, along with climate change, mean that new varieties will be needed to respond to these challenges.

[25] In an effort to improve the diversity available to breeders, and ensure the future of the field genebanks, experts have drawn up A Global Strategy for the Conservation and Use of Cacao Genetic Resources, as the Foundation for a Sustainable Cocoa Economy.

However, a recent study of genetic diversity and predicted climates[16] suggests that many of those protected areas will no longer be suitable for cacao by 2050.

Other projects, such as the International Cocoa Quarantine Centre, aim to combat cacao diseases and preserve genetic diversity.

This method was found to be quick, reproducible, and accurate showing promising results in the future to prevent damage to Theobroma cacao by various phytopathogens.

The genome sequence enables cacao molecular biology and breeding for elite varieties through marker-assisted selection, in particular for genetic resistance to fungal, oomycete and viral diseases responsible for huge yield losses each year.

[34] The cacao tree, native of the Amazon rainforest, was first domesticated at least 5,300 years ago, in equatorial South America from the Santa Ana-La Florida (SALF) site in what is present-day southeast Ecuador (Zamora-Chinchipe Province) by the Mayo-Chinchipe culture before being introduced in Mesoamerica.

[35] In Mesoamerica, ceramic vessels with residues from the preparation of cacao beverages have been found from the Early Formative (1900–900 BC) period.

For example, one such vessel found at an Olmec archaeological site on the Gulf Coast of Veracruz, Mexico dates cacao's preparation by pre-Olmec peoples as early as 1750 BC.

[36] On the Pacific coast of Chiapas, Mexico, a Mokaya archaeological site provides evidence of even earlier cacao beverages, to 1900 BC.

In a similar creation story, the Mexica (Aztec) god Quetzalcoatl discovered cacao (cacahuatl: "bitter water"), in a mountain filled with other plant foods.

The cacao beverage was used as a ritual only by men, as it was believed to be an intoxicating food unsuitable for women and children.

At one point, the Aztec empire received a yearly tribute of 980 loads (Classical Nahuatl: xiquipilli) of cacao, in addition to other goods.

[46] The first European knowledge about chocolate came in the form of a beverage which was first introduced to the Spanish at their meeting with Moctezuma in the Aztec capital of Tenochtitlan in 1519.

[citation needed] Cortés and others noted the vast quantities of this beverage the Aztec emperor consumed, and how it was carefully whipped by his attendants beforehand.