Analysis of the chocolate genome could lead to improved crops and products

“The large amount of information generated by this project dramatically changes the status of this tropical plant and its potential interest for the scientific community,” said Guiltinan, professor of plant molecular biology, Penn State.

The researchers not only sequenced the genome of this ancient plant, but assembled 76 percent of the genome linking 82 percent of those genes to the 10 cacao chromosomes. This analysis identified a variety of gene families that may have future impact on improving cacao trees and fruit either by enhancing their attributes or providing protection from fungal diseases and insects that effect cacao trees.

“Relics of the ancestral Criollo first cultivated by Olmec or Maya people can still be encountered in old Mesoamerican plantations or in forests where the Maya live,” said Siela Maximova, associate professor of horticulture and a member of the research team. “Our genome sequence is derived form a Belizean Criollo plant collected in the Mayan mountains.”

Cocoa production began in Mesoamerica 3,000 years ago, and the Criollo variety was the first domesticated. Because these trees self-pollinate, they are generally highly homozygous — possessing two identical forms of each gene, making this particular variety a good choice for accurate genome assembly.

Although originally a new-world crop, cacao trees — scientifically designated Theobroma cocao — are now grown and cultivated in humid, tropical areas around the world. About 3.7 million tons of cocoa are produced annually worldwide and contribute greatly to the income of small farmers. Cacao trees, because they are grown in shade, are also ideal for environmental preservation because they contribute to diversity and land rehabilitation.

“We believe that Theobroma cacao is the first early domesticated tropical tree fruit crop to be sequenced,” said Guiltinan. “Interestingly, only 20 percent of the genome was made up of transposable elements.”

Transposable elements or transposons are one of the natural pathways through which genetic sequences changes. They do this by moving around the chromosomes, changing the order of the genetic material. Smaller amounts of transposons than average could lead to slower evolution of the chocolate plant.

Guiltinan and his colleagues are interested in specific gene families that could link to specific cocoa qualities or disease resistance. They hope that mapping these gene families will lead to a source of genes directly involved in variations in the plant that are useful for acceleration of plant breeding programs.

“We hope this achievement will encourage greater investment in research of Theobroma cacao, the 'food of the Gods' whose magic flavor has spread worldwide since the time of the Maya and Aztec civilizations, and whose continued study will benefit developing countries for which cocoa is of high economic importance,” said Guiltinan.

A summary of the paper appears in Nature Precedings at http://precedings.nature.com/documents/4908/version/1

Penn State researchers involved in this study include Guiltinan and Maximova, department of horticulture; Yufan Zhang and Zi Shi, graduate students, plant biology; Stephen Schuster, department of biochemistry and molecular biology; John E. Carlson, School of Forest Resources and M.J. Axtell and Z. Ma, department of biology.

Other researchers involved were from CIRAD, Institut National de la Recherche Agronomique UMR, Universite d'Evry, INRA-CNRS LIPM Laboratoire des Interactions Plantes Micro-organismes, Universite de Perpignan, Unite de Biometrie et d'Intelligence Artificielle , Institut des Sciences du vegetal, Chocolaterie Valrhona, all in France.

Also included are researchers from the University of Arizona; Cold Spring Harbor Laboratory; Institute des Sciences du Vegetal, Ivory Coast; CEPLAC, Brazil and Centro Nacional de Biotecnologia Agricola, Instituto de Estudios Avanzados,Venezuela.

CIRAD, the Agropolis foundation, the Région Languedoc Roussillon, Agence Nationale de la Recherche (ANR), Valrhona, the Venezuelan Ministry of Science, Technology and Industry, Hershey Corp., the American Cocoa Research Institute Endowment and National Science Foundation supported this work.