The USDA Agricultural Research Service (ARS) has been working for many years to develop and apply molecular markers to accelerate the process of breeding our important crops. The USDA-ARS cacao breeding program began in 1999 with the objective of selecting new cultivars with resistance to witches’ broom (Moniliophthora perniciosa) and frosty pod (Moniliophthora roreri), which have devastated cocoa production in Central and South America. Mars Inc. joined the effort in 2000, providing financial and scientific support to what has become a very successful public/private partnership focused on developing a Marker-Assisted-Selection (MAS) program for cacao.  During the past ten years, molecular markers have been identified, genetic linkage maps produced and Quantitative Trait Loci (QTL) determined by this research program, headed by Raymond J. Schnell at the ARS Subtropical Horticulture Research Station (SHRS) in Miami, FL. These QTLs have already been applied to accelerate the process of selecting superior cacao seedlings in the major cacao breeding programs in the Americas, West Africa and Oceania.
 
The cacao genome sequencing project was undertaken to generate additional information that would expand the current ARS-Mars MAS program. The QTL associated with resistance to cacao diseases such as witches’ broom and frosty pod did not provide the precision needed to identify the actual genes that regulate the trait. Recent technological advances in DNA sequencing have now enabled the entire cacao genome to be sequenced, thus enabling those disease resistance genes to be identified and characterized.

Part of the cacao genome was sequenced by Brian Scheffler’s research group at the ARS Genomics and Bioinformatics Research Unit (GBRU) in Stoneville, MS. In addition, David Kuhn at SHRS has developed single-nucleotide polymorphism (SNP) markers for the disease resistance genes, as well as other important genes. Researchers in cocoa-producing countries can apply these markers to identify germplasm with the favorable traits and accelerate the breeding process by allowing screening of progeny at the seedling stage. These SNP markers are already in use at the Cocoa Research Institute of Ghana (CRIG).
 
More information on the project objectives can be found at the ARS project website. This project is part of the Agricultural Research Service's National Program 301, Plant Genetic Resources, Genomics, and Genetic Improvement Action Plan; additional information regarding this National Program is available from Peter Bretting, National Program Leader for Plant Germplasm and Genomes,  Beltsville, MD (peter.bretting@ars.usda.gov).