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United States Department of Agriculture

Agricultural Research Service

Related Topics

Research Project: Genetic Improvement of Theobroma Cacao

Location: Subtropical Horticulture Research

2012 Annual Report


1a.Objectives (from AD-416):
The primary goal of this Trust Fund Cooperative Agreement No. 58-6631-1-002 (“Agreement”) project is to set out the terms and conditions of the project to develop and disseminate new productive disease resistant cultivars of cacao. To attain that goal we have developed tools and breeding enhancement techniques that efficiently facilitate recurrent genetic improvement. These tools and techniques are being implemented in the project and have been made available to international breeding programs. Research performed in genetic resource evaluation, molecular genetics, statistics, bioinformatics, plant pathology, and practical field selection are all part of a global strategy to develop superior planting material for farmers. The project has eight (8) specific goals: 1. Fine mapping DNA based markers associated with resistance to cacao diseases and other agronomic traits through linkage mapping or genome wide association (GWAS) to obtain useful information for developing cacao breeding strategies. 2. Establish families combining traits of interest and develop a Marker Assisted Selection (MAS) program to genetically improve cacao for resistance to these diseases and to provide new cultivars with enhanced production. This objective requires cooperation with a number of national and international research organizations in Central and South America, West Africa, and South Asia. The South and Central American institutes are the Tropical Agricultural Research and Education Center (CATIE) in Turrialba, Costa Rica, and the Instituto Nacional de Investigaciones Agricolas y Pecuarias (INIAP) Estacion Experimental Pichilingue (EET Pichilingue) in Quevedo, Ecuador. Collaboration with West African institutes is through the support of the United States Agency for the Development (USAID) and the International Institute for Tropical Agriculture (IITA) in Nigeria and directly with the Cocoa Research Institute of Ghana (CRIG). In Asia our main collaborator is the Coconut and Cacao Institute (CCI) in Papua New Guinea. To ensure access to these populations, specific cooperative agreements (SCA) have been established with these institutions. 3. Develop new molecular marker methodologies for massive screening of plants and implement those methodologies in the Marker Assisted Selection process. 4. Identify genes involved with major agronomic traits and investigate the molecular basis of their expression. 5. Develop biostatistical expertise for cacao genetics for whole genome map development, identification of marker-trait associations, molecular systematic analysis, and development of a genetic relational database. 6. Apply the biostatiscal expertise developed in the analyses of segregating populations and germplasm collections existing in the above mentioned research institutes. 7. Implement evaluation of improved material in farmers’ fields. 8. To share information on genotypic identity, breeding values of the genotypes studied available through our database or the database established in collaboration with Washington State University (WSU).


1b.Approach (from AD-416):
Markers associated with the key agronomic traits will be used in MAS programs to select for new varieties emphasizing the resistance to the most important cacao pathogens. Candidate gene markers along with microsatellite markers were used to produce the first definitive saturated linkage map of Theobroma cacao. One major and one minor Quantitative Trait Locus (QTL) were discovered controlling resistance to witches’ broom and three QTLs have been identified for resistance to frosty pod. One QTL has also been identified regulating reproductive self-incompatibility in cacao. Assays are being developed to use these markers for selection in current breeding populations. These assays will be used to pre-select genotypes for field testing allowing greater efficiency in the identification of superior individuals. These QTLs are also being used to locate the respective genes in the cacao genome.


3.Progress Report:

This research relates to inhouse project objective: The development and implementation of an international Marker Assisted Selection (MAS) program for cacao is the major objective of this project.

The goals of this project are to develop new DNA based markers and utilize them to differentiate populations of cacao (the plant that chocolate is made from) that are segregating for resistance to frosty pod rot, black pod, witches’ broom, vascular streak dieback, cocoa pod borer and mirids. Markers associated with the resistance genes are being used in marker-assisted selection (MAS) programs to select for new varieties with resistance to these diseases and pests. Providing productive, disease resistant cultivars for farmers will ensure a plentiful supply of cocoa beans for the American confectionary industry, as well as pharmaceutical and cosmetic industries. More importantly, these improved cultivars will provide an alternative planting material to drug crops currently grown in South America.

This is the second year of a new Trust Agreement (the third five year commitment from Mars, Inc. for $500,000 per year for a total commitment of $7,500,000 for the breeding project). These funds are used to support the overseas field testing for disease resistance and productivity traits. The Trust continues to support our breeding program and yield trials in Costa Rica, Ecuador, Ghana, and Papua New Guinea where phenotypic and disease resistance evaluations continue. In addition, the funds support travel and laboratory expenses associated with the molecular evaluations. They also support one post doctoral fellow and part of a lab technician in the Miami lab. The project has been managed through visits to the Miami Lab from Mars personal, regular conference calls and emails with Mars senior managers and with daily interaction with the senior Mars breeder who is stationed at the Miami lab.


Last Modified: 4/15/2014
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