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United States Department of Agriculture

Agricultural Research Service

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Location: Subtropical Horticulture Research

Project Number: 6038-21000-017-11
Project Type: Trust

Start Date: Dec 27, 2005
End Date: Dec 27, 2010

The primary goal of this project is to develop and disseminate new productive disease resistant cultivars of cacao. To attain that goal we are developing tools and breeding enhancement techniques that will 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 four specific goals: Objective 1. Develop DNA based markers associated with resistance to Moniliophthora perniciosa, Moniliophthora roreri, Phytophthora spp., and Ceratocystis fimbrata and evaluate germplasm in the international collections to obtain useful information for developing cacao breeding strategies. Objective 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 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 International Institute for Tropical Agriculture (IITA) in Nigeria and with the Cocoa Research Institute of Ghana (CRIG) and in Asia with 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. Objective 3. Identify genes involved with disease resistance reactions and investigate the molecular basis of resistance. Objective 4. 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. Analysis of single nucleotide polymorphism (SNP) data and association mapping analysis cannot be performed in house. A Specific Cooperative Agreement (SCA) has been established to accomplish the work.

Markers associated with the resistance genes will be used in MAS programs to select for new varieties with resistance to these four diseases. Candidate gene markers were developed from Resistance Gene Homologues and WRKY genes using Single Strand Conformational Polymorphism-Capillary Array Electrophoresis (SSCP-CAE). These, 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. The microsatellite loci linked to the QTL are now being used to locate the disease resistance genes in a Bacterial Artificial Chromosome (BAC) library. Assays are being developed to use these markers for selection in current breeding populations.

Last Modified: 11/30/2015
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