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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Research Project #430568

Research Project: Genomic Enhancement of Theobroma Cacao

Location: Subtropical Horticulture Research

Project Number: 6038-21000-025-12-T
Project Type: Trust Fund Cooperative Agreement

Start Date: Feb 1, 2016
End Date: Mar 31, 2020

The primary goal of this project is to develop and disseminate new, productive, disease resistant cultivars of cacao. To attain that goal we have developed tools and breeding enhancement techniques such as disease resistance QTLs identification that efficiently facilitate recurrent genetic improvement. These tools and techniques are being implemented in the current cacao breeding program 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 six (6) specific goals: Objective 1. Identification, mapping, and characterization of genes associated with resistance to cacao diseases, insect pests, and agronomic traits in segregating populations and germplasm collections through the use of DNA markers, as well as linkage and association mapping methodologies. Objective 2. Evaluation of disease resistance gene expression by sequencing the RNA from time course inoculations of resistant and susceptible plants. Objective 3. Conduct cacao performance trials at national and international locations, development of segregating populations, phenotypic evaluations of breeding populations and implementation of a genomic-assisted breeding program by use of DNA markers associated with disease resistance and agronomic traits of importance. This objective requires cooperation with a number of national and international research organizations in Puerto Rico, Hawaii, Central and South America, West Africa, and South Asia. To ensure access to land and other research resources, Non-Assistance Cooperative Agreements (NACAs) and material transfer agreements have been established with institutions located in these states and countries. Objective 4. Conduct cacao performance trials to evaluate newly released clones in farmers' fields in Hawaii and Puerto Rico. Objective 5. Standardize the screening methodology used in the selection of disease resistant cacao clones. Objective 6. Update the current cacao database with information related to molecular markers, identification of marker-trait associations, genetic identity, breeding values of evaluated genotypes, molecular systematic analysis and gene modeling.

Using the cacao genome database, markers associated with the key disease resistance and agronomically important traits, will be used in genomic–assisted breeding programs to select parental genotypes that will be used to develop new breeding populations segregating for resistance to the most important cacao pathogens and insects. In addition, candidate genes recently identified by Single Nucleotide Polymorphism (SNP) markers using linkage and association mapping approaches will be used to select outstanding plants in current segregating populations. These selected plants will be subjected to further field testing, allowing improved selection efficiency and thus improvement in the identification of outstanding varieties.