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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Research Project #431493

Research Project: Development of Clones of Theobroma cacao With Resistance to Frosty Pod and Black Pod Using Genomics-assisted Breeding Methodology

Location: Subtropical Horticulture Research

Project Number: 6038-21000-025-14-A
Project Type: Cooperative Agreement

Start Date: Aug 12, 2016
End Date: Dec 31, 2020

The main goal of this collaborative research project is to develop cacao clones with resistance to Frosty Pod and Black Pod through the application of genomic assisted breeding approaches. The project has four specific objectives: (1) discover SNP markers associated with resistance to Frosty Pod, Black Pod and self-incompatibility in cacao segregating populations as well as in germplasm accessions; (2) identify the genes responsible for resistance to Frosty Pod, Black Pod, and self-incompatibility in cacao; (3) develop additional SNP markers that could be successfully applied in the genomic-assisted breeding program; and (4) release cacao clones that are self-compatible with resistance to Frosty Pod and Black Pod, high yielding, with good flavor characteristics that deliver a high value for farmers.

Cacao production in the Americas is beset with disease causing very serious production losses. Also the release of cultivars without evaluation of their self-incompatibility characteristics could also be responsible for yield reduction. Therefore, the development of disease resistant and self-compatible cultivars is a priority. SNP markers have been developed using sequence data from two cacao genomes. However, precise pollination and disease scoring data are crucial for for the use of association mapping methodology. If there is an absence of uniform pollination and disease rating data, association mapping results will lack the necessary precision. The primary goal of a genomics-assisted breeding program is the development of high yielding cacao cultivars utilizing the new molecular genetic tools to increase the efficiency of the selection process. Seven field trials involving 1.7 ha of land and 1,472 trees are currently part of CATIE/USDA-ARS project from the previous three agreements. Agronomic practices such as: maintenance of shade species; pruning of the cacao trees, weed and ant control; cleaning of the drainage system; fertilizer applications, and substitution of dead cacao plants with new seedlings will continue to be applied to all the experimental plots during the new phase of the project: Disease incidence and pod yield will be documented by individual trees on a monthly basis. Traditional mapping, association mapping methodologies will be used in the discovery of new QTLs for resistance to frosty pod and black pod diseases. In addition, genomic selection methodology will be utilized in the development of new cacao clones. The following experiments will be pursued: CATIE mapping population “Pound-7 x UF-273” (T4): This population has been used for the identification of genes associated with FP and BP resistance and will continue to be used for the discovery of genes self-incompatible in cacao. For this purpose two field workers skilled in pollinating cacao should be hired and used to perform all the needed pollinations. Mapping populations (L8 and L9): Segregating populations, L8 (‘ICS-43’ X IMC-60’) and L9, an F2 population originated from the selfing of the tree‘55/Isla 2’ from the F1 population ’Pound-7’ x ‘UF-273’ were planted on the La Lola farm beginning in October 2003. These populations will be used for FP and BP resistance studies as well as self-incompatibility studies. Progeny Trial (T16) Population “CC-267 (Matina 1-6) X Criollo-13” and their parents, an F1 segregating population, was developed by crossing the accessions CC-267 (Matina 1-6) by Criollo-13. A yield trial was planted in La Montaña Farm in August 2009 with the two parents and 32 plants that were previously selected and clonally propagated with eight replicates per plant. Agronomic maintenance and artificial pollination are going to be required in this trial.