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United States Department of Agriculture

Agricultural Research Service

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Research Project: Genetic and Phenotypic Evaluation of Basic Germplasm, Mapping Populations, Advanced Full-Sib Families, and Selected Clones of Theobroma Cacao

Location: Subtropical Horticulture Research

2012 Annual Report


1a.Objectives (from AD-416):
1. To select superior cultivars from current breeding trials that are resistant to Frosty Pod (FP) and Black Pod (BP) diseases, high yielding (greater than 2000 kg/ha) and with flavor characteristics that impart high value for producers.

2. To investigate the genetic basis of self-compatibility, disease resistance, tree architecture, flavor and fat characteristics using previously identified Quantitative Trait Loci (QTLs) and correlate genes in these areas of the genome with phenotypic responses.

3. Using the newly developed Single Nucleotide Polymorphism (SNP) chip, identify marker/trait associations in current field trials using phenotypic data.

4. Using these marker/trait associations and the completed reference cacao genome sequence, investigate the genetic control of these complex horticultural traits.


1b.Approach (from AD-416):
Ten field trials involving 11 ha of land and 13,000 trees are currently under the umbrella of the CATIE/USDA project from the previous two SCA. The following agronomic practices will continue in the experimental areas during the new project period: maintenance of shade species, pruning of the cacao trees, weed and ant control, cleaning of the drainage system, three fertilizer applications per year, substitution of dead cacao plants with new seedlings. Monthly evaluations of yield and disease incidence will also be recorded on a tree-by-tree basis in some of the trials as indicated below. In addition new QTLs identified for resistance to frosty pod and black pod diseases will be identified using traditional mapping and association genetics. Validation of the efficiency of selection using the markers and using phenotypic data from field screenings will be completed.

‘CC-267’ (‘Matina’) x ‘Criollo-13’ Progeny Trial

Thirty-two selected cloned progeny from this cross are planted in a RCB with four replications at the La Montana Farm in 2009. These progeny will be used for molecular studies and phenotypic data, including number of healthy pods, number of pods affected by FP or BP and fresh weight of seed for each production cycle each year, will be collected starting in 2012, and continue for the duration of the project.

Nine Families Hybrids Trial (L18)

Nine hybrid families from superior clones previously identified in the breeding program were produced and planted at the ‘La Lola’ research farm in 2009. Over 1500 seedlings have been established. The experiment is planted in a RCB design with four replication/family. Each seedling will be evaluated for number of healthy pods, number of pods affected by FP or BP and fresh weight of seed for each production cycle each year for the duration of the project. Molecular studies will be conducted on selected individuals within this population.

160 Superior Clones Field Trial (L12)

This clonal trial was established in La Lola Farm in June-July 2005. The experiment involves 160 superior clones represented by 25 plants each randomly distributed in nearly four ha of land. The experimental area comprises 4.000 experimental trees. Most clones were obtained by grafting superior trees selected from the oldest trials established by the CATIE´s Breeding Program in La Lola and Turrialba. Selection of the trees was made by using records of yield and disease reaction to FP and BP taken monthly during nearly 10 years and on a tree-by-tree basis.

Molecular data together with two more yield of field data, will be used to select the best clones of the trial for larger trials or distribution to farmers.


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.

Phenotypic data continues to be collected on our experimental plots at the La Lola farm and among the mapping population at Turrialba. The location of QTL's (quantitative trait loci) associated with self-compatibility in cacao have been identified in the F1mapping population of ‘Pound 7’ x ‘UF 273’. Analysis of differential gene expression has been done to identify genes involved in the self -incompatibility reaction. In addition, a population from the selfing of ‘UF 273 Type 1’, F2 mapping population of ‘UF 273’ x ‘Pound 7’ and Matina x Criollo progeny have been used in the fine mapping of genes involved self-compatibility.


Last Modified: 10/21/2014
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