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United States Department of Agriculture

Agricultural Research Service

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Research Project: Evaluation of Germplasm, Mapping Populations, and Advanced Families of Theobroma Cacao for Disease Resistance, Productivity Traits

Location: Subtropical Horticulture Research

2013 Annual Report


1a.Objectives (from AD-416):
A. Germplasm evaluation: Phenotypic evaluation for the INIAP germplasm collections will be continued from the previous agreement. B. Evaluation of mapping populations and hybrid cocoa selections. C. Breeding for Witches Broom resistance: During the previous Trust Agreement, two breeding schemes were developed to select high yielding WB tolerant cultivars. Each breeding involved a number of controlled crosses to develop full-sib families. These full-sib families were then evaluated as seedlings under extremely high inoculum pressure for WB disease. Resistant seedlings were cloned and placed into yield trials as clones. D. Irrigation improvements.


1b.Approach (from AD-416):
1. Nacional cacao collections CGN collection - For the CGN collection genetic variability has been enriched with several new genotypes selected in farmer´s fields. Local breeding selections have also been added and the entire collection will be evaluated for productivity traits (bean weight, pod characteristics and number), disease resistance traits (Frosty Pod [FP], Witches’ Broom [WB], and Black Pod [BP]) and flavor characteristics (physical, chemical and sensorial studies).

SNA collection - Highest yielding clones in the SNA collection are SNA 0614, EB 0501, SNA 0602 and SNA 0701. From the 97 accessions under evaluation, more than half presented averages of 0 to 1 vegetative brooms per tree, indicating the importance of these particular genotypes as a possible source of resistance against WB. This collection will continue to be evaluated for WB resistance and for flavor characteristics (physical, chemical and sensorial studies). 2. Amazonian cacoa collections Allen collection - The Allen Collection consists of material collected along the river Napo in eastern Ecuador. Evaluation of this collection began in late 2009 and continued during 2010 under the previous agreement for dry bean weight and other productivity parameters. These will continue to be evaluated over the next five years along with disease resistance traits (FP, WB, and BP). The evaluation of flavor characteristics (physical, chemical and sensorial studies) will also be added under this agreement.

Chalmers collection - For the Chalmers Collection the accessions have been fully characterized both morphologically and genetically. However, there is a high probability of fine or flavor genotypes among these clones, as some exhibit pale or even white beans. These traits are usually associated with aromatic type cocoas. Over the agreement period physical, chemical and sensorial study of the beans will be undertaken.

Other miscellaneous collections - In addition to the aforementioned collections hundreds of new accessions have been introduced in recent years. These include a duplicate of a large group of accessions that were located at the East Napo station as well as old collections from East Pichilingue. Over the agreement period physical, chemical and sensorial study of the beans will be undertaken, as well as observations on disease reactions and productivity. 3. Genetic recombination mapping and QTL analysis The following mapping populations will continue to be characterized during the period 2011-2012: ‘EET 95’ × ‘SIL 1’ (7A Sección A), ‘SCA 12’ × ‘Desconocido’ (7A Sección B), ‘SCA 12’ × ‘SIL 5’ (7A Sección D), ‘SCA6’ × ‘SIL 1’ (7A Sección C), ‘SCA 12’ × ‘SIL 1’ (7A Sección E), ‘SCA 6’ × ‘SIL 5’ (7A Sección F). In addition to characterization for yield and disease incidence, these populations will be manually self pollinated to evaluate their self-incompatibility reactions, the pods issued from the self-pollination characterization will be microfermented for flavor mapping. Two post graduate students from INIAP will focus their academic research in the genetic analysis of two of the mapping populations.


3.Progress Report:

This Research is directly related to inhouse objective 3: Apply association mapping and genomic selection approaches to genomic and phenotypic data to accelerate the breeding of cacao having improved productivity, host-plant resistance to biotic stresses, tolerance to environmental extremes and superior product quality.

Twenty six new selections from the breeding populations at INIAP were transferred to the Miami quarantine facility. These clones have FP and WB resistance combined with high productivity. After quarantine the new clones will be distributed to other cacao breeding programs. In addition, self pollinations of the cultivar CCN-51 are being conducted in support of the project for the fine mapping of genes involved with self-compatibility.

New mapping populations are being analyzed to identify additional QTL markers for WB and FP. This project has been managed through regular conference calls, emails, and one visit by a Miami scientist to the location in the past year.


Last Modified: 7/31/2014
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