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United States Department of Agriculture

Agricultural Research Service

Research Project: MOLECULAR CHARACTERIZATION AND DIVERSITY ASSESSMENT OF COCOA GERMPLASM IN THE AMERICAS

Location: Sustainable Perennial Crops

2011 Annual Report


1a.Objectives (from AD-416)
The goal of this project is to develop and implement scientific approaches for managing and facilitating the use of cacao germplasm. Over the next 5 years we will focus on the following objectives:

Objective 1: Rationalize ex situ cacao collections in international and non-U.S. national genebanks.

Sub-objective 1.A. Maximize diversity coverage and reduce mislabeling and redundancy in international and non-U.S. national collections. Sub-objective 1.B. Improve the integration and expand the scope of phenotype, pedigree, and molecular data in International Cacao Databases. This objective will assure that germplasm collections are representative of the diversity available and that breeders are using correctly labeled and described breeding parents.

Objective 2: Develop complementary conservation methods, including in situ and on-farm conservation methods that can improve cacao productivity while maintaining or enhancing genetic diversity. This will be carried out with partners in developing country centers of diversity.

Objective 3: Characterize and evaluate targeted economic/agronomic traits of cacao and identify likely sources of new genes for breeders. This will serve as a guide to breeders as to what germplasm may contain the traits in which they are interested.


1b.Approach (from AD-416)
The project will continue to genotype cacao samples from ex situ collections from various cocoa producing countries in Latin America. These genotypes developed with a standard set of 15 SSR markers will continue to be used to fingerprint the cacao collections from Ecuador, Colombia, Bolivia, and several small collections in Central America and the Caribbean, following our established protocol of DNA extraction, SSR analysis and allele sizing. The generated multi-locus SSR data, together with those previously obtained from the two International genebanks and other non-U.S. national collections, will be compiled and used for the identification of duplicates within and among collections. After the elimination of mislabeled and duplicate accessions, summary statistics for measuring genetic diversity will be conducted to analyze the geographical distribution of cacao germplasm and identify “hotspots” and geographical areas that have complementary levels of diversity. A minimum of two gap-collecting expeditions will be carried out in areas lacking representation in the ex situ collections. The information on genetic identities obtained in Sub-objective 1.A will serve as the foundation for correcting the existing nomenclatures in the two international databases, as well as the International Cocoa Quarantine Centre, Reading (ICQC, R), which serves as the source for the dissemination of disease-free (post-quarantine) accessions for the global cacao community. Comparison of on-farm diversity with the natural populations in the Peruvian Amazon will be implemented using the populations previously collected from Ucayali, Huallaga, and Mararon River valleys to develop complementary conservation methods, including on-farm conservation methods. Finally phenotypic and genetic analyses will be conducted to characterize and evaluate targeted economic/agronomic traits of cacao and identify likely sources of new genes for breeders.


3.Progress Report
Traditional cacao varieties suitable for the production of fine flavored chocolate still exist in farmers’ fields in tropical America. Identification of traditional cacao varieties using microsattelite and single nucleotide polymorphism (SNP) markers was carried out in Peru. A total of 856 farmer selections from tropical America were analyzed in 2011. In southern Peru, a traditional variety called “Cacao Chuncho” was identified in the Urubamba Valley. This variety has a unique genetic profile and is native to southern Peru. This variety was directly domesticated from the wild cacao around the Urubamba valley. In northern Peru, a unique farmer variety was identified in Jaen, Cajamarca. This variety shares a similar genetic profile with the original “Nacional” cacao from coastal Ecuador, but it has white or pink beans. Moreover, this variety is well adapted in the tropical highland, grows well at 1,200 meters above sea level, and thus represents a unique cacao population in tropical highlands.

Java cocoa is a well-known fine cocoa specialty product in Indonesia. Genetic diversity and population structure of Java cocoa was assessed using simple sequence repeat (SSR) markers. The result shows that the Java cocoa is heterogeneous in genetic structure, including genetic background of Trinitario, Upper Amazon and Lower Amazon Forastero. Parentage analysis supports the Venezuela origin of the original Java Criollo. The resultant information improved our understanding of the diversity and ancestry of Java cocoa.

The development of single nucleotide polymorphism (SNP) markers in cacao offers the opportunity to use a high throughput genotyping system for cacao germplasm characterization. The SNP genotyping result was compared with the multi-locus data generated with 15 SSR loci, in terms of probability of identity, genetic distance, F-statistics, individual assignment probability in model based clustering analysis and parentage analysis. The comparison shows that high throughput genotyping using a small set of SNP markers is highly accurate and a cost-effective tool for cacao germplasm characterization.


4.Accomplishments
1. Two traditional cacao varieties were identified in Peru. In southern Peru, a traditional variety called “Cacao Chuncho” was identified in the Urubamba Valley. Ancestry analysis shows that “Cacao Chuncho” is native to southern Peru and was directly domesticated from the wild cacao around the Urubamba Valley. In northern Peru, a unique farmer variety was identified in Jaen, Cajamarca. This farmer variety shares similar genetic profile as the pure “Nacional” cacao from coast Ecuador, but it has white or pink beans. Moreover, this variety is well adapted in the tropical highland at 1,200 meters above sea level. Both varieties have unique flavor qualities that are of interest to the fine flavor chocolate industry. These findings have stimulated the conservation and production of these types in Peru and have helped to promote the utilization of the Nacional type in numerous new chocolate products in the U.S., Europe and Peru.


Review Publications
Motilal, L., Zhang, D., Pathmanathan, U., Mischke, B.S., Pinney, S.M., Meinhardt, L.W. 2011. Microsatellite fingerprinting in the International Cocoa Genebank, Trinidad: Accession and plot homogeneity information for germplasm management. Plant Genetic Resources. 9:430-438.

Zhang, D., July, W., Johnson, E., Somarriba, E., Philips-Mora, W., Astorga, C., Mischke, B.S., Meinhardt, L.W. 2011. Genetic diversity and spatial structure in cacao (Theobroma cacao L.) germplasm from Bolivia. Genetic Resources and Crop Evolution. DOI: dx.doi.org/10.1007/s10722-011-9680-y.

Zhang, D., Gardini, E.A., Baligar, V.C., Bailey, B.A., Meinhardt, L.W. 2011. Dissecting genetic structure in farmer selections of Theobroma cacao in the Peruvian Amazon: implications for on-farm conservation and rehabilitation. Tropical Plant Biology. 4:106-116.

Last Modified: 4/16/2014
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