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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC RESOURCE MANAGEMENT OF TROPICAL/SUBTROPICAL GENETIC RESOURCES AND ASSOCIATED INFORMATION

Location: Tropical Crops and Germplasm Research

Title: Microsatellite Fingerprinting of the USDA-ARS Tropical Agriculture Research Station Cacao (Theobroma cacao L.) Germplasm Collection.

Authors
item Irish, Brian
item Goenaga, Ricardo
item Zhang, Dapeng
item Schnell Ii, Raymond
item Brown, James
item Motamayor, Juan Carlos -

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 21, 2009
Publication Date: February 17, 2010
Citation: Irish, B.M., Goenaga Portela, R.J., Zhang, D., Schnell Ii, R.J., Brown, J.S., Motamayor, J. 2010. Microsatellite Fingerprinting of the USDA-ARS Tropical Agriculture Research Station Cacao (Theobroma cacao L.) Germplasm Collection. Crop Science. 50:656-667.

Interpretive Summary: Pods from cacao trees are the main source of raw material for the production of chocolate. Most cacao is produced in developing countries; however most of the chocolate industry is in developed countries. A germplasm collection consisting of close to 1000 cacao trees has been maintained at the USDA-ARS Tropical Agriculture Research Station, in Mayaguez, Puerto Rico, for many years. This collection is maintained, characterized and distributed as a source of genetic material for cacao breeding programs and/or for farmers worldwide. A high degree of genetic diversity in the collection is desirable to satisfy the needs of cacao improvement programs. An experiment was conducted with molecular markers on DNA extracted from all of the trees in the collection. The research was carried out in an effort to estimate genetic diversity in the germplasm collection. Results from the study showed that the collection consists of trees with a diverse genetic background that represents the geographic origins of cacao. Nevertheless, gaps in genetic diversity were also identified and new germplasm will be introduced to include underrepresented germplasm.

Technical Abstract: Cacao (Theobroma cacao L.) is an important cash crop in many tropical countries. Cacao accessions must be propagated vegetatively to conserve genetic integrity due to its allogamous nature and its seed recalcitrance. Therefore, cacao germplasm is usually maintained as living trees in field collections and has resulted in varying rates of misidentification and duplication. Using a high throughput genotyping system with 15 microsatellite loci, all 924 trees in the USDA-ARS Mayaguez cacao collection were fingerprinted. Nineteen accessions (12.3%) were found to have intra-plant errors while fourteen (9.1%) synonymous sets were identified, that included replicates of 49 accessions. The average number of alleles (8.8; SE=0.56) and gene diversity (HE=0.66; SE=0.026) indicate a high allelic diversity in this collection. A distance based cluster analysis and a Bayesian assignment test showed that the cacao accessions can be classified into four distinct clusters, with their geographical origins covering most of the cacao growing regions in the Americas. Assessment of the representative diversity of the collection led to the identification of several genetic gaps, including underrepresented genetic populations and particular traits of economic/agronomic value. The improved understanding of identities and structure in the USDA-ARS cacao collection will contribute to more efficient use of cacao in conservation and breeding.

Last Modified: 8/30/2014
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