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United States Department of Agriculture

Agricultural Research Service

Title: Genetic Diversity and Population Structure of Cocoa (Theobroma Cacao L.) in the Hullaga and Ucayali Valleys of Peru

Authors
item Zhang, Dapeng
item Arevalo, Enrique - ICT, TARAPOTO, PERU
item Mischke, Barbara
item Zuniga, Luis - ICT, TARAPOTO, PERU
item Barreto, Alejandro - ICT, TARAPOTO, PERU

Submitted to: Annals Of Botany
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 30, 2006
Publication Date: July 15, 2006
Citation: Zhang, D., Arevalo, E.G., Mischke, B.S., Zuniga, L.C., Barreto, A.C. 2006. Genetic diversity and population structure of cocoa (theobroma cacao l.) in the hullaga and ucayali valleys of peru. Annals Of Botany. 98:647-655

Interpretive Summary: Cocoa is the source of chocolate for the confectionery industry. Conservation of cocoa genetic resources is of great importance for the cocoa economy in the world. Incorrect labeling of plant material and lack of understanding about their genetic diversity limits conservation efforts and use of cocoa genetic resources. Using DNA technology, we identified the mislabeled plant material in an important cocoa collection from Peru. These results will allow efficient use of the cocoa collection and allow breeding of better cocoa varieties thus benefiting the chocolate consumers and cocoa farmers in the world.

Technical Abstract: The cocoa germplasm from the Huallaga and Ucayali valley of Peru is fundamentally important for cocoa breeding because of their resistances to cocoa diseases. Using a set of 15 microsatellite markers, we fingerprinted cocoa germplasm collected from these two valleys in the 1980s. Out of the 109 accessions, we identified 10 synonymous groups including 20 accessions. Population structure was revealed using a Bayesian clustering analysis. Most of these accessions (93.8%) were assigned into two source populations with their geographical labels correctly corresponding to their population membership. The divergence between the two populations was also supported by a highly significant FST (0.207, P<0.001). The level of genetic diversity was higher in the Ucayali population than in the Huallaga population, both in terms of allelic richness and of gene diversity. Analysis of Molecular Variance (AMOVA) showed that 20.8% of the total genetic variation resided between populations, whereas 79.2% resided within individuals. However, significant gene flow was observed between the two populations (Nm = 1.12). The results support our hypothesis that the Peruvian Amazon hosted a high level of cocoa genetic diversity, and the diversity distribution is stratified by the major river systems but has had significant gene flow.

Last Modified: 10/1/2014
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