Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/13/2009
Publication Date: 5/23/2009
Citation: Zhang, D., Boccara, M., Motilal, L., Mischke, B.S., Johnson, E.S., Butler, D., Bailey, B.A., Meinhardt, L.W. 2009. Molecular characterization of an earliest cacao (Theobroma cacao L.) collection from Peruvian Amazon using microsatllite DNA markers. Tree Genetics and Genomes. http://dx.doi.org/10.1007/s11295-009-0212-2. Interpretive Summary: Cocoa is an important tropical crop since it is the source of cocoa butter and powder for the confectionery industry. Genetic resources of cocoa are important for breeding new cocoa varieties and thus are of great importance for sustainable cocoa production. Incorrect labeling of the trees and a lack of knowledge regarding their genetic diversity are the main limitations to conservation and to use of cocoa genetic resources. In the present study, we fingerprinted 612 cacao accessions collected in the 1930s to 1940s from the Peruvian Amazon. We identified 180 cases of mislabeling and 116 duplicated clones. Based on the DNA fingerprints, we also reconstructed the family relationship. The result indicates that the genetic diversity in wild cacao is structured by the river systems of the Peruvian Amazon. In addition, our results demonstrate that these germplasm were collected from a small area in Peruvian Amazon. The vast majority of the Peruvian Amazon have not been covered by collecting expeditions. These results improve our understanding of the genetic diversity that exists in this cocoa collection. These findings will be used by collection curators, plant breeders and cocoa farmers.
Technical Abstract: Cacao (Theobroma cacao L.) is indigenous to the Amazon region of South America. The Peruvian Amazon harbors a large number of diverse cacao populations. Since the 1930s, several numbers of populations have been collected from the Peruvian Amazon and maintained as ex situ germplasm repositories in various countries, with the largest one held in the International Cacao Genebank in Trinidad. The lack of information on population structure and pedigree relationship and the incorrect labeling of accessions are major concerns for efficient conservation and use of cacao germplasm. In the present study, we assessed the individual identity, sibship, and population structure in cacao populations collected from the Amazon region of Peru in the 1930-1940s. Using a capillary electrophoresis genotyping system, we analyzed the SSR variation of 612 cacao accessions collected from the Marañon, Nanay and Ucayali river systems. A total of 180 cases of mislabeling were identified using a Bayesian clustering method for admixture detection. In addition, forty five duplicate groups, including 116 accessions, were identified by multilocus matching of SSR profiles. Using maximum likelihood-based methods, we reconstructed 78 fullsib families nested in 48 half-sib families, indicating that the pods collected in the 1930s were from 48 mother trees in maximum. Likelihood simulation also identified eight probable parents that are responsible for 117 pairs of mother-offspring relationships in this collection. Principal Coordinate Analysis (PCA) and the Bayesian clustering method cohesively demonstrate a pronounced structure of genetic diversity stratified by the river systems of the Peruvian Amazon. Our results also shows that in spite of the high level of allelic diversity in this collection, this collection was composed of a large number of related family members collected from a small area, including a couple of sites in the Ucayali and Nanay rivers, as well as the lower Marañon river near Iquitos. The vast majority of the Peruvian Amazon, especially the upper Marañon river and its tributaries, have not been covered by collecting expeditions. The improved understanding of the individual identities, genealogical relationships and geographical origin of cacao germplasm in this collection will contributed to a more efficient conservation and use of the Peruvian cacao germplasm. Additionally, this study also provides baseline information to help guide the future collecting expeditions in the Peruvian Amazon.