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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 Title: Elucidating genetic identities of cacao germplam in an international cacao collection using molecular markers

Authors
item Motilal, Lambert -
item Zhang, Dapeng
item Umaharanl, Pathmanathan -
item Boccara, Michel -
item Mischke, Barbara
item Sankar, Antoinette -
item Meinhardt, Lyndel

Submitted to: Plant Genetic Resources: Characterization and Utilization
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 30, 2012
Publication Date: October 23, 2012
Citation: Motilal, L., Zhang, D., Umaharanl, P., Boccara, M., Mischke, B.S., Sankar, A., Meinhardt, L.W. 2012. Elucidating genetic identities of cacao germplam in an international cacao collection using molecular markers. Plant Genetic Resources: Characterization and Utilization. 10(3):232-241.

Interpretive Summary: Cacao (Theobroma cacao L.) is a tree crop from which cocoa butter and chocolate are derived. The conservation of cacao germplasm requires maintaining living trees in field genebanks in tropical regions. The International Cocoa Genebank, Trinidad, is one of the largest cacao germplasm collections in the world. The objective of the present study was to elucidate the extent of mislabeling and genetic diversity in this collection using molecular markers. The study focused on the Refractario group which were collected from 12 farms in the coastal region of Ecuador in the 1920s. A total of 387 cacao varieties were genotyped. Based on the DNA fingerprints, relationships among the Refractario groups from different farms were analyzed. The 12 farms were grouped into four sub-clusters. The information framework generated in this study will allow the curators to improve the efficiency in conservation and utilization of this cacao collection. This information will be used by researchers, germplasm curators and plant breeders.

Technical Abstract: The conservation of cacao (Theobroma cacao L.) germplasm requires maintaining living trees in field genebanks in tropical regions. The International Cocoa Genebank, Trinidad is one of the largest cacao germplasm collections in the world. The objective of the present study was to elucidate the extent of mislabeling and genetic diversity in this collection using 26 selected Single Sequence Repeats (SSR) markers. The study focused on the Refractario accessions which were collected from 12 farms in the coastal region of Ecuador in the 1920s. A total of 484 leaf samples, representing 387 cacao accessions, were genotyped.DNA fingerprints were analyzed for multi-locus matching, computation for probabilities of identity and population assignment. A synonymous rate of 7.5% and an error rate of 39.4% were found. Result of clustering analysis revealed relationship among the Refractario accessions from different farms and grouped the the 12 farms into four sub-clusters, including OB1 (B and SJ), OB2 (AM, CL, CLM and LP), OB3 (JA, LV, LX, LZ, SLA, SLC, SJ) and OB4 (MOQ). The information framework generated is discussed in relation to the assessment of genetic diversity, germplasm enhancement and genebank management.

Last Modified: 11/22/2014
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