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United States Department of Agriculture

Agricultural Research Service

Title: Increasing accuracy and throughput in large-scale microsatellite fingerprinting of cacao field germplasm collections

Authors
item Motilal, Lambert - CRU, WEST INDIES
item Zhang, Dapeng
item Umaharan, Pathmanathan - UNIV WEST INDIES
item Mischke, Barbara
item Boccara, Michael - CRU, WEST INDIES
item Pinney, Stephen

Submitted to: Tropical Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: September 15, 2008
Publication Date: October 1, 2008
Citation: Motilal, L., Zhang, D., Umaharan, P., Mischke, B.S., Boccara, M., Pinney, S.M. 2008. Increasing accuracy and throughput in large-scale microsatellite fingerprinting of cacao field germplasm collections. Tropical Plant Biology. 2:23-37.

Interpretive Summary: Cacao is an important tropical crop because it is the source of cocoa butter and powder for the confectionery industry. Genetic resources of cacao are important for breeding new cacao varieties and thus are of great importance for sustainable cacao production. A lack of knowledge about the genetic diversity in cacao limits the conservation and use of these new cacao resources. In the present study, we report on a method of improving efficiency and accuracy of determining mislabelled accessions in a cacao collection. We tested the use of small pools of DNA to reduce the number of trees required, a reduced number of molecular markers to decrease the time required for fingerprinting and the best available markers for separating different cacao varieties. We identified a set of nine makers that reveal the same accuracy for identifying mislabelling as that made by a complete set of 37 markers. These results improve our understanding about the accuracy and efficiency of using molecular marker technology in cacao genebank management. This information will contribute to a more efficient management of cacao germplasm and will improve the breeding of better cacao varieties. These results will be useful to plant breeders, germplasm curators and cacao farmers and will benefit chocolate consumers.

Technical Abstract: Microsatellite-based DNA fingerprinting has been increasingly applied in crop genebank management. However, efficiency and cost-saving remain a major challenge for large scale genotyping, even when middle or high throughput genotyping facility is available. In this study we report on increasing the rate and accuracy of determining mislabelling errors in Theobroma cacao L. germplasm collections when fingerprinted with microsatellite loci in medium to high throughput capillary sequencing systems. The use of small pools of DNA to reduce the number of effective trees, a reduced number of microsatellite loci to decrease the time required for fingerprinting and the best available microsatellite loci for separating accessions to increase accuracy were examined. There was a relatively high level of mixture within plots (59% of 54 plots examined) of the field genebank which opposed the use of a pooling strategy in fingerprinting the collection. However, a set of nine informative loci that could separate sixty accessions into the same genetic groupings as the complete set of 37 loci was found. Stringent probability of identity values (chance of unique accession) was highly influenced (r = -0.996; P<0.001) by the number of alleles utilised in the fingerprinting set but the composition of the primer set was more important when choosing discriminatory loci.

Last Modified: 7/25/2014