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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Publications at this Location » Publication #249443
Title: A SNP assay for genotyping Theobroma cacao suitable for use under field conditions

Author
item Livingstone, Donald
item Freeman, Barbara - Barbie
item MOTAMAYOR, JUAN - Mars, Inc
item DADZIE, ABU - Cocoa Research Institute Of Ghana
item TAKRAMA, JEMMY - Cocoa Research Institute Of Ghana
item Schnell Ii, Raymond
item Kuhn, David

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/15/2010
Publication Date: 1/15/2010
Citation: Livingstone, D., Freeman, B.L., Motamayor, J.C., Dadzie, A.M., Takrama, J., Schnell Ii, R.J., Kuhn, D.N. 2010. A SNP assay for genotyping Theobroma cacao suitable for use under field conditions. Plant and Animal Genome Conference. a.

Interpretive Summary: The ability to genotype the tropical tree crop, Theobroma cacao L., on site in producer countries would help to speed the introduction of improved germplasm to farmers. Currently, many cacao producing regions simply lack the resources necessary to perform genotyping experiments on site, forcing samples to be shipped to other laboratories. This outsourcing of genotype analysis has prolonged the identification of desired trees causing a loss of both time and resources. We describe a Single Nucleotide Polymorphism (SNP) marker-based method to successfully genotype cacao plants under conditions similar to those found in most cacao producing areas. This field SNP assay forgoes expensive realtime machines and automated sequencers, in favor of less expensive standard thermocyclers and a microplate reader. This simple, effective method to genotype cacao seedlings in the field should allow for more efficient resource management in breeding programs, and is currently being implemented in Ghana.

Technical Abstract: The tropical tree crop Theobroma cacao L. is grown commercially for its beans, which are used in the production of cocoa butter and chocolate. Although the upper Amazon region of South America is the center of origin for cacao, 70% of the world’s supply of cocoa beans currently comes from small farms in Africa where harvested beans serve as the primary cash crop. While cacao breeding programs in producer nations continue to serve as an invaluable source of improved planting material, modern marker-based breeding is difficult to perform due to the lack of genotyping facilities in these areas. We describe a SNP marker-based method to successfully genotype cacao plants under conditions similar to those found in most cacao producing areas. This field SNP assay forgoes expensive realtime machines and automated sequencers, in favor of less expensive standard thermocyclers and a microplate reader. The assay was tested under field conditions by planting open pollinated seeds of seven pods from three different maternal plants. The resulting 171 seedlings were successfully genotyped with 19 SNP markers representing 13 loci. The ability to use temperature stable reagents and rapid DNA extraction methods is also explored. Additionally, by examining the seedling genotypes from the SNP markers and 13 additional microsatellite markers we investigate whether seeds in a pod are the result of single or multiple pollination events. This simple, effective method to genotype cacao seedlings in the field should allow for more efficient resource management in breeding programs, and is currently being implemented in Ghana.