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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Publications at this Location » Publication #258344
Title: Applying SNP marker technology in the cacao breeding program at the Cocoa Research Institute of Ghana

Author
item TAKRAMA, J - Cocoa Research Institute Of Ghana
item DADZIE, A - Cocoa Research Institute Of Ghana
item OPOKU, S - Cocoa Research Institute Of Ghana
item PADI, F - Cocoa Research Institute Of Ghana
item ADOMAKO, B - Cocoa Research Institute Of Ghana
item ADU-AMPOMAH, Y - Cocoa Research Institute Of Ghana
item LIVINGSTONE, D - Cocoa Research Institute Of Ghana
item MOTAMAYOR, J - Mars, Inc
item Schnell Ii, Raymond
item Kuhn, David

Submitted to: African Crop Science Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/5/2012
Publication Date: 3/1/2012
Citation: Takrama, J., Dadzie, A., Opoku, S.Y., Padi, F., Adomako, B., Adu-Ampomah, Y., Livingstone, D., Motamayor, J.C., Schnell II, R.J., Kuhn, D.N. 2012. Applying SNP marker technology in the cacao breeding program at the Cocoa Research Institute of Ghana. African Crop Science Journal. 20(1):67-75.

Interpretive Summary: In this investigation 45 parental cacao plants and five progeny derived from the parental stock studied were genotyped using six SNP markers to determine off-types or mislabeled clones and to authenticate crosses made in the Cocoa Research Institute of Ghana (CRIG) breeding program. Investigation was based on the 5’ nuclease SNP assay using Illustra Hot Start mix Ready-To-Go PCR strips and BioTek FLx800TBP Fluorescence Microplate Reader. In a group of six cacao plants labeled as PA150 clones and another five labeled as Pound7, one clone in each group was unambiguously determined as off-type or mislabeled. Similarly, in a cohort of 23 PA7 "clones", four genotypes were differentiated. Cross-checking the fidelity of five progeny from the parental stock under study, it was established that no errors were made in the crossing. The most significant outcome of this study, however, was that out of the four categories of 23 PA7 candidate parental trees only one category can be comparable to the reference clone in the International Cacao Germplasm collection, Trinidad (ICG,T); thus informing the need for further work to find the correct clone among these for the breeding program. It was thus concluded that this simple yet cutting-edge genotyping procedure can be used in applied cocoa breeding programmes in a cocoa producing country. This work represents a first step in the genotypic characterisation of the CRIG germplasm collection and Seed Gardens.

Technical Abstract: In this investigation 45 parental cacao plants and five progeny derived from the parental stock studied were genotyped using six SNP markers to determine off-types or mislabeled clones and to authenticate crosses made in the Cocoa Research Institute of Ghana (CRIG) breeding program. Investigation was based on the 5’ nuclease SNP assay using Illustra Hot Start mix Ready-To-Go PCR strips and BioTek FLx800TBP Fluorescence Microplate Reader. In a group of six cacao plants labeled as PA150 clones and another five labeled as Pound7, one clone in each group was unambiguously determined as off-type or mislabeled. Similarly, in a cohort of 23 PA7 "clones", four genotypes were differentiated. Cross-checking the fidelity of five progeny from the parental stock under study, it was established that no errors were made in the crossing. The most significant outcome of this study, however, was that out of the four categories of 23 PA7 candidate parental trees only one category can be comparable to the reference clone in the International Cacao Germplasm collection, Trinidad (ICG,T); thus informing the need for further work to find the correct clone among these for the breeding program. It was thus concluded that this simple yet cutting-edge genotyping procedure can be used in applied cocoa breeding programmes in a cocoa producing country. This work represents a first step in the genotypic characterisation of the CRIG germplasm collection and Seed Gardens.