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ARS Home » Southeast Area » Mayaguez, Puerto Rico » Tropical Crops and Germplasm Research » Research » Publications at this Location » Publication #213703

Title: Microsatellite fingerprinting of the cacao (Theobroma cacao) germplasm collection at the USDA-ARS, Tropical Agriculture Reserarch Station.

item Irish, Brian
item Goenaga, Ricardo
item Schnell Ii, Raymond
item Brown, James
item Zhang, Dapeng

Submitted to: Caribbean Food Crops Society Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 8/18/2007
Publication Date: 9/16/2007
Citation: Irish, B.M., Goenaga, R.J., Schnell Ii, R.J., Motamayor, J.C., Brown, J.S., Zhang, D. 2007. Microsatellite fingerprinting of the cacao (Theobroma cacao) germplasm collection at the USDA-ARS, Tropical Agriculture Reserarch Station.. Caribbean Food Crops Society Proceedings 43:219.

Interpretive Summary:

Technical Abstract: Cacao (Theobroma cacao L.) is an important cash crop in many tropical countries. Because of its outcrossing nature, cacao accessions must be propagated vegetatively to conserve their genetic integrity. Therefore, cacao germplasm is usually maintained as living trees in collections in tropical regions around the world. The large number of varieties and selections, its clonal propagation, the transfer between locations and the long term field maintenance has resulted in mislabeling of accessions in germplasm collections worldwide. To study this potential problem in the USDA-ARS collection, all 924 trees (154 accessions x 3 blocks x 2 trees/block) were fingerprinted using an internationally recognized standard set of 15 microsatellite (SSR) primers. Intra-clone error (mislabeling among multiple trees within the same accession) was estimated at 12.3%. Inter-clone error (the mismatch between the DNA fingerprint profile of an accession in this collection and the fingerprint profile in source collection) was estimated at 25%. The results of descriptive statistics showed that the 15 loci had an average of 8.8 alleles per locus. The observed and expected mean heterozygosity values were 0.65 and 0.66, respectively. Cluster analysis showed that accessions generally grouped together according to their known genetic background (Trinitario, Forastero and Criollo), with sub-clusters consisting of accessions from common breeding programs and/or geographic origins. Also, 14 synonymous sets (plants with identical fingerprint profiles) were identified and the number of duplicated accessions ranged from 2 to 19 in each set. The relatively high values for allele number and heterozygosity suggest high genetic diversity in the collection. The microsatellite fingerprint profiles generated in this study are highly useful and will aid in the correction of misidentified cacao accessions. Fingerprint profiles for cacao accessions will become available through the USDA National Plant Germplasm System Germplasm Resource Information Network (GRIN) database