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United States Department of Agriculture

Agricultural Research Service

Title: Genetic diversity assessment of sub-samples of cacao, Theobroma cacao L. collections in West Africa using simple sequence repeats marker.

item Aikpokpodion, Peter
item Kolesnikova-allen, M
item Adetimirin, V
item Motamayor, Juan-carlos
item Adu-ampomah, Y
item Eskes, A
item Schnell Ii, Raymond

Submitted to: Tree Genetics & Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/1/2009
Publication Date: 7/18/2009
Citation: Aikpokpodion, P.O., Kolesnikova-Allen, M., Adetimirin, V.O., Motamayor, J., Adu-Ampomah, Y., Eskes, A.B., Schnell Ii, R.J. 2009. Genetic diversity assessment of sub-samples of cacao, Theobroma cacao L. collections in West Africa using simple sequence repeats marker.. Tree Genetics & Genomics. DOI 10.1007/s11295-009-0221-1

Interpretive Summary: West Africa is the most important supplier in the world of cocoa beans, the seed of Theobroma cacao L.. The tree is native to South America and a limited number of Amelonado seed were introduced into Africa late in the 19th century from Brazil by the Portuguese. This Amelonado type was grown extensively in West Africa and became known as West African Amelonado. The outbreak of cocoa swollen shoot disease in the 1930s in Ghana, Togo, and Nigeria almost destroyed the industry due to insufficient genetic variability in the base population. New genetic material collected in the Upper Amazon basin was introduced from Trinidad in 1944 and these were used in the West African Research Institute breeding program in Ghana and Nigeria. A new generation of hybrid families was developed and distributed to farmers and these were widely grown throughout the region. The objective of this investigation was to survey the genetic diversity in farmers' fields, using molecular markers, and to compare it with the introduced Upper Amazon Clones and the original local clones. Our goal was to determine the contribution of the Upper Amazon parents to current commercial plantings in West Africa. To accomplish this we used 12 markers known as microsatellites. These have genetic properties that make them useful for these types of studies. The results of the study indicate that there has been a significant replacement of the Amelonado cacao, grown from the late 19th century until the 1950's, with the Upper Amazon and Amazon x Amelonado hybrids. A significant gene flow occurred between the genebank populations and farmers' populations, indicating that varieties developed in the breeding programs have a significant impact on what is now grown in farmers' plantations.

Technical Abstract: Knowledge of genetic diversity, particularly in an introduced crop species, is crucial to the management and utilization of the genetic resources available. Using capillary electrophoresis system, microsatellite markers were used to determine genetic diversity in 574 accessions of cacao, Theobroma cacao L. representing eight populations covering parental, genebank and farmers’ populations in West Africa. From the 12 microsatellite markers used, a total of 144 alleles were detected with a mean allelic richness of 4.39 alleles/locus. While the largest genetic diversity was found in the Upper Amazon parent population (Hnb = 0.730) and the 1944 Posnette’s Introduction (Hnb = 0.704), genetic diversity was lowest in the Local parent population (Hnb = 0.471). Although gene diversity was appreciably high in the farmers’ populations (Hnb = 0.563 – 0.624), the effective number of alleles was lower than found in the genebank’s Posnette’s population. Fixation index estimates indicated deficiency of heterozygotes in the Upper Amazon and the Local parent populations (FIS = 0.209 and 0.160, respectively), and excess of heterozygotes in the Trinitario parent population (FIS = - 0.341). Although, these estimates indicated the presence of inbreeding in the Upper Amazon and the Local parent populations, the presence of substructure (Wahlund effect) was also suggested. A significant gene flow (Nm = 5.11 – 29.46) occurred between the genebank’s population and farmers’ populations indicating that varieties developed in the breeding programmes have had significant impact on what is grown in farmers’ plantations. From this study, we showed that appreciable genetic diversity is present in the West African cacao collections that can be exploited for crop improvement, mitigate the effect of a narrow genetic base of cacao planted in commercial plantations and guarantee the future of cocoa supply to the world market. This report describes the first comprehensive study of the diversity of cacao grown in the world’s largest producing region, West Africa.

Last Modified: 06/25/2017
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