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Title: Genetic diversity and structure of farm and genebank accessions of cacao (Theobroma cacao L.) in Cameroon revealed by microsatellite markers

item Efombagan, I.
item Motamayor, Juan
item Sounigo, O
item Eskes, A
item Nyasse, S
item Cilas, C
item Schnell Ii, Raymond
item Manzanares-dauleux, M
item Kolesnikova-allen, M

Submitted to: Tree Genetics & Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/26/2008
Publication Date: 6/1/2008
Citation: Efombagan, I.B., Motamayor, J.C., Sounigo, O., Eskes, A.B., Nyasse, S., Cilas, C., Schnell Ii, R.J., Manzanares-Dauleux, M., Kolesnikova-Allen, M. 2008. Genetic diversity and structure of farm and genebank accessions of cacao (Theobroma cacao L.) in Cameroon revealed by microsatellite markers. Tree Genetics & Genomics. DOI 10.1007/s11295-008-0155-z

Interpretive Summary: Genetic diversity among West African cacao populations grown in farmers' fields has been limited by early introduction bottlenecks and by the use of farmer selected plants as parents for the establishment of new plantings. Recent efforts have been made to estimate genetic diversity in farmers' fields in Nigeria, Ghana, Ivory Coast, and Cameroon using molecular markers. In this study 12 microsatellite molecular markers were used to estimate genetic diversity in farmers' fields and to compare that with genetic diversity in genebanks and among breeding populations in Cameroon. The results indicate that most of the genes in the farmers' accessions originate from the Lower Amazon Forastero germplasm introduced into Cameroon in the 1950s. Significant amounts of Upper Amazon Forastero, and Criollo alleles were also found among the farmers accessions with most of the farmers' accessions containing genes from all three genetic groups. This means that a significant amount of recombination has taken place in the seed gardens with more advanced selections being grown on farms. The traditional Trinitario types, originally introduced to Cameroon, have also disappeared from farmers fields. This work has direct application for cacao breeding in Cameroon because the use of selected farm accessions will depend on the genetic background and the level of heterozygosity.

Technical Abstract: The genetic diversity of 400 accessions collected in cacao farms, 95 genebank and 31 reference accessions was analyzed using 12 microsatelitte markers. The genebank and reference accessions were sub-divided into 12 accession groups (AG) that belong to the traditional cacao genetic groups (GG) Lower Amazon Forastero (LA), Upper Amazon Forastero (UA), Trinitario (Tr) and Criollo (Cr). The 12 microsatelite loci revealed a total of 125 alleles, 113 of which were present in the farm accession group (FA). The within and between group variation for all AGs accounted respectively for 81% and 19% of total molecular variation. The average Fis for the FA was 0.15 suggesting a moderate level of inbreeding. Significant differences for the level of gene diversity (GD) were found between the farm (0.50), genebank (0.42 to 0.62) and reference (0.10 to 0.60) AGs. Genetic differentiation among AGs was variable with Fst values varying between 0.14 and 0.57 for the different AGs. Analysis using a Bayesian model-based method showed the existence of a high level of admixture for the farm accessions group. The LA genes were most represented in the FA (54%), followed by UA (33%) and Cr (1%). The genes of LA were also the most represented in the genebank (48%), followed by UA (24%) and Cr (14%). Only 14% and 6% of the genes of the genebank and farm accessions, respectively, could not be attributed to any of the reference GGs. The results suggest the predominating presence of LA genes in the Cameroon farm accessions and a high level of admixture, with apparent presence of genes of more than three GGs in most accessions. The traditional Trinitario types appear to have almost disappeared from farmers' fields. The admixture must be the result of hybridization and recombination of these genes from different GGs in seed gardens and in farmers’ fields. The data generated have a direct value for breeding because the use of selected farm accessions will depend on the GG it belongs to and also on their level of heterozygozity