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Title: Genetic diversity and population structure of cacao landraces in Northern and Central coastal Ecuador

Author
item Zhang, Dapeng
item AMORES, FREDDY - INIAP, ECUADOR
item CEDENO, ANGELA PALACIOS - INIAP, ECUADOR
item HERMANN, MICHAEL - BIOVERSITY, COLOMBIA
item Meinhardt, Lyndel

Submitted to: Conservation Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/8/2007
Publication Date: 6/5/2007
Citation: Zhang, D., Amores, F., Cedeno, A., Hermann, M., Meinhardt, L.W. 2008. Genetic diversity and population structure of cacao landraces in Northern and Central coastal Ecuador. Conservation Genetics. 9(2) 327-337.

Interpretive Summary: Cacao is an important tropical crop because it is the source of cocoa butter and powder for the confectionery industry. Genetic resources of cacao are important for breeding new cacao varieties and thus are of great importance for sustainable cacao production. A lack of knowledge about the genetic diversity in cacao limits the conservation and use of these cacao resources. In the present study, we assessed genetic diversity and population structure in a group of farmer selections from the Northern and Central coastal Ecuador using DNA finger printing technology. The result showed that a large number of landraces still exist in the traditional farms in Ecuador. These landraces have a moderately high level of genetic diversity and a distinctive genetic profile among all of the known cacao groups. These results improve our understanding of the genetic structure in the fine flavored cacao in Ecuador and should help cacao researchers establish conservation priority. These results improve our understanding of on-farm diversity and will help cacao researchers establish conservation priority. This information will contribute to a more efficient management of cacao germplasm and will improve the breeding of better cacao varieties. These results will be useful to plant breeders, germplasm curators and cacao farmers and will benefit chocolate consumers.

Technical Abstract: Knowledge about genetic diversity among the landraces is essential for developing on-farm conservation strategy in modern agroecosystems. The “arriba” cacao is a group of landraces that are still used today for cacaoa production in the coastal plains and valleys of Ecuador. The strongly rising demand for fine-flavoured cocoa for use in high-end chocolate in the US and in Europe and corresponding price premiums for distinct cocoa flavour profiles can provide economic incentives to conserve these varieties on farm. Using a high-throughput genotyping system with 15 microsatellite loci, we genotyped 123 cacao accessions including 100 “arriba” cacao sampled from ten traditional farms in northern (Esmeraldas) and central (Naranjal) Ecuador. A high varietal and gene diversity was observed in these two regions. The allele richness averaged 6.7 allele per loci and the gene diversity of 0.604 in these landraces. Analysis of Molecular Variance (AMOVA) revealed a significant difference between the north (Esmeraldas) and the cental (Naranjal) populations. Inter- and within-farm variations are highly significant and account for 6% and 84% of the total variation respectively. These landraces have a unique genetic profile in comparison with known Forastero, Trinitario and Criollo germplasm, but shared high similarity with Ecuadorian Nacional hybrids. A substantial gene introgression from exotic germplasm, mostly upper Amazon forastero, was detected in these landraces. Contrary to the common belief, the Venezuela Trinitario only contributed a small fraction of parentage to these landraces. The results suggest that a large number of landraces still exist in the traditional farms in Ecuador. These landraces comprise a wide array of different genotypes, which are genetically unique among the known cacao germplasm groups/populations. The unique genetic profile of these landraces highlight the need for further collecting of these new types of arriba cacao germplasm in these regions. The rich genotype and gene diversity among these landraces is also advantageous for promoting on farm conservation.