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Title: Dissecting genetic structure in farmer selections of Theobroma cacao in the Peruvian Amazon: implications for on-farm conservation and rehabilitation

item Zhang, Dapeng
item Baligar, Virupax
item Bailey, Bryan
item Meinhardt, Lyndel

Submitted to: Tropical Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/21/2011
Publication Date: 1/1/2011
Citation: Zhang, D., Gardini, E.A., Baligar, V.C., Bailey, B.A., Meinhardt, L.W. 2011. Dissecting genetic structure in farmer selections of Theobroma cacao in the Peruvian Amazon: implications for on-farm conservation and rehabilitation. Tropical Plant Biology. 4:106-116.

Interpretive Summary: Cacao is an important tropical crop since 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 new cacao resources. In the present study, we analysed the population structure and genetic ancestry in 220 farmer selections of cacao from the Peruvian Amazon using DNA finger printing technology. The results showed that the farmer selections in the Peruvian Amazon have a high level of genetic diversity, which is comparable to the wild cacao found in Peru. We identified a new native population in farmers' fields, which is genetically different from all of the known cacao in Peru. 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: Natural evolution and human intervention have both contributed to on-farm diversity of crop species. Knowledge of genetic structure in farmer selections is essential to identify genetic entities that have conservation priority in farmers’ fields. Using a high-throughput genotyping system with 15 microsatellite loci, we analyzed population structure in 220 farmer selections of cacao from the Peruvian Amazon. A high level of genetic diversity was observed in these farmer selections. Allelic variation in this cultivated population is comparable to that of the natural populations in the Peruvian Amazon. Ancestry inference identified a multi-cluster admixture in farmer selections, among which we identified a new group of domesticated Forastero cacao that is native to the Peruvian Amazon. This domesticated population is genetically different from known natural populations in the Peruvian Amazon, but is similar to the cultivated population in Huallaga. This native Forastero population contributed 46% of the ancestry for the 220 farmer selections, whereas the introduced international parental clones accounted for 37%, among which parentage analysis identified 16 international clones as probable female parents and 11 clones as probable male parents for these farmer selections. Together the top three international clones ICS-1, IMC-67, and SCA-6 contributed 73% of the identified parentage. The distinctive population profile of the native cacao identified in farmer selections highlights the need for assessing on-farm genetic diversity and identifying conservation gaps in the Peruvian Amazon. The results will also be used to assist rational deployment of farmers’ elite clones in rehabilitation programs, as well as for breeding programs.