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United States Department of Agriculture

Agricultural Research Service

Research Project: MOLECULAR CHARACTERIZATION AND DIVERSITY ASSESSMENT OF COCOA GERMPLASM IN THE AMERICAS Title: Complex origin of Trinitario-type Theobroma cacao (Malvaceae) revealed using plastid genomics

Authors
item Yang, Ji Yong -
item Scascitelli, Moira -
item Motilal, Lambert -
item Sveinsson, Saemundur -
item Engels, Johannes -
item Kane, Nolan -
item Dempewolf, Hannes -
item Zhang, Dapeng
item Maharaj, Kamaldeo -
item Cronk, Quentinue -

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 9, 2013
Publication Date: February 21, 2013
Citation: Yang, J., Scascitelli, M., Motilal, L., Sveinsson, S., Engels, J., Kane, N., Dempewolf, H., Zhang, D., Maharaj, K., Cronk, Q. 2013. Complex origin of Trinitario-type Theobroma cacao (Malvaceae) revealed using plastid genomics. Tree Genetics and Genomes. 9(3):829-840.

Interpretive Summary: Genetic resources of cacao are important for breeding new cacao varieties and thus are of great importance for sustainable cacao production. Traditional cacao varieties in Trinidad and Tobago, the so-called “Trinitario” cultivar group, have been widely considered to be of elite quality. The origin of Trinitario cacao is however unclear, although it is generally considered to be of hybrid origin. Using a new technology called massive parallel sequencing, we identified two new types of genetic markers from chloroplasts in 95 cacao trees collected from old farms in Trinidad. We compared their DNA patterns to a reference set of ten completely sequenced chloroplast genomes and only found three types were present in the sampled Trinitario trees, corresponding to Upper Amazon Forastero (UAF), Lower Amazon Forastero (LAF) and Criollo (CRI) types. These three types likely represented the three founding types introduced to Trinidad and Tobago. All three types were widely distributed in Trinidad and Tobago. These results are useful to plant breeders, germplasm curators and cacao farmers and will benefit chocolate consumers.

Technical Abstract: Trinidad and Tobago has a long history of producing high quality cacao (Theobroma cacao L.) flavor, despite this industry having been threatened in the past by disease and changing economic fortunes. Cacao genotypes in Trinidad and Tobago are of a highly distinctive kind, the so-called “Trinitario” cultivar group, widely considered to be of elite quality. The origin of Trinitario cacao is however unclear, although it is generally considered to be of hybrid origin. We used massive parallel sequencing to identify polymorphic plastidic single nucleotide polymorphisms (cpSNPs) and polymorphic plastidic simple sequence repeats (cpSSRs) in order to determine the origin of the Trinitario cultivar group by comparing patterns of polymorphism to a reference set of ten completely sequenced chloroplast genomes (nine Theobroma cacao and one outgroup, T. grandiflorum (Willd. ex Spreng.) Schum). Only three cpSNP haplotypes were present in the Trinitario cultivars sampled, corresponding to Upper Amazon Forastero (UAF), Lower Amazon Forastero (LAF) and Criollo (CRI) haplotypes. These three cpSNP haplotypes likely represented the three founding introductions of cacao to Trinidad and Tobago. The cpSSRs were more variable, giving eight haplotypes, but these clustered into three groups corresponding to the three cpSNP haplotypes. All haplotypes were widely distributed in Trinidad and Tobago. We therefore concluded that the Trinitario cultivar group is of complex hybrid origin and has derived from at least three original introduction events.

Last Modified: 10/22/2014
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