First Microsatellite Markers Developed from Cupuassu ESTs: Application in Diversity Analysis and Cross-Species Transferability to Cacao

The cupuassu tree (Theobroma grandiflorum) (Willd. ex Spreng.) Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit´s pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate....

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Published in:	PloS one Vol. 11; no. 3; p. e0151074
Main Authors:	Ferraz Dos Santos, Lucas, Moreira Fregapani, Roberta, Falcão, Loeni Ludke, Togawa, Roberto Coiti, Costa, Marcos Mota do Carmo, Lopes, Uilson Vanderlei, Peres Gramacho, Karina, Alves, Rafael Moyses, Micheli, Fabienne, Marcellino, Lucilia Helena
Format:	Journal Article
Language:	English
Published:	United States Public Library of Science 07-03-2016 Public Library of Science (PLoS)
Subjects:	Annotations Barley Biodiversity Biology and life sciences Breeding Cacao Cacao - genetics Cell cycle Chocolate Deoxyribonucleic acid Disease resistance DNA DNA sequencing Expressed sequence tags Expressed Sequence Tags - metabolism Food industry Food production Fungal diseases Gene mapping Gene polymorphism Genetic aspects Genetic markers Genetics Genomes Genotype Genotypes Identification Markers Microsatellite Repeats - genetics Microsatellites Mutation Physiological aspects Plant breeding Plant diseases Polymorphism Polymorphism, Genetic Pulp Quality Research and Analysis Methods Seeds Sequence Analysis, DNA Species Species diversity Studies Theobroma cacao Theobroma grandiflorum Trees Witches' broom France Brazil
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Summary:	The cupuassu tree (Theobroma grandiflorum) (Willd. ex Spreng.) Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit´s pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate. In order to support the cupuassu breeding program and to select plants presenting both pulp/seed quality and fungal disease resistance, SSRs from Next Generation Sequencing ESTs were obtained and used in diversity analysis. From 8,330 ESTs, 1,517 contained one or more SSRs (1,899 SSRs identified). The most abundant motifs identified in the EST-SSRs were hepta- and trinucleotides, and they were found with a minimum and maximum of 2 and 19 repeats, respectively. From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation, focusing on pulp and seed quality, as well as resistance to pathogens. The 70 ESTs selected contained 77 SSRs, and among which, 11 were polymorphic in cupuassu genotypes. These EST-SSRs were able to discriminate the cupuassu genotype in relation to resistance/susceptibility to witches' broom disease, as well as to pulp quality (SST/ATT values). Finally, we showed that these markers were transferable to cacao genotypes, and that genome availability might be used as a predictive tool for polymorphism detection and primer design useful for both Theobroma species. To our knowledge, this is the first report involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transferability from cupuassu to cacao. Moreover, these markers might contribute to develop or saturate the cupuassu and cacao genetic maps, respectively.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Conceived and designed the experiments: FM LHM. Performed the experiments: LFS RMF LLF RCT MMCC RMA. Analyzed the data: LFS UVL KPG FM LHM. Contributed reagents/materials/analysis tools: RMA FM LHM. Wrote the paper: LFS FM. Advised LFS: FM LHM. Responsible for the financial support of the work: RMA FM. Competing Interests: The authors have declared that no competing interests exist.
ISSN:	1932-6203 1932-6203
DOI:	10.1371/journal.pone.0151074