Abstract
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.
Highlights
The cupuassu tree, Theobroma grandiflorum (Willd. ex Spreng.) Schum., belonging to the Malvaceae family, is a fruitful species native to the Amazon [1]–as the cacao tree (Theobroma cacao L.) whose seeds are used as raw material for chocolate production
From the 1,517 expressed sequence tag (EST) containing simple sequence repeat (SSR), 70 ESTs were selected based on their functional annotation focusing mainly on sequences potentially involved in the pulp and seed quality characteristics or development, and in other potentially interesting regulating sequences or sequences related to resistance (Fig 3; S1 Table)
24.29% were related to primary metabolism, including lipid (10%) and sugar metabolisms (1.43%), 21.43% were related to gene expression and RNA metabolism, 12.86% to protein synthesis and processing, 12.85% to drought, seed development and other abiotic stresses, 10% to chromatin and DNA metabolism, 8.57% to signal transduction and post-translational regulation, 2.86% to stress resistance, defense and detoxification
Summary
The cupuassu tree, Theobroma grandiflorum (Willd. ex Spreng.) Schum., belonging to the Malvaceae family, is a fruitful species native to the Amazon [1]–as the cacao tree (Theobroma cacao L.) whose seeds are used as raw material for chocolate production. Ex Spreng.) Schum., belonging to the Malvaceae family, is a fruitful species native to the Amazon [1]–as the cacao tree (Theobroma cacao L.) whose seeds are used as raw material for chocolate production. The cupuassu tree is considered one of the main tree crops in the Amazon region [2,3], being economically important in Brazil, with great potential at international level due to the multiple uses of its fruit pulp and seeds. Due to its potential for the “chocolate” industry — in the actual period of announced cacao beans and chocolate shortage [12, 13]– studies related to cupuassu species are increasing at molecular and breeding level [14,15,16,17]. The genetic proximity of cupuassu with cacao—that has been thoroughly studied during the last 10 years [18,19,20,21]–allowed the transfer of data and technologies, as well as comparison for improvement of breeding programs related to different characteristics such as pulp/seed quality and disease resistance
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