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.
Citation: Ferraz dos Santos L, Moreira Fregapani R, Falcão LL, Togawa RC, Costa MMdC, Lopes UV, et al. (2016) First Microsatellite Markers Developed from Cupuassu ESTs: Application in Diversity Analysis and Cross-Species Transferability to Cacao. PLoS ONE 11(3): e0151074. https://doi.org/10.1371/journal.pone.0151074
Editor: Xiaoming Pang, Beijing Forestry University, CHINA
Received: December 12, 2015; Accepted: February 23, 2016; Published: March 7, 2016
Copyright: © 2016 Ferraz dos Santos et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All relevant data are within the paper and its Supporting Information files.
Funding: This research was supported by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior and the Empresa Brasileira de Pesquisa Agropecuária project called “Theobroma” (coordinated by FM), and by the Empresa Brasileira de Pesquisa Agropecuária/Macroprogram project called "Geneaçu" (coordinated by RMA).
Competing interests: The authors have declared that no competing interests exist.
Abbreviations: ATT, titratable acidity; EST, expressed sequence tag; NGS, next generation sequencing; ORF, open reading frame; UTR, untranslated region; SSR, simple sequence repeat; SST, total soluble solids
The cupuassu tree, Theobroma grandiflorum (Willd. ex Spreng.) Schum., belonging to the Malvaceae family, is a fruitful species native to the Amazon –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. From the pulp, several products are manufactured, such as juices, ice creams, liquors, jams, jellies, creams and sweets [2, 3]. Cupuassu seeds have a high quality fat, composed mainly of oleic and stearic acid [4, 5], from which a product similar to chocolate, called cupulate, can be obtained [6–8]. Moreover, cupuassu received attention because of its proteolytic activity, useful in food industry , its antioxidant and cytotoxic activity, as well as its action in increasing glucose tolerance [9–11]. Due to its potential for the “chocolate” industry—particularly 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 [14–17]. Moreover, the genetic proximity of cupuassu with cacao—that has been thoroughly studied during the last 10 years [18–21]–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.
Considering that in Brazil, the main phytopathological problem that affects the Theobroma genus is the witches’ broom disease—caused by the hemibiotrophic basidiomycete Moniliophthora perniciosa –the cupuassu breeding program should integrate the selection of lines that present both pulp/seed quality and resistance to this fungus. Such selection could be assisted by microsatellites (SSRs) markers that are short repeat motifs with high polymorphism due to indel mutation-type in one or more repeats . SSRs distribution is considered as nonrandom across both coding and noncoding regions of genomic DNA, and some of these SSR structures are important for different cell function (e.g. gene transcription, chromatin organization, DNA replication, cell cycle), indicating that some of the SSR groups may not be neutral . In plant genetics, the SSRs were preferred due to their high variability, abundance, multiallelic nature, reproducibility, polymorphism, transferability as well as their codominant inheritance, chromosome-specific location and wide genomic distribution [23–25]. SSRs, in many species, were widely used for genetic diversity studies, molecular mapping, molecular fingerprint and conservation strategies .
When these SSRs are identified in expressed sequence tags (ESTs), the selection of interesting plant genotypes could be quite efficient mainly because the markers are physically associated to coding regions and can enhance the evaluation of plant populations by enabling the variation assay in expressed genes with known function . With the advent of low cost next generation sequencing (NGS) technologies, it is now possible to easily obtain thousands of ESTs that could be the main source for in silico SSR identification (then named EST-SSRs). Identification of EST-SSRs is also important in the study of different species from the same genus [28–32], in which gene function and biological processes could be conserved [24, 33] and may be related to the same responses to biotic and/or abiotic stresses. Therefore, the transferability of SSRs or EST-SSRs between species may support the idea of similar existing function, as well as to contribute to comparative genomics and diversity analysis [34–36].
For this reason, herein, we focused on: i) the identification and description of SSRs from new generation sequencing-obtained ESTs of cupuassu; ii) the analysis of the related EST function; iii) the validation of the SSRs on cupuassu genotypes with varied pulp quality and resistance to witches’ broom disease and diversity study in relation to both characteristics; iv) the transferability of cupuassu SSR to cacao genotypes. To our knowledge this is the first work involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transfer from cupuassu to cacao.
Material and Methods
Cupuassu genotypes used for EST-SSR validation were selected focusing on subsequent applications in breeding program for pulp quality improvement and/or witches’ broom disease resistance. Sixteen cupuassu genotypes from Embrapa Amazonia Oriental were used (Tables 1 and 2) in this study. Among them, fourteen were resistant to witches’ broom disease and two susceptible (Table 2; personal communication R.M. Alves). The genotypes 174 (Coari) and 1074, resistant and susceptible to witches’ broom disease, respectively, were the genitors of several of the progenies used in the breeding programs in Brazil (Table 1) . For marker transferability analysis, three Theobroma cacao L. genotypes, from Ceplac (Bahia, Brazil) were used: two resistant, SCA6 and TSH 516, and one susceptible, ICS1. The TSH 516 genotype corresponds to the SCA6 x ICS1 cross .
AM: Amazon State from Brazil; AP: Amapá State from Brazil; PA: Pará State from Brazil.
Cupuassu pulp quality analyses
For the pulp quality analyses, five cupuassu fruits were harvested from three different plants (n = 15) for each of the sixteen cupuassu genotypes described (Table 2). For the evaluation of the pulp characteristics (°Brix, acidity, humidity and pH), 20 g of pulp from each fruit were collected and analyzed as previously described . The Brix was determined using a refractometer PR-101 (ATAGO). The total acidity, expressed in citric acid percentage, was determined by titration using 0.1 N NaOH. The pH was determined using a Horiba F-21 pH-meter. For the determination of humidity, the samples were oven dried at 105°C until weight stabilization.
EST sequencing, EST-SSR identification, and primer design
In this study, pulp and seed of the cupuassu genotype (Coari 174) (Theobroma grandiflorum [Willd. ex Spreng.] Schumm.; see also Plant material) grown at the experimental station of Embrapa Amazonia Oriental (Belém, Pará, Brazil) were sequenced using the 454 platform / Roche Applied Sciences. The raw sequences were trimmed and assembled using the est2assembly  and Mira  software resulting on 8,330 contig sequences. The sequences are available on the cupuassu restricted databases at http://lbi.cenargen.embrapa.br/cupuacu/. The ESTs were screened for the presence of SSRs using the MISA software  according to the following criteria: i) nucleotide motif/minimum number of repeats of 1/10, 2/6, 3/4, 4/2, 4/3, 5/3, 6/5, 7/2, 8/2 and 9/2; and ii) maximum difference between two SSRs of 100 bp. For putative function determination and annotation, EST sequences containing SSRs were compared with the public sequence database using BLASTX against the non-redundant (NR) protein database (http://www.ncbi.nih.gov/BLAST/; ) and with the cacao protein-coding sequence database (http://cocoagendb.cirad.fr; ). Alignments showing similarity with an expected value (e-value) ≤1.10−7 were considered significant. The GO annotation for the ESTs containing SSRs were performed using Gene Ontology Consortium tools (http://www.geneontology.org/)  and then manually inspected and classified as previously described . The primers were designed using the Primer3 software (http://primer3.wi.mit.edu/) according to the following criteria: i) amplicon size of 100–300 bp; ii) primer length of 17–23 bases; iii) melting temperature of 56–60°C; and iv) GC content of 40%-60%. See Fig 1 for the general scheme of data mining for SSR identification.
Location of the EST-SSR in relation to the coding sequence of the cDNA
The open reading frame (ORF) of the 70 chosen ESTs was determined using the ORF Finder program (http://www.ncbi.nlm.nih.gov/gorf/gorf.html) and by comparison with cacao genome (http://cocoagendb.cirad.fr; ), and the SSR was localized in relation to the ORF. The possible locations were: in the 5’ untranslated region (5’UTR), in the ORF region, or in the 3’ untranslated region (3’UTR). In some cases, due to the EST sequence length or quality, it was not possible to clearly determine the ORF and consequently the location of the SSR.
DNA extraction, PCR amplification and electrophoresis conditions
Cupuassu and cacao DNA were extracted from young leaves as previously described  and quantified using Nanodrop 2000 (Thermo Scientific). The optimization phase of the 77 primers designed was performed using the cupuassu genotypes 174 and 1074 (see Plant material). For the optimization phase, PCR was performed in 13 μl containing 7.5 ng of DNA, 0.25 mmol.l-1 of each dNTPs, 10 mmol.l-1 of Tris-HCl pH 8.3, 50 mmol.l-1 of KCl, 2 mmol.l-1 of MgCl2, 0.2 μmol.l-1 of each primer, and 1U of Taq DNA polymerase (Phoneutria). Amplifications were performed using the Mastercycler PCR 5333 thermocycler (Eppendorf), using the following conditions: 96°C for 2 min, 30 cycles at 94°C for 1 min, 58°C for 1 min, 72°C for 1 min, and a final extension step at 72°C for 7 min. Amplified fragments were analyzed by electrophoresis on 4% denaturing TBE acrylamide gels. Polymorphism was evaluated by scoring the SSR bands. When comparing the genotypes, the presence or absence of a determined band (similar size) indicated similarity or dissimilarity between genotypes, respectively. The 10-bp molecular marker (Invitrogen) was used as a reference to score the bands. For the confirmation of the polymorphic primers, the amplifications were made on the 16 cupuassu genotypes (Table 1). PCR was performed as described above, excepted for the primers that were labelled with the M13 tail, and with the increase in the reaction of 0.2 μmol.l-1 of M13 primer labelled with NEDTM fluorescence, and 10 μmol.l-1 of 6-FAM. The amplification products were analyzed on the ABI3500 sequencer (Applied Biosystems) using GeneScan™ 500 LIZ™ dye (Life Technologies) as internal size standard. The allele size was defined using the GeneMarker software. The transferability of the developed EST-SSR primers was carried out by cross-species amplification on genomic DNA of three T. cacao genotypes (SCA6, ICS1, TSH516) using the same PCR and electrophoretic conditions (4% denaturing TBE acrylamide gel) as described above.
Sequencing of amplicons for marker confirmation
PCR amplifications were carried out in 20 μl reaction volume containing PCR buffer 1X (Invitrogen), 0.375 mM of each primer (see S1 Table), 10 ng/μl of cupuassu DNA (genotypes 1074 and 174) and 0.5 U of Taq polymerase (Invitrogen). Thermocycling conditions consisted of an initial melt at 95°C for 5 min followed by 28 cycles of 95°C for 30 s, 58°C for 90 s, 72°C for 30 s and a final extension step of 72°C for 10 min. All amplifications were performed in a MyCycler thermocycler (Bio-Rad Laboratories). PCR amplification reactions were checked on electrophoresis on 1.8% agarose gel stained with Gel-red I (Invitrogen). PCR products were cleaned with ExoSap-IT (USB) according to the manufacturer’s instructions. Sequencing was performed on the ABI3100 equipment (Applied Biosystems) at Ceplac (Bahia, Brasil). The confirmation of the SSR marker was based on the comparison of number of repeated sequences of each allele among the different genotypes.
Genetic diversity and statistical analysis
The amplified SSR DNA bands representing different alleles were scored on the different genotypes. The genetic diversity parameters were assessed in terms of observed number of alleles (Na), observed heterozygosity (Ho), and expected heterozygosity (He) using the Genetic Data Analysis software . Polymorphic information content (PIC) was obtained for each locus as previously described  and null alleles were examined using Micro-checker software, v.2.2.3 . Factorial Component Analysis (FCA) was made with the GENETIX software . Correlation test between molecular data and pulp quality or resistance to witches’ broom disease was realized using the SAS program .
In silico comparison of Theobroma grandiflorum loci with Theobroma cacao var. Criollo
For cupuassu/cacao loci comparison, T. grandiflorum ESTs were compared to cacao genome var. Criollo (CacaoGenDB; http://cocoagendb.cirad.fr) using the blastn tool of the CacaoGenDB configured with the following parameters: blast against gene sequences (including UTRs and introns) and expected e-value of 1.10−10 . Specific repeat motifs observed in cupuassu loci were searched in the corresponding region of the cacao sequence (ORF or UTRs). Primers used for SSR analysis in cupuassu and for transferability study in cacao were also blasted on the cacao genome using the specific Primer Blaster tool from CocoaGenDB, with an acceptability of up to three mismatches. Each cupuassu EST and the corresponding cacao sequences were compared and aligned using the Clustal Omega program (http://www.ebi.ac.uk/Tools/msa/clustalo/).
Frequency, distribution and function of SSRs in cupuassu ESTs
Among a total of 8,330 EST sequences from cupuassu (pulp and seeds), 1,517 ESTs containing 1,899 SSRs were identified (Fig 1). Two-hundred and eighty ESTs contained more than one SSR (data not shown). From the 1,899 EST-SSRs, nine types of motifs were identified: mononucleotides (9%), dinucleotides (7.5%), trinucleotides (25.4%), tetranucleotides (10.7%), pentanucleotides (2.0%), hexanucleotides (0.3%), heptanucleotides (29.3%), octanucleotides (8.2%) and nonanucleotides (7.6%) (Fig 2A). Within the mononucleotides, A and T were the most frequents (4.53% and 4.27%, respectively); within the dinucleotides, AT, AG and TC were the most frequent (1.58%, 1.47% and 1.42%, respectively), followed by the GAA (1.32%), AAG (1.26%), CTT (1.21%), TCT and TTC (1.16%) trinucleotides (S2 Table). The tetra-, penta-, hexa-, hepta-, octa- and nonanucleotides presented similar low frequency, mostly <0.7% (S2 Table). The motifs were found with a minimum and maximum of 2 and 19 repeats, respectively (Fig 2B, S2 Table). From the 1,517 EST-SSRs, 44.6, 17.8, 11.3 and 7.75% presented 2, 4, 3 and 10 repeats, respectively (Fig 2B). The other highest categories were 5, 6, 7, 8 and 11 repeats (6%, 4.1%, 2.3%, 1.7% and 1.3%, respectively) followed by the lowest categories (12, 9, 13, 14, 15, 16, 17, 19 repeats, all <1%; Fig 2B). The mono-, di- and trinucleotides were the most repeated (repeat number 6 to 19; Fig 2C). Tetranucleotides were repeated three to six times, pentanucleotides three to five times, hexanucleotides five times, hepta- and nonanucleotides two to four times and octanucleotides two times (Fig 2C). From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation focusing mainly on sequences potentially involved in the pulp and seed quality characteristics or development, but also in other potentially interesting regulating sequences (e.g. transcription factors) or sequences related to resistance (Fig 3; S1 Table). From these, 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. The other categories corresponded to 7.14% (Fig 3). The 70 selected ESTs contained 77 SSRs for which primers were designed (Fig 1; S1 Table). Considering these 77 SSRs in relation to the coding sequence position, 33.7% were found in the ORF, 22.1% in the 5’UTR and 11.7% in the 3’UTR; for 32.5% of the SSRs, the localization in relation to the ORF was not possible (Fig 4A). The 5’UTR contained mono-, di-, tri-, tetra- and heptanucleotides, while the 3’UTR contained mono-, di-, and trinucleotides (Fig 4B). The ORF mainly contained tri- and mononucleotides, followed by di-, tetra- and nonanucleotides (Fig 4B).
A. Frequency of EST-SSRs with mono-, di-, tri-, tetra-, penta-, hexa-, hepta-, octa- and nonanucleotide motifs. B. Frequency of EST-SSRs with 2 to 19 repeat motifs. C. Frequency of mono-, di-, tri-, tetra-, penta-, hexa-, hepta-, octa- e nonanucleotide motifs for each repeat number category.
The frequency of each category was indicated.
Polymorphism detection in cupuassu genotypes and diversity analysis
From the 77 SSRs selected, 22 were pre-selected, and finally 11 were confirmed as polymorphic (Fig 1, Table 3) when tested in the cupuassu genotypes described in Table 1. The number of alleles per EST-SSR ranged from 2 to 6 with an average of 3.18. The observed heterozygosity (Ho) values ranged from 0 to 0.88 with an average of 0.51, and the expected heterozygosity (He) values ranged from 0.083 to 0.76 with an average of 0.5. PIC values of the EST-SSR ranged from 0.32 to 0.7 with an average of 0.5 (Table 3). Eight of the SSRs were located in the ORF of the corresponding EST (72.7%) and 3 in the 5’UTR (27.3%) (Table 3). These 11 markers used in the genetic diversity analysis revealed a clusterization according to the resistance vs susceptibility of the cupuassu genotypes; the susceptible genotypes 62 and 1074 were discriminated from the others (Fig 5). Interestingly, the genotype 1074, that present the higher deviation, also came from a different geographic origin (Parintins—AM; Table 1) than the other genotypes. The diversity analysis also showed a tendency of genotype clusterization according to the SST/ATT parameter, discriminating into two groups: i) SST/ATT ≤ 7.0 (genotypes 32, 44, 46, 48, 51, 56, 61, 62, 215, 1074); ii) SST/ATT > 7.0 (genotypes 42, 47, 57, 63, 64 and 174) (Fig 5, Table 2).
The susceptible cupuassu genotypes were indicated by squares (62 and 1074); the other ones were susceptible and indicated by diamonds. The cupuassu genotypes with SST/ATT parameter >7.0 were indicated in red; those with SST/ATT parameter ≤ 7.0 were indicated in blue. Orange circle separated the susceptible genotypes to the resistant ones (green circle).
Transferability of EST-SSRs
The transferability of the cupuassu EST-SSRs to T. cacao was analyzed by cross-species amplification. From the 22 pre-selected EST-SSRs (polymorphic or not in cupuassu; Fig 1), 17 amplified cacao DNA, which corresponds to a transferability rate of 77% (Table 4). The amplifications were within the expected size, and 14 of the 17 cupuassu SSRs were polymorphic in cacao (Table 4). From the 11 EST-SSRs polymorphic in cupuassu, 8 were transferable to cacao and 6 were also polymorphic in this species (Tables 3 and 4). The 11 polymorphic locus of cupuassu were also compared to the cacao genome database (cacao var. Criollo) and several homolog sequences were encountered (Table 5). Eight cupuassu loci presented polymorphism when compared to cacao: six of them presented the same repeat motif, but with less repeats (c2723, c5718, c70, c180, c193B, c203B) for at least one homolog sequence, and 2 of them did not present the repeat motif (c3202/3202B, c733; Table 5). Two loci showed the same motif/repeat number in cupuassu and cacao (c339, c431B; Table 5). The in silico analysis showed that some primers were transferable allowing the identification of a polymorphic locus (e.g. c2723; Fig 6A, Tables 4 and 5). Some primers were transferable but the locus was non-polymorphic (e.g. c339; Fig 6B, Tables 4 and 5). The two other situations corresponded to primers that were not able to amplify the cacao gene, whatever if the locus was polymorphic or not (e.g. c193, c733; Fig 6C, Tables 4 and 5). It is interesting to note that some loci were transferable to cacao but presented different polymorphism depending on the cacao variety analyzed: for example, the c431B locus is polymorphic in SCA6/ICS1/TSH516 varieties (Table 4) but did not presented potential polymorphism in the in silico analysis using the Criollo variety (Table 5).
A. Transferable primers and polymorphic locus. B. Transferable primers and non-polymorphic locus. C. Untransferable primer and polymorphic locus. D. Untransferable and non-polymorphic locus.
In this article we obtained and analyzed a large number of ESTs from Theobroma grandiflorum (cupuassu) with the objective to identify new SSR markers useful for marker assisted selection in cupuassu with respect to both quality and resistance to witches’ broom disease. Both of these characteristics are important from a practical point of view for increasing the development of cupulate production or pulp-derived products, as an alternative to chocolate production declared in crisis [12, 13]. Moreover, the cupuassu breeding program needs the insertion of new markers for genetic fine mapping and selection of genome regions specifically involved in quality and/or resistance, in order to complement previous genetic analysis of cupuassu population [14, 15, 17]. Here we obtained SSR markers from NGS ESTs of cupuassu genotypes with different levels of resistance to witches’ broom disease and pulp quality. It is important to highlight that we produced the first EST database from cupuassu as well as the first EST-SSRs for this species. In cacao, more than 200,000 ESTs from different plant genotypes and organs submitted or not to different biotic and abiotic stresses [18, 44, 51–54], and more than 2,000 SSRs (whose 1631 [81%] were EST-SSRs) were already obtained (S3 Table) whereas in cupuassu, only genomic SSR were previously found (unpublished data, R.M. Alves). Furthermore, ESTs for use in molecular studies related to pulp or bean quality from the Theobroma genus are rare [18, 53].
Under these conditions, our results are highly relevant due to the large amount of ESTs generated (8,330) as well as the functional data associated to some of the EST-SSR identified (Fig 3). SSRs were detected in 18% of the ESTs analyzed (Fig 1), which corresponds to a high frequency comparing to data produced from other crops [24, 55, 56] with similar technical approaches (e.g. NGS, Misa analysis). Here, the highest proportions of EST-SSRs identified were hepta- and trinucleotides (29.3% and 25.4%, respectively; Fig 2A). Trinucleotides were generally considered as the most abundant class of SSRs in plant ESTs [27, 55–57] but other works also indicated dinucleotides [33, 58]. Since the addition or deletion of three nucleotides within translated regions usually does not affect the ORFs, it is not uncommon to detect a high abundance of these repeat motifs in EST-SSRs [59, 60], as we observed in our results (Fig 4B). But generally, it is accepted that the abundance of one or other SSR class may be due to the search criteria used for EST mining [26, 58, 61]. Nevertheless, the search criteria used for EST mining influences the frequency of the repeat number of the SSRs motifs; here the most frequent repeat number were 2, 4, 3 and 10 (44.6%, 17.8%, 11.3% and 7.75%, respectively; Fig 2B). Moreover, the SSRs containing the highest repeat numbers (10 to 19) were also the ones that contained exclusively mono- and dinucleotides (Fig 2C), while the SSRs with the lowest repeat numbers (2 to 6) contained larger motifs (tetra- to nonanucleotides; Fig 2C).
From the 1,899 EST-SSRs identified, 77 were tested as to their polymorphism in 16 cupuassu genotypes and 11 were polymorphic (Table 3). The PIC values (average 0.5; Table 3) observed here was closed to the ones found in cacao and cupuassu studies using genomic SSR [14, 62]. Such polymorphism was associated to genetic diversity of cupuassu according to the resistance parameter (characteristic that better discriminated the cupuassu genotypes) and, to a lesser extent, to SST/ATT parameter (Fig 5). The ATT data found in our study were consistent with the results obtained in other evaluations [63, 64], and 13 of the 16 genotypes studied (81%) presented ATT values higher than the minimum required (1.5; Table 2) . The pH of cupuassu genotypes used here also showed values closed to those observed in other studies [63, 64, 66, 67] and all the genotypes (100%) presented values higher as to the required limit for good cupuassu quality (2.6; Table 2) . The SST content also were consistent with other studies  and higher to the required limit  (Table 2); it is important to note that the harvesting period could influence the pulp quality as observed in other analyses where the SST values were lower than the expected values [64, 67]. Genotypes 63 and 64 showed the highest SST/ATT and for this reason may be considered as good candidate for breeding programs (Table 2). Generally, these data suggested that the cupuassu germplasm collection, as well as the cupuassu breeding program, generated material with high genetic variability related to pulp quality, and that the marker found here could be used for subsequent analysis of new crosses for cupuassu population and potentially for use in other Theobroma species.
Because EST-SSRs are generated from coding and expressed sequences, which are generally well conserved between species, the possibility to find conserved primers flanking the repeats—and possibly polymorphic—motifs, is high [26, 41]. Here we observed in vitro and in silico marker transferability between cupuassu and different varieties of cacao (resistant and susceptible to witches’ broom disease; Tables 4 and 5). Generally, the in silico analysis confirmed the in vitro results, and different transferability situations were observed (Table 5 and Fig 6). Transferability requires not only polymorphism between cuapuassu and cacao sequences, but also good primer design, able to amplify the polymorphic regions (Fig 6A). Therefore, the availability of the cacao genome and the study of the family of genes with interesting function can help to design primers able to amplify—and consequently to be efficiently transferred—between different species from the same genus. It is important to note that we report the first cupuassu-cacao marker transferability; whereas only a few studies of transferability between the two Theobroma species have been already reported and always from cacao to cupuassu [38, 68]. The first report used cacao markers previously developed  (S3 Table) to define the natural mating system of Theobroma grandiflorum in its putative center of diversity  while the second specifically deals with marker transferability from cacao to cupuassu . The polymorphism rate calculated in these studies was lower (43.8%; Alves et al., 2006) than the one obtained here from EST-SSRs (77%; Fig 1, Table 4). Generally, in the work presented here we obtained a higher transferability (77%) than presented in other tests regarding marker transferability between correlated species [31, 35, 70]. The success of transferability between species as observed for coffee , rice , bananas , barley  and gerbera  is due to saving time and costs in the development of new markers.
Here we obtained the first EST-SSRs from cupuassu. These markers were polymorphic in cupuassu and allowed diversity analysis of the studied genotypes, mainly in relation to pulp quality. Moreover, these markers were transferable to cacao genotypes. The detection of EST-SSRs was also an important point regarding sequence function; the sequences containing ESTs will be good candidates for functional studies related to pulp and seed quality as well as to resistance to witches’ broom disease. Moreover, these markers may contribute to develop or saturate both the cupuassu and cacao genetic maps, respectively.
S1 Table. Characteristics of the 77 EST-SSRs designed in this study.
S2 Table. Frequency of different SSR types identified in 1517 ESTs from cupuassu seeds and pulp.
We thank Raner José Santana Silva (Embrapa Cenargen) for technical support in RNA extraction prior NGS, Dr. Fernanda Amato Gaiotto and Horley Vitória Ribeiro (UESC) for supplying reagents for SSR analysis, Didier Clement (Cirad) for kindly providing cacao DNA, and Dr. Claudia Fortes Ferreira (Embrapa CNPMF, Brazil) for English language revision.
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.
- 1. Clement C, De Cristo-Araújo M, Coppens D’Eeckenbrugge G, Alves Pereira A, Picanço-Rodrigues D. Origin and domestication of native amazonian crops. Diversity. 2010;2(1):72–106.
- 2. Calzavara BBG, Muller CH, Kahwage ONN. Fruticultura Tropical: o cupuaçuzeiro—cultivo, beneficiamento e utilização do fruto. Belém: EMBRAPA-CPATU; 1984. 101 p.
- 3. Cohen KO, Jackix MNH. Estudo do liquor de cupuaçu. Food Science and Technology (Campinas). 2005;25:182–90.
- 4. Lannes SCS, Medeiros ML, Gioielli LA. Physical interactions between cupuassu and cocoa fats. Grasas y Aceites. 2003;54(3): 253–8.
- 5. Vasconcelos MNL, da Silva ML, Maia JGS, GO R.. Estudo químico de sementes do cupuaçu. Acta Amazonica. 1975;5:293–5.
- 6. Lannes SCdS, Medeiros ML. Processamento de achocolatado de cupuaçu por spray-dryer. Revista Brasileira de Ciências Farmacêuticas. 2003;39:115–23.
- 7. Lannes SCdS, Medeiros ML, Amaral RL. Formulação de "chocolate" de cupuaçu e reologia do produto líquido. 2002. 2002;38(4):7. Epub 2002-12-01.
- 8. Reisdorff C, Rohsius C, Claret de Souza AdG, Gasparotto L, Lieberei R. Comparative study on the proteolytic activities and storage globulins in seeds of Theobroma grandiflorum (Willd ex Spreng) Schum and Theobroma bicolor Humb Bonpl, in relation to their potential to generate chocolate-like aroma. Journal of the Science of Food and Agriculture. 2004;84(7):693–700.
- 9. de Oliveira TB, Genovese MI. Chemical composition of cupuassu (Theobroma grandiflorum) and cocoa (Theobroma cacao) liquors and their effects on streptozotocin-induced diabetic rats. Food Research International. 2013;51(2):929–35.
- 10. Yang H, Protiva P, Cui B, Ma C, Baggett S, Hequet V, et al. New bioactive polyphenols from Theobroma grandiflorum (“Cupuaçu”). Journal of Natural Products. 2003;66(11):1501–4. pmid:14640528
- 11. de Oliveira TB, Rogero MM, Genovese MI. Poliphenolic-rich extracts from cocoa (Theobroma cacao L.) and cupuassu (Theobroma grandiflorum Willd. Ex Spreng. K. Shum) liquors: A comparison of metabolic effects in high-fat fed rats. PharmaNutrition. 2015;3(2):20–8.
- 12. Sayid R. Chocolate could run out in 2020 due to worldwide shortage of cocoa. The Daily Mirror online. 2013 31/12/2013; Sect. World News.
- 13. Wexler A. World's sweet tooth heats up cocoa. Growing demand from emerging markets is pushing up prices for key ingredient in chocolate. The Wall Street Journal. 2014 13/02/2014.
- 14. Alves RM, Silva CRS, Silva MSC, Silva DCS, Sebbenn AM. Diversidade genética em coleções amazônicas de germoplasma de cupuaçuzeiro [Theobroma grandiflorum (Willd. ex Spreng.) Schum.]. Revista Brasileira de Fruticultura. 2013;35:818–28.
- 15. Alves RM, Resende MDV, Bandeira BS, Pinheiro TM, Farias DCR. Evolução da vassoura-de-bruxa e avaliação da resistência em progênies de cupuaçuzeiro. Revista Brasileira de Fruticultura. 2009;31:1022–32.
- 16. Kuhn DN, Figueira A, Lopes U, Motamayor JC, Meerow AW, Cariaga K, et al. Evaluating Theobroma grandiflorum for comparative genomic studies with Theobroma cacao. Tree Genetics & Genomes. 2010;6(5):783–92.
- 17. Alves RM, Resende MDVd, Bandeira BdS, Pinheiro TM, Farias DCR. Avaliação e seleção de progênies de cupuaçuzeiro (Theobroma grandiflorum), em Belém, Pará. Revista Brasileira de Fruticultura. 2010;32:204–12.
- 18. Argout X, Fouet O, Wincker P, Gramacho K, Legavre T, Sabau X, et al. Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions. BMC Genomics. 2008;9(1):512.
- 19. Argout X, Salse J, Aury J-M, Guiltinan MJ, Droc G, Gouzy J, et al. The genome of Theobroma cacao. Nat Genet. 2011;43:101–8. pmid:21186351
- 20. Feltus F, Saski C, Mockaitis K, Haiminen N, Parida L, Smith Z, et al. Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes. BMC Genomics. 2011;12(1):379.
- 21. Micheli F, Guiltinan M, Gramacho KP, Wilkinson MJ, Figueira AVdO, Cascardo JCdM, et al. Chapter 3—Functional genomics of cacao. In: Jean-Claude K, Michel D, editors. Advances in Botanical Research. Volume 55: Academic Press; 2010. p. 119–77.
- 22. Aime MC, Phillips-Mora W. The causal agents of witches' broom and frosty pod rot of cacao (chocolate, Theobroma cacao) form a new lineage of Marasmiaceae. Mycologia. 2005;97(5):1012–22. pmid:16596953
- 23. Li Y-C, Korol AB, Fahima T, Beiles A, Nevo E. Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Molecular Ecology. 2002;11(12):2453–65. pmid:12453231
- 24. Su Haq, Jain R, Sharma M, Kachhwaha S, Kothari SL. Identification and characterization of microsatellites in Expressed Sequence Tags and their cross transferability in different plants. International Journal of Genomics. 2014;2014:863948. PMC4217358. pmid:25389527
- 25. Agarwal M, Shrivastava N, Padh H. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Reports. 2008;27(4):617–31. pmid:18246355
- 26. Varshney R, Graner A, Sorrells M. Genic microsatellite markers in plants: features and applications. Trends in Biotechnology. 2005;23(1):48–55. pmid:15629858
- 27. Nicot N, Chiquet V, Gandon B, Amilhat L, Legeai F, Leroy P, et al. Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theoretical and Applied Genetics. 2004;109(4):800–5. pmid:15146317
- 28. Taniguchi F, Fukuoka H, Tanaka J. Expressed sequence tags from organ-specific cDNA libraries of tea (Camellia sinensis) and polymorphisms and transferability of EST-SSRs across Camellia species. Breeding Science. 2012;62(2):186–95. PMC3405963. pmid:23136530
- 29. Fan L, Zhang MY, Liu QZ, Li LT, Song Y, Wang LF, et al. Transferability of Newly Developed Pear SSR Markers to Other Rosaceae Species. Plant Molecular Biology Reporter / Ispmb. 2013;31(6):1271–82. PMC3881569.
- 30. Lee G-A, Song J, Choi H-R, Chung J-W, Jeon Y-A, Lee J-R, et al. Novel microsatellite markers acquired from Rubus coreanus Miq. and cross-amplification in other Rubus Species. Molecules. 2015;20(4):6432–42. pmid:25867828
- 31. Santos JCS, Barreto MA, Oliveira FA, Vigna BBZ, Souza AP. Microsatellite markers for Urochloa humidicola (Poaceae) and their transferability to other Urochloa species. BMC Research Notes. 2015;8:83. PMC4365966. pmid:25889143
- 32. Adal A, Demissie Z, Mahmoud S. Identification, validation and cross-species transferability of novel Lavandula EST-SSRs. Planta. 2015;241(4):987–1004. pmid:25534945
- 33. Sahu J, Das Talukdar A, Devi K, Choudhury MD, Barooah M, Modi MK, et al. E-microsatellite markers for Centella asiatica (Gotu Kola) genome: validation and cross-transferability in Apiaceae family for plant omics research and development. OMICS: A Journal of Integrative Biology. 2015;19(1):52–65. pmid:25562200
- 34. Shrivastava D, Verma P, Bhatia S. Expanding the repertoire of microsatellite markers for polymorphism studies in Indian accessions of mung bean (Vigna radiata L. Wilczek). Molecular Biology Reports. 2014;41(9):5669–80. pmid:24913033
- 35. Raveendar S, Lee G-A, Jeon Y-A, Lee Y, Lee J-R, Cho G-T, et al. Cross-amplification of Vicia sativa subsp. sativa microsatellites across 22 Other Vicia Species. Molecules. 2015;20(1):1543–50. pmid:25608853
- 36. Bhawna , Abdin MZ, Arya L, Verma M. Transferability of cucumber microsatellite markers used for phylogenetic analysis and population structure study in Bottle Gourd (Lagenaria siceraria (Mol.) Standl.). Applied Biochemistry and Biotechnology. 2015;175(4):2206–23. pmid:25471016
- 37. Faleiro FG, Queiroz VT, Lopes UV, Guimarães CT, Pires JL, Yamada MM, et al. Mapping QTLs for witches' broom (Crinipellis perniciosa) resistance in cacao (Theobroma cacao L.). Euphytica. 2006;149(1–2):227–35.
- 38. Alves RM, Garcia AAF, Cruz ED, Figueira A. Seleção de descritores botânico-agronômicos para caracterização de germoplasma de cupuaçuzeiro. Pesquisa Agropecuaria Brasileira. 2003;38:807–18.
- 39. Papanicolaou A, Stierli R, ffrench-Constant R, Heckel D. Next generation transcriptomes for next generation genomes using est2assembly. BMC Bioinformatics. 2009;10(1):447.
- 40. Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Müller WEG, Wetter T, et al. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Research. 2004;14(6):1147–59. pmid:15140833
- 41. Thiel T, Michalek W, Varshney R, Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics. 2003;106(3):411–22. pmid:12589540
- 42. Altschul S, Gish W, Miller W, Myers E, Lipman D. Basic local alignment search tool. Journal of Molecular Biology. 1990;215(3):403–10. pmid:2231712
- 43. Consortium GO. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Research. 2004;32(suppl 1):D258–D61.
- 44. Gesteira AS, Micheli F, Carels N, Da Silva A, Gramacho K, Schuster I, et al. Comparative analysis of expressed genes from cacao meristems infected by Moniliophthora perniciosa. Ann Bot. 2007;100(1):129–40. Epub 2007/06/15. mcm092 [pii] pmid:17557832; PubMed Central PMCID: PMC2735303.
- 45. Doyle JJ, Doyle JL. Isolation of plant DNA from fresh tissue1990.
- 46. Lewis PO, Zaykin D. Genetic Data Analysis. 1.0. ed2001.
- 47. Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME. Optimizing parental selection for genetic linkage maps. Genome. 1993;36(1):181–6. pmid:18469981.
- 48. Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P. micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes. 2004;4(3):535–8.
- 49. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F. GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Montpellier (France): Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II; 1996–2004
- 50. SAS I. SAS/STAT user’s guide. Release 6.03 ed. SAS Institute Inc., Cary, NC 10281988.
- 51. Leal G, Albuquerque P, Figueira A. Genes differentially expressed in Theobroma cacao associated with resistance to witches' broom disease caused by Crinipellis perniciosa. Molecular Plant Pathology. 2007;8(3):279–92. pmid:20507499
- 52. Verica J, Maximova S, Strem M, Carlson J, Bailey B, Guiltinan M. Isolation of ESTs from cacao (Theobroma cacao L.) leaves treated with inducers of the defense response. Plant cell reports. 2004;23(6):404–13. pmid:15340758
- 53. Jones P, Allaway D, Gilmour D, Harris C, Rankin D, Retzel E, et al. Gene discovery and microarray analysis of cacao (Theobroma cacao L.) varieties. Planta. 2002;216(2):255–64. pmid:12447539
- 54. Naganeeswaran SA, Subbian EA, Ramaswamy M. Analysis of expressed sequence tags (ESTs) from cocoa (Theobroma cacao L.) upon infection with Phytophthora megakarya. Bioinformation. 2012;8(2):65–9. PMC3282258. pmid:22359437
- 55. Asadi A, Rashidi Monfared S. Characterization of EST-SSR markers in durum wheat EST library and functional analysis of SSR-containing EST fragments. Molecular Genetics and Genomics. 2014;289(4):625–40. pmid:24652471
- 56. Kumari K, Muthamilarasan M, Misra G, Gupta S, Subramanian A, Parida SK, et al. Development of eSSR-Markers in Setaria italica and their applicability in studying genetic diversity, cross-transferability and comparative mapping in Millet and Non-Millet Species. PLoS ONE. 2013;8(6):e67742. PMC3689721. pmid:23805325
- 57. Kantety R, La Rota M, Matthews D, Sorrells M. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Molecular Biology. 2002;48(5–6):501–10. pmid:11999831
- 58. Lima LS, Gramacho KP, Pires JL, Clement D, Lopes UV, Carels N, et al. Development, characterization, validation, and mapping of SSRs derived from Theobroma cacao L.–Moniliophthora perniciosa interaction ESTs. Tree Genetics & Genomes. 2010;6(5):663–76.
- 59. Bosamia TC, Mishra GP, Thankappan R, Dobaria JR. Novel and stress relevant EST derived SSR markers developed and validated in Peanut. PLoS ONE. 2015;10(6):e0129127. pmid:26046991
- 60. Metzgar D, Bytof J, Wills C. Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Research. 2000;10(1):72–80. PMC310501. pmid:10645952
- 61. Aggarwal R, Hendre P, Varshney R, Bhat P, Krishnakumar V, Singh L. Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theoretical and Applied Genetics. 2007;114(2):359–72. pmid:17115127
- 62. Santos R, Clement D, Lemos L, Legravre T, Lanaud C, Schnell R, et al. Identification, characterization and mapping of EST-derived SSRs from the cacao–Ceratocystis cacaofunesta interaction. Tree Genetics & Genomes. 2013;9(1):117–27.
- 63. Gonçalves MVVA, da Silva JPL, Mathias SP, Rosenthal A, Calado VMA. Caracterização fisico-chimica e reologica da polpa de cupuaçu congelada (Theobroma grandiflorum Schum). Perspectivas Online Exatas e Engenharia. 2013; 3(7).
- 64. Santos GM, Maia GA, Sousa PHM, Figueiredo RW, Costa JMC, Fonseca AVV. Atividade antioxidante e correlações com componentes bioativos de produtos comerciais de cupuaçu. Ciência Rural. 2010;40:1636–42.
- 65. Regulamento técnico geral para fixação dos padrões de identidade e qualidade para polpa de fruta conforme consta do Anexo I desta Instrução Normativa., Instrução normativa n°01 (2000).
- 66. Costa MC, Maia GA, Souza Filho MdSM, Figueiredo RWd, Nassu RT, Monteiro JCS. Conservação de polpa de cupuaçu [Theobroma grandiflorum (Willd. Ex Spreng.) Schum] por métodos combinados. Revista Brasileira de Fruticultura. 2003;25:213–5.
- 67. Bueno SM, Lopes MRV, Graciano RAS, Fernandes ECB, Garcia-Cruz CH. Quality evaluation of frozen fruit pulp. Rev Inst Adolfo Lutz. 2002;62(2):121–6.
- 68. Alves RM, Sebbenn AM, Artero AS, Figueira A. Microsatellite loci transferability from Theobroma cacao to Theobroma grandiflorum. Molecular Ecology Notes. 2006;6(4):1219–21.
- 69. Lanaud C, Risterucci AM, Pieretti I, Falque M, Bouet A, Lagoda PJL. Isolation and characterization of microsatellites in Theobroma cacao L. Molecular Ecology. 1999;8(12):2141–3. pmid:10632866
- 70. Wang L, Chen H, Bai P, Wu J, Wang S, Blair M, et al. The transferability and polymorphism of mung bean SSR markers in rice bean germplasm. Molecular Breeding. 2015;35(2):1–10.
- 71. Ferrão L, Caixeta E, Pena G, Zambolim E, Cruz C, Zambolim L, et al. New EST–SSR markers of Coffea arabica: transferability and application to studies of molecular characterization and genetic mapping. Molecular Breeding. 2015;35(1):1–5.
- 72. Backiyarani S, Uma S, Varatharj P, Saraswathi MS. Mining of EST-SSR markers of Musa and their transferability studies among the members of order the Zingiberales. Applied Biochemistry and Biotechnology. 2013;169(1):228–38. pmid:23179283
- 73. Castillo A, Budak H, Varshney RK, Dorado G, Graner A, Hernandez P. Transferability and polymorphism of barley EST-SSR markers used for phylogenetic analysis in Hordeum chilense. BMC Plant Biology. 2008;8:97-. PMC2569940. pmid:18822176
- 74. Gong L, Deng Z. EST-SSR markers for gerbera (Gerbera hybrida). Molecular Breeding. 2010;26(1):125–32.