Cacao biotechnology: current status and future prospects

Selected Mesoamerican Crops - Anti-Obesity Potential and Health Promotion. A Review

Mesoamerica is the center of origin of a great number of food crops that nowadays are part of a healthy diet. Pre-Columbian civilizations utilized more than 90% of these foods as ingredient or in main dishes, as well as for remedies and religious ceremonies. Since several years ago, Mesoamerican foods have been recognized by their outstanding concentration of bioactive compounds, including, phenolic compounds, pigments, essential fatty acids, amino acids, peptides, carbohydrates and vitamins, which provide a great number of health benefits. As a result of their unique composition, these ancient crops have several positive effects, such as hypoglycemic, antioxidant, anti-obesity, anti-inflammatory, anti-ageing, neuroprotective, anti-diarrheal, and anti-hypercholesterolemic capacity. Hence, this review is focused mainly in the anti-obesity and antioxidant potential of some of the most cultivated, harvested, as well as commercialized and consumed, food crops native of Mesoamerica, like, nopal and its fruit (Opuntia ficus indica spp.), chia (Salvia hispanica L.), pumpkin (Cucurbita spp.) and cacao (Theobroma cacao).

Using ddRADseq to assess the genetic diversity of in-farm and gene bank cacao resources in the Baracoa region, eastern Cuba, for use and conservation purposes

The Baracoa region, eastern Cuba, hosts around 80 % of the country cacao (Theobroma cacao L.) plantations. Cacao plants in farms are diverse in origin and propagation, with grafted and hybrid plants being the more common ones. Less frequent are plants from cuttings, TSH progeny, and traditional Cuban cacao. A national cacao gene bank is also present in Baracoa, with 282 accessions either prospected in Cuba or introduced from other countries. A breeding program associated with the gene bank started in the 1990s based on agro-morphological descriptors. The genetic diversity of cacao resources in Baracoa has been poorly described, except for traditional Cuban cacao, affecting the proper development of the breeding program and the cacao planting policies in the region. To assess the population structure and genetic diversity of cacao resources in Baracoa region, we genotyped plants from both cacao gene bank (CG) and cacao farms (CF) applying a new ddRADseq protocol for cacao. After data processing, two SNPs datasets containing 11,425 and 6,481 high-quality SNPs were generated with 238 CG and 135 CF plants, respectively. SNPs were unevenly distributed along the 10 cacao chromosomes and laid mainly in noncoding regions of the genome. Population structure analysis with these SNP datasets identified seven and four genetic groups in CG and CF samples, respectively. Clustering using UPGMA and principal component analysis mostly agree with population structure results. Amelonado was the predominant cacao ancestry, accounting for 49.22 % (CG) and 57.73 % (CF) of the total. Criollo, Contamana, Iquitos, and Nanay ancestries were detected in both CG and CF samples, while Nacional and Marañon backgrounds were only identified in CG. Genetic differentiation among CG (FST ranging from 0.071 to 0.407) was higher than among CF genetic groups (FST: 0.093-0.282). Genetic diversity parameters showed similar values for CG and CF samples. The CG and CF genetic groups with the lowest genetic diversity parameters had the highest proportion of Amelonado ancestry. These results should contribute to reinforcing the ongoing breeding program and updating the planting policies on cacao farms, with an impact on the social and economic life of the region.

Cocoa Apoplastome Contains Defense Proteins Against Pathogens

The apoplast performs important functions in the plant, such as defense against stress, and compounds present form the apoplastic washing fluid (AWF). The fungus Moniliophthora perniciosa, the causal agent of witches' broom disease (WBD) in Theobroma cacao, initially colonizes the apoplast in its biotrophic phase. In this period, the fungus can remain for approximately 60 days, until it changes to its second phase, causing tissue death and consequently large loss in the production of beans. To better understand the importance of the apoplast in the T. cacao-M. perniciosa interaction, we performed the first apoplastic proteomic mapping of two contrasting genotypes for WBD resistance (CCN51-resistant and Catongo-susceptible). Based on two-dimensional gel analysis, we identified 36 proteins in CCN-51 and 15 in Catongo. We highlight PR-proteins, such as peroxidases, β-1,3-glucanases, and chitinases. A possible candidate for a resistance marker of the CCN-51 genotype, osmotin, was identified. The antioxidative metabolism of the superoxide dismutase (SOD) enzyme showed a significant increase (P < 0.05) in the AWF of the two genotypes under field conditions (FD). T. cacao AWF inhibited the germination of M. perniciosa basidiospores (>80%), in addition to causing morphological changes. Our results shed more light on the nature of the plant's defense performed by the apoplast in the T. cacao-M. perniciosa interaction in the initial (biotrophic) phase of fungal infection and therefore make it possible to expand WBD control strategies based on the identification of potential targets for resistance markers and advance scientific knowledge of the disease.

The selenium-independent phospholipid hydroperoxide glutathione peroxidase from Theobroma cacao (TcPHGPX) protects plant cells against damages and cell death

Proteins from the glutathione peroxidase (GPX) family, such as GPX4 or PHGPX in animals, are extensively studied for their antioxidant functions and apoptosis inhibition. GPXs can be selenium-independent or selenium-dependent, with selenium acting as a potential cofactor for GPX activity. However, the relationship of plant GPXs to these functions remains unclear. Recent research indicated an upregulation of Theobroma cacao phospholipid hydroperoxide glutathione peroxidase gene (TcPHGPX) expression during early witches' broom disease stages, suggesting the use of antioxidant mechanisms as a plant defense strategy to reduce disease progression. Witches' broom disease, caused by the hemibiotrophic fungus Moniliophthora perniciosa, induces cell death through elicitors like MpNEP2 in advanced infection stages. In this context, in silico and in vitro analyses of TcPHGPX's physicochemical and functional characteristics may elucidate its antioxidant potential and effects against cell death, enhancing understanding of plant GPXs and informing strategies to control witches' broom disease. Results indicated TcPHGPX interaction with selenium compounds, mainly sodium selenite, but without improving the protein function. Protein-protein interaction network suggested cacao GPXs association with glutathione and thioredoxin metabolism, engaging in pathways like signaling, peroxide detection for ABA pathway components, and anthocyanin transport. Tests on tobacco cells revealed that TcPHGPX reduced cell death, associated with decreased membrane damage and H2O2 production induced by MpNEP2. This study is the first functional analysis of TcPHGPX, contributing to knowledge about plant GPXs and supporting studies for witches' broom disease control.

Evaluation of rations containing bioconverted cacao pod as fiber source for small ruminant

This study aimed to evaluate the potential use of bioconverted cacao pod (BCP) as a substitute for forage in the total mixed ration (TMR) for a small ruminant. In the in vitro experiment, the control TMR (30% forage and 70% concentrate) was substituted with two different levels of BCP (15% and 30%) and two different types of BCP ( BCP-pc and BCP-tv). Based on the in vitro evaluation, the best ration was then chosen for the in vivo experiment, in which male goats were fed a control TMR, the TMR containing 15% BCP-pc (RC), and TMR containing 15% bioconverted palm kernel meal (RP). The results showed that TMRs with 15% BCP-pc and BCP-tv substitution had significantly lower gas production and digestibility than the control ration. However, the TMR with 15% or 30% BCP substitution showed no significant difference in rumen fermentation characteristics, methane production, and total protozoa. In the in vivo experiment, the RC showed no significant difference in all nutrient intakes, the average daily gain of animals, feed conversion ratio value, and crude fiber digestibility but reduced dry and organic matter digestibility. In comparison, the RP resulted in reduced parameters. Therefore, the study concluded that BCP-pc at a level of 15% could be used as a substitute for forage in TMR for male goats without compromising the fermentability of rumen, nutrient intakes, and their average daily gain and feed conversion ratio. Overall, this study suggests the potential of BCP-pc as an alternative feed ingredient.

Fungal Pathogens of Cacao in Puerto Rico

Cacao production is a rapidly expanding industry in Puerto Rico, with new farmers planting ~20,000 trees in the past few years. To determine the etiology and extent of diseases affecting cacao in Puerto Rico, a survey was performed at eight sites around the island. Pod rot and/or branch dieback were observed at all sites. Most organisms isolated from symptomatic pod and stem samples were identified as Diaporthe spp. (48%) and Lasiodiplodia spp. (25%) based on sequences of the internal transcribed spacer and large subunit regions. Within these genera, Diaporthe tulliensis and Lasiodiplodia theobromae were the most prevalent species and were used in inoculation studies to determine their relative virulence on pods and stems. Phytophthora palmivora served as a positive control due to its well-established pathogenicity in all tissues. On pods, L. theobromae and P. palmivora caused significantly larger lesions (6.1 and 5.9 cm, respectively) than D. tulliensis (2.7 cm) four days post-inoculation. All three species caused disease on stems, with no differences found among species. Although P. palmivora was thought to be the primary pathogen affecting cacao in Puerto Rico, this study identifies L. theobromae and D. tulliensis as the common pathogens on the island. This improved understanding will help scientists and farmers control disease by selecting fungicides effective against both oomycetes and fungi.

The damage caused by Cd toxicity to photosynthesis, cellular ultrastructure, antioxidant metabolism, and gene expression in young cacao plants are mitigated by high Mn doses in soil

Manganese (Mn) is one of the essential mineral micronutrients most demanded by cacao. Cadmium (Cd) is highly toxic to plants and other living beings. There are indications that Mn can interact with Cd and mitigate its toxicity. The objective of this study was to evaluate the action of Mn on the toxic effect of Cd in young plants of the CCN 51 cacao genotype, subjected to different doses of Mn, Cd, and Mn+Cd in soil, through physiological, biochemical, molecular, and micromorphological and ultrastructural changes. High soil Mn doses favored the maintenance and performance of adequate photosynthetic processes in cacao. However, high doses of Cd and Mn+Cd in soil promoted damage to photosynthesis, alterations in oxidative metabolism, and the uptake, transport, and accumulation of Cd in roots and leaves. In addition, high Cd concentrations in roots and leaf tissues caused irreversible damage to the cell ultrastructure, compromising cell function and leading to programmed cell death. However, there was a mitigation of Cd toxicity when cacao was grown in soils with low Cd doses and in the presence of Mn. Thus, damage to the root and leaf tissues of cacao caused by Cd uptake from contaminated soils can be attenuated or mitigated by the presence of high Mn doses in soil.

Assessing the functional diversity of rhizobacteria from cacao by partitioning root and shoot biomasses

Plant-microbe interactions are critical for the sustainability of agricultural production. In this study, our aims were to characterize the genetic and functional diversity of the culturable bacterial community associated with the cacao rhizosphere and access their potential for growth promotion of cacao seedling. Culture-dependent and molecular methods were used to characterize the population densities and diversity of bacterial communities from soil and cacao plants at two locations and two plant ages. A total of 63 strains were identified through hsp60 sequencing. Pseudomonas and Enterobacter were the most abundant genera in association with the cacao rhizosphere, whereas Bacillus was more numerous in soil. Parameters of seedling growth promotion were evaluated 60 days after inoculation of seeds, with partition of the assessments into root and shoot weight. Each isolate showed beneficial, neutral or deleterious effects on plant growth, depending on the isolate and on the parts of plant assessed. Interestingly, although an apparent overall decrease in total biomass of seedlings (roots + shoots dry matters) was observed for the majority of isolates (89%), 94% of all isolates, in fact, revealed an increase in plant roots/shoots dry biomass ratio. Despite that part of the isolates (35%) appeared to significantly decrease plant height, and that 65% did not influence plant height (neutral effect), 18 had significantly increased root dry biomass; nevertheless, seven of these root growth-increasing isolates simultaneously decreased shoots-related growth parameters. The results of this study evidentiated the functional diversity of culturable cacao rhizobacteria and how the partitioning of roots and shoots in the assessment of plant growth parameters could reveal the biotechnological potential of these isolates for promoting growth of clones for rehabilitation of commercial cacao plantations. KEY POINTS: • The most common culturable bacteria in cacao roots were Pseudomonas and Enterobacter • Most culturable bacteria from cacao roots increased the root/shoot ratio • Roots and shoots should be examined separately to detect cacao beneficial bacteria.

Quantitative Analysis and 2D/3D Elemental Imaging of Cocoa Beans Using X-ray Fluorescence Techniques

As an important raw material for the confectionery industry, the cocoa bean (Theobroma cacao L.) has to meet certain legal requirements in terms of food safety and maximum contaminant levels in order to enter the cocoa market. Understanding the enrichment and distribution of essential minerals but also toxic metals is of utmost importance for improving the nutritional quality of this economically important raw food material. We present three X-ray fluorescence (XRF) techniques for elemental bio-imaging of intact cocoa beans and one additional XRF technique for quantitative analysis of cocoa pellets. The interrelation of all the methods presented gives a detailed picture of the content and 3D-resolved distribution of elements in complete cocoa beans for the first time.

Mexican Ancestral Foods (Theobroma cacao, Opuntia ficus indica, Persea americana and Phaseolus vulgaris) Supplementation on Anthropometric, Lipid and Glycemic Control Variables in Obese Patients: A Systematic Review and Meta-Analysis

Diet containing Mexican ancestral foods such as cocoa, nopal, avocado, and common bean have been individually reported to have beneficial effects on obesity and comorbidities. Methods: A systematic review and meta-analysis on the effect of Mexican ancestral foods on the anthropometric, lipid, and glycemic control variables in obese patients was performed following PRISMA guidelines. Data were analyzed using a random-effects model. Results: We selected 4664 articles from an initial search, of which only fifteen studies satisfied the inclusion criteria. Data for 1670 participants were analyzed: 843 in the intervention group and 827 in the control group. A significant reduction in body mass index (mean difference: −0.80 (−1.31 to −0.30)) (95% confidence interval), p = 0.002, heterogeneity I2 = 92% was showed after the ingestion of cocoa, nopal, avocado, or common bean. The mean difference for body weight was −0.57 (−1.93 to 0.79), waist of circumference: −0.16 (−2.54 to −2.21), total cholesterol: −5.04 (−11.5 to 1.08), triglycerides: −10.11 (−27.87 to 7.64), fasting glucose: −0.81 (−5.81 to 4.19), and insulin: −0.15 (−0.80 to 0.50). Mexican ancestral food supplementation seems to improve anthropometric, lipid, and glycemic control variables in obesity; however, more randomized controlled trials are needed to have further decisive evidence about dosage and method of supplementation and to increase the sample size.

Application of HPP for the Development of a Dessert Elaborated with Casein and Cocoa for a Dysphagia Diet

In this study, the application of high-pressure processing (HPP) for optimizing the texture of a cocoa dessert rich in casein and developed for people with dysphagia was investigated. Different treatments (250 MPa/15 min; 600 MPa/5 min) and protein concentrations (10-15%) were combined and evaluated for choosing the optimum combination leading to an adequate texture. The selected formulation was a dessert containing 4% cocoa and 10% casein and subjected to 600 MPa for 5 min. It showed a high nutritional value (11.5% protein) and high antioxidant capacity, which was slightly affected by the HPP processing. The rheological and textural properties showed that HPP had a clear effect on the dessert structure. The loss tangent decreased from 2.692 to 0.165, indicating the transition from a liquid to a gel-like structure, which is in a suitable range for dysphagia foods. During storage (14 and 28 days at 4 °C), progressive significant changes in the structure of the dessert were observed. A decrease in all rheological and textural parameters occurred, except for the loss of tangent, which increased its value. In any case, at 28 days of storage, samples maintained the weak gel-like structure (0.686 loss tangent) that is acceptable for dysphagia management.

Genome-wide SNP genotyping as a simple and practical tool to accelerate the development of inbred lines in outbred tree species: An example in cacao (Theobroma cacao L.)

Cacao is a globally important crop with a long history of domestication and selective breeding. Despite the increased use of elite clones by cacao farmers, worldwide plantations are established mainly using hybrid progeny material derived from heterozygous parents, therefore displaying high tree-to-tree variability. The deliberate development of hybrids from advanced inbred lines produced by successive generations of self-pollination has not yet been fully considered in cacao breeding. This is largely due to the self-incompatibility of the species, the long generation cycles (3–5 years) and the extensive trial areas needed to accomplish the endeavor. We propose a simple and accessible approach to develop inbred lines based on accelerating the buildup of homozygosity based on regular selfing assisted by genome-wide SNP genotyping. In this study we genotyped 90 clones from the Brazilian CEPEC´s germplasm collection and 49 inbred offspring of six S₁ or S₂ cacao families derived from self-pollinating clones CCN-51, PS-13.19, TSH-1188 and SIAL-169. A set of 3,380 SNPs distributed across the cacao genome were interrogated on the EMBRAPA multi-species 65k Infinium chip. The 90 cacao clones showed considerable variation in genome-wide SNP homozygosity (mean 0.727± 0.182) and 19 of them with homozygosity ≥90%. By assessing the increase in homozygosity across two generations of self-pollinations, SNP data revealed the wide variability in homozygosity within and between S₁ and S₂ families. Even in small families (<10 sibs), individuals were identified with up to ~1.5 standard deviations above the family mean homozygosity. From baseline homozygosities of 0.476 and 0.454, offspring with homozygosities of 0.862 and 0.879 were recovered for clones TSH-1188 and CCN-51 respectively, in only two generations of selfing (81–93% increase). SNP marker assisted monitoring and selection of inbred individuals can be a practical tool to optimize and accelerate the development of inbred lines of outbred tree species. This approach will allow a faster and more accurate exploitation of hybrid breeding strategies in cacao improvement programs and potentially in other perennial fruit and forest trees.

Genome-Wide Identification and Analysis of the R2R3-MYB Gene Family in Theobroma cacao

The MYB gene family is involved in the regulation of plant growth, development and stress responses. In this paper, to identify Theobroma cacao R2R3-MYB (TcMYB) genes involved in environmental stress and phytohormones, we conducted a genome-wide analysis of the R2R3-MYB gene family in Theobroma cacao (cacao). A total of 116 TcMYB genes were identified, and they were divided into 23 subgroups according to the phylogenetic analysis. Meanwhile, the conserved motifs, gene structures and cis-acting elements of promoters were analyzed. Moreover, these TcMYB genes were distributed on 10 chromosomes. We conducted a synteny analysis to understand the evolution of the cacao R2R3-MYB gene family. A total of 37 gene pairs of TcMYB genes were identified through tandem or segmental duplication events. Additionally, we also predicted the subcellular localization and physicochemical properties. All the studies showed that TcMYB genes have multiple functions, including responding to environmental stresses. The results provide an understanding of R2R3-MYB in Theobroma cacao and lay the foundation for a further functional analysis of TcMYB genes in the growth of cacao.

Genetic diversity and population structure of fine aroma cacao (Theobroma cacao L.) from north Peru revealed by single nucleotide polymorphism (SNP) markers

Cacao (Theobroma cacao L.) is the basis of the lucrative confectionery industry with “fine or flavour” cocoa attracting higher prices due to desired sensory and quality profiles. The Amazonas Region (north Peru) has a designation of origin, Fine Aroma Cacao, based on sensory quality, productivity and morphological descriptors but its genetic structure and ancestry is underexplored. We genotyped 143 Fine Aroma Cacao trees from northern Peru (Bagua, Condorcanqui, Jaén, Mariscal Cáceres, and Utcubamba; mainly Amazonas Region), using 192 single nucleotide polymorphic markers. Identity, group, principal coordinate, phylogenetic and ancestry analyses were conducted. There were nine pairs of matched trees giving 134 unique samples. The only match within 1,838 reference cacao profiles was to a putative CCN 51 by a Condorcanqui sample. The “Peru Uniques” group was closest to Nacional and Amelonado-Nacional genetic clusters based on FST analysis. The provinces of Bagua and Utcubamba were genetically identical (Dest = 0.001; P = 0.285) but differed from Condorcanqui (Dest = 0.016–0.026; P = 0.001–0.006). Sixty-five (49%) and 39 (29%) of the Peru Uniques were mixed from three and four genetic clusters, respectively. There was a common and strong Nacional background with 104 individuals having at least 30% Nacional ancestry. The fine aroma of cacao from Northern Peru is likely due to the prevalent Nacional background with some contribution from Criollo. A core set of 53 trees was identified. These findings are used to support the continuance of the fine or flavour industry in Peru.

Cost Analysis of Cacao (Theobroma cacao L.) Plant Propagation through the Somatic Embryogenesis Method

In vitro cacao (Theobroma cacao L.) production via somatic embryogenesis (SE) is being implemented to mass propagate clonal plant material with the donor material’s prominent characteristics. Though it is an advanced technology, it is con-sidered expensive compared to other propagation techniques. This work focused on identifying the critical financial feasi-bility factors for the SE productive process. The process's costs were estimated, identifying factors influencing each la-boratory's standardized ES process. A Monte Carlo Simulation (MCS) was performed to evaluate different variables upon increasing productive scale in a biofactory (commercial-scale production). The projected lot volume was 100,000 plantlets in solid media, considering the process flow from in vitro introduction to acclimation. A biofactory operational model was projected, establishing time and operator movements and identifying direct and indirect costs. Costs were defined by the standardized or integral method, with estimated and budgeted calculations to set the cost per plantlet. The identified cost components were culture medium (CM), indirect manufacturing costs (IMC), labor (direct and indirect) and operating expenses. Labor had the most significant share of the costs, at 53%, followed by operating expenses, at 30%, CM, at 12%, and IMC, at 5%. The MCS helped define that the variables with the highest impact on unit price were the embryos’ response in the germination-acclimation stage and the proliferation coefficient during the maturation stage. This projection yielded a figure of US $0.73 per plantlet. However, strategies to reduce this cost have been proposed. These strategies are mainly conducive to optimizing labor and implementing practices that increase multiplication. Keywords. Plant Tissue culture, Cost analysis, Large-scale production, Biofactory, Monte Carlo Simulation (MCS)

Cocoa By-Products: Characterization of Bioactive Compounds and Beneficial Health Effects

The annual production of cocoa is approximately 4.7 million tons of cocoa beans, of which only 10% corresponds to the cocoa bean and the remaining value corresponds to a high number of residues, cocoa bean shell, pulp and husk. These by-products are a source of nutrients and compounds of notable interest in the food industry as possible ingredients, or even additives. The assessment of such by-products is relevant to the circular economy at both environmental and economic levels. Investigations carried out with these by-products have shown that cocoa husk can be used for the production of useful chemicals such as ketones, carboxylic acids, aldehydes, furans, heterocyclic aromatics, alkylbenzenes, phenols and benzenediols, as well as being efficient for the removal of lead from acidic solutions, without decay in the process due to the other metals in this matrix. The fibre present in the cocoa bean shell has a considerable capacity to adsorb a large amount of oil and cholesterol, thus reducing its bioavailability during the digestion process, as well as preventing lipid oxidation in meats, with better results compared to synthetic antioxidants (butylated hydroxytoluene and β-tocopherol). Finally, cocoa pulp can be used to generate a sweet and sour juice with a natural flavour. Thus, this review aimed to compile information on these by-products, focusing mainly on their chemical and nutritional composition, simultaneously, the various uses proposed in the literature based on a bibliographic review of articles, books and theses published between 2000 and 2021, using databases such as Scopus, Web of Science, ScieLO, PubMed and ResearchGate.

Lowering the Toxicity of Cd to Theobroma cacao Using Soil Amendments Based on Commercial Charcoal and Lime

Carbonaceous and calcareous materials are commonly used as amendments to decrease the Cd mobility in contaminated soils. This study evaluated the effect of amendments applied to cocoa seedlings in the greenhouse, considering the mobilization of soil cadmium toward the seedlings as the main response. The experimental conditions considered soil artificially contaminated with Cd at a concentration of 50 mg Cd kg⁻¹ and applications of amendments in different treatments with the presence of charcoal dust and calcium carbonate. The charcoal was characterized by microscopy and by adsorption tests, and it proved to be a material with macropores, with a maximum capacity of 8.06 mg Cd g⁻¹ and favorable kinetic behavior according to the adjustment of the data obtained to the pseudo-second-order model. The results also showed that the application of liming decreased the mobility of Cd toward the seedlings, with the liming combined with charcoal leading to the absence of Cd in the cocoa seedlings, considering a residual concentration of Cd in the soil of 35 mg Cd kg⁻¹. The results, although limited to a small scale, demonstrated the possibility of applying low-cost and easy-to-handle amendments for the control of Cd in cocoa plantations.

Utilizing CRISPR-Cas in Tropical Crop Improvement: A Decision Process for Fitting Genome Engineering to Your Species

Adopting modern gene-editing technologies for trait improvement in agriculture requires important workflow developments, yet these developments are not often discussed. Using tropical crop systems as a case study, we describe a workflow broken down into discrete processes with specific steps and decision points that allow for the practical application of the CRISPR-Cas gene editing platform in a crop of interest. While we present the steps of developing genome-edited plants as sequential, in practice parts can be done in parallel, which are discussed in this perspective. The main processes include 1) understanding the genetic basis of the trait along with having the crop’s genome sequence, 2) testing and optimization of the editing reagents, development of efficient 3) tissue culture and 4) transformation methods, and 5) screening methods to identify edited events with commercial potential. Our goal in this perspective is to help any lab that wishes to implement this powerful, easy-to-use tool in their pipeline, thus aiming to democratize the technology.

Ceratocystis cacaofunesta differentially modulates the proteome in xylem-enriched tissue of cocoa genotypes with contrasting resistance to Ceratocystis wilt

Decreased accumulation of polyphenol oxidase, H₂O₂ accumulation, effective regulation of programmed cell death, and a protein predicted as allergenic can play key roles in cacao defense against Ceratocystis cacaofunesta. Ceratocystis wilt, caused by the fungus Ceratocystis cacaofunesta, has destroyed millions of Theobroma cacao trees in several countries of the Americas. Through proteomics, systems biology, and enzymatic analyses of infected stems, it was possible to infer mechanisms used by resistant (TSH1188) and susceptible (CCN51) cacao genotypes during infection. Protein extraction from xylem-enriched tissue of stems inoculated with the fungus and their controls 1 day after inoculation was carried out, followed by separation through two-dimensional gel electrophoresis and identification by mass spectrometry. Enzyme activity was determined at 1, 3, 7 and 15 days after inoculation. A total of 50 differentially accumulated distinct proteins were identified in the treatments of both genotypes and were classified into 10 different categories. An interaction network between homologous proteins from Arabidospsis thaliana was generated for each genotype, using the STRING database and Cytoscape software. Primary metabolism processes were apparently repressed in both genotypes. The resistance factors suggested for genotype TSH1188 were: H₂O₂ accumulation, effective regulation of programmed cell death, production of phytoalexins derived from tryptophan and furanocoumarins, and participation of a predicted allergenic protein with probable ribonuclease function inhibiting the germination and propagation of the fungus. In the susceptible genotype, it is possible that its recognition and signaling mechanism through proteins from the SEC14 family is easily overcome by the pathogen. Our results will help to better understand the interaction between cacao and one of its most aggressive pathogens, to create disease control strategies.

African and Asian Medicinal Plants as a Repository for Prospective Antiviral Metabolites Against HIV-1 and SARS CoV-2: A Mini Review

Introduction: The worldwide burden of viral infections has triggered a resurgence in the search for new and more efficient antiviral drugs. Scientists are also repurposing existing natural compounds such as the antimalarial drug artemisinin from Artemesia annua L. as potential drug candidates for some of the emerging and re-emerging viral infections such as covid-19

Aim: The aim of this review was to analyse the existing literature to explore the actual or potential natural antiviral compounds from African and Asian medicinal plants as lead compounds in the drug discovery process.

Methods: We searched the literature on African and Asian medicinal plant species as antiviral agents for HIV-1 and the novel coronavirus (SARS-CoV-2) in various databases and search engines such as Web of Science, Google Scholar and PubMed. The search was limited to in vitro, in vivo, and clinical studies and excluded in silico studies.

Results: We present 16 plant species with actual or potential antiviral activity against HIV-1 and SARS-CoV-2. These plant species span the continents of Africa and Asia where they are widely used for treating several other ailments.

Conclusion: Natural compounds from plants can play a significant role in the clinical management of HIV/AIDS and the covid-19 pandemic. More research needs to be conducted to investigate the potential toxicities of the various compounds and their efficacies in clinical settings.

Chemical and biological properties of cocoa beans affected by processing: a review

Cocoa (Theobroma cacao L.) is widely cultivated in tropical countries. The cocoa beans are a popular ingredient of confectionery. Cocoa beans contain various chemicals that contribute to their bioactivity and nutritional properties. There has been increasing interest in developing cocoa beans for "healthy" food products. Cocoa beans have special combination of nutrients such as lipids, carbohydrates, proteins and other compounds of biological activities. The bioactive phytochemicals include methylxanthines, polyphenols, biogenic amines, melanoidins, isoprostanoids and oxalates. These phytochemicals of cocoa are related to various in vivo and in vitro biological activities such as antioxidation, anti-cancer, anti-microbial, anti-inflammation, anti-diabetes, cardiovascular protection, physical improvement, anti-photoaging, anti-depression and blood glucose regulation. The potential of bioactive compounds in cocoa remains to be maximized for food and nutritional applications. The current processing technology promotes the degradation of beneficial bioactive compounds, while maximizing the flavors and its precursors. It is not optimized for the utilization of cocoa beans for "healthy" product formulations. Modifications of the current processing line and non-conventional processing are needed to better preserve and utilize the beneficial bioactive compounds in cocoa beans.

The Effect of Yellow Tea Leaves Camellia sinensis on the Quality of Stored Chocolate Confectionery

Chocolate and tea leaves are considered the most valuable sources of highly bioactive polyphenols due to their potential anti-cancer properties and beneficial effects on the cardiovascular and nervous systems. The objective of the present study was the development of a sensory profiling modality that is correlated with the taste of the chocolate enriched with yellow tea phytochemicals. The additive concentration was optimized in white chocolate and the designed product was evaluated using the sensory profiling method. It was shown that the yellow tea extract in chocolate had a significant effect on the taste and color of the product. Addition of 2.0% yellow tea powdered extract increased the value of color acceptance and caused an intensification of the aromas, particularly the leafy taste, compared to the control samples. The next step of the study was to determine the influence of tea addition in white, milk and dark chocolate subjected to 6 months of storage. The designed chocolates were tested for their activity as antioxidants (DPPH, ABTS and ORAC assay) and cholinesterase inhibitors (AChE, BChE assay). It was confirmed that the yellow tea addition affected the activity of prepared chocolates with respect to radical scavenging activity and was highest for dark chocolate with yellow tea where the values were as follows: 4373 mg Tx/100 g (DPPH), 386 mg Tx/100 g (ABTS) and 4363 µM Tx/100 g (ORAC). An increase in the anti-radical activity of chocolate with yellow tea was found after 3 months of storage, but the subsequent 3 months of storage resulted in its reduction. AChE values ranged from 0.118 to 0.730 [µM eserine/g dw] and from 0.095 to 0.480 [µM eserine/g dw] for BChE assay. Total capacity to inhibit AChE and BChE differed depending on the type of chocolate and was negatively influenced by the half-year storage. Summarizing tested values for individual samples were higher, with increasing content of cocoa liquor and yellow tea extract in the product. The results of the research show that the use of yellow tea in confectionery is promising and may appoint a new direction in functional foods.

Cacao Bean Polyphenols Inhibit Cardiac Hypertrophy and Systolic Dysfunction in Pressure Overload-induced Heart Failure Model Mice

Pathological stresses such as pressure overload and myocardial infarction induce cardiac hypertrophy, which increases the risk of heart failure. Cacao bean polyphenols have recently gained considerable attention for their beneficial effects on cardiovascular diseases. This study investigated the effect of cacao bean polyphenols on the development of cardiac hypertrophy and heart failure. Cardiomyocytes from neonatal rats were pre-treated with cacao bean polyphenols and then stimulated with 30 µM phenylephrine. C57BL/6j male mice were subjected to sham or transverse aortic constriction surgery and then orally administered with vehicle or cacao bean polyphenols. Cardiac hypertrophy and function were examined by echocardiography. In cardiomyocytes, cacao bean polyphenols significantly suppressed phenylephrine-induced cardiomyocyte hypertrophy and hypertrophic gene transcription. Extracellular signal-regulated kinase 1/2 and GATA binding protein 4 phosphorylation induced by phenylephrine was inhibited by cacao bean polyphenols treatment in the cardiomyocytes. Cacao bean polyphenols treatment at 1200 mg/kg significantly ameliorated left ventricular posterior wall thickness, fractional shortening, hypertrophic gene transcription, cardiac hypertrophy, cardiac fibrosis, and extracellular signal-regulated kinase 1/2 phosphorylation induced by pressure overload. In conclusion, these findings suggest that cacao bean polyphenols prevent pressure overload-induced cardiac hypertrophy and systolic dysfunction by inhibiting the extracellular signal-regulated kinase 1/2-GATA binding protein 4 pathway in cardiomyocytes. Thus, cacao bean polyphenols may be useful for heart failure therapy in humans.

The History of Cacao and Its Diseases in the Americas

Cacao is a commodity crop from the tropics cultivated by about 6 million smallholder farmers. The tree, Theobroma cacao, originated in the Upper Amazon where it was domesticated ca. 5450 to 5300 B.P. From this center of origin, cacao was dispersed and cultivated in Mesoamerica as early as 3800 to 3000 B.P. After the European conquest of the Americas (the 1500s), cacao cultivation intensified in several loci, primarily Mesoamerica, Trinidad, Venezuela, and Ecuador. It was during the colonial period that cacao diseases began emerging as threats to production. One early example is the collapse of the cacao industry in Trinidad in the 1720s, attributed to an unknown disease referred to as the "blast". Trinidad would resurface as a production center due to the discovery of the Trinitario genetic group, which is still widely used in breeding programs around the world. However, a resurgence of diseases like frosty pod rot during the republican period (the late 1800s and early 1900s) had profound impacts on other centers of Latin American production, especially in Venezuela and Ecuador, shifting the focus of cacao production southward, to Bahia, Brazil. Production in Bahia was, in turn, dramatically curtailed by the introduction of witches' broom disease in the late 1980s. Today, most of the world's cacao production occurs in West Africa and parts of Asia, where the primary Latin American diseases have not yet spread. In this review, we discuss the history of cacao cultivation in the Americas and how that history has been shaped by the emergence of diseases.

Plants-Derived Biomolecules as Potent Antiviral Phytomedicines: New Insights on Ethnobotanical Evidences against Coronaviruses

SARS-CoV-2 infection (COVID-19) is in focus over all known human diseases, because it is destroying the world economy and social life, with increased mortality rate each day. To date, there is no specific medicine or vaccine available against this pandemic disease. However, the presence of medicinal plants and their bioactive molecules with antiviral properties might also be a successful strategy in order to develop therapeutic agents against SARS-CoV-2 infection. Thus, this review will summarize the available literature and other information/data sources related to antiviral medicinal plants, with possible ethnobotanical evidence in correlation with coronaviruses. The identification of novel antiviral compounds is of critical significance, and medicinal plant based natural compounds are a good source for such discoveries. In depth search and analysis revealed several medicinal plants with excellent efficacy against SARS-CoV-1 and MERS-CoV, which are well-known to act on ACE-2 receptor, 3CLpro and other viral protein targets. In this review, we have consolidated the data of several medicinal plants and their natural bioactive metabolites, which have promising antiviral activities against coronaviruses with detailed modes of action/mechanism. It is concluded that this review will be useful for researchers worldwide and highly recommended for the development of naturally safe and effective therapeutic drugs/agents against SARS-CoV-2 infection, which might be used in therapeutic protocols alone or in combination with chemically synthetized drugs.

Phytophthora palmivora-Cocoa Interaction

Phytophthora palmivora (Butler) is an hemibiotrophic oomycete capable of infecting over 200 plant species including one of the most economically important crops, Theobroma cacao L. commonly known as cocoa. It infects many parts of the cocoa plant including the pods, causing black pod rot disease. This review will focus on P. palmivora’s ability to infect a plant host to cause disease. We highlight some current findings in other Phytophthora sp. plant model systems demonstrating how the germ tube, the appressorium and the haustorium enable the plant pathogen to penetrate a plant cell and how they contribute to the disease development in planta. This review explores the molecular exchange between the oomycete and the plant host, and the role of plant immunity during the development of such structures, to understand the infection of cocoa pods by P. palmivora isolates from Papua New Guinea.

Food-derived bioactive compounds with anti-aging potential for nutricosmetic and cosmeceutical products

Besides providing essential nutrients for humans, food contains bioactive compounds that exert diverse biological activities such as anti-microbial, anti-cancerogenic, anti-viral, anti-inflammatory and antioxidant. The cosmetic industry is interested in natural bioactive compounds for their use in nutricosmetic and cosmeceutical products. These products aimed to reduce skin aging, inflammation or provide photoprotection against UV radiation. As a result, nutricosmetics and cosmeceuticals are becoming innovative self-care products in the beauty market. These products contain phytochemicals as active compounds obtained from fruits, vegetables, legumes, medicinal herbs and plants with anti-aging potential. This review summarizes the information within the last 5 years related to bioactive compounds present in fruits, vegetables, herbs and spices commonly used for human consumption. Their antioxidant and biological potential for modulating molecular markers involved in the aging process, as well as their mechanism of action. Diverse natural foods and their byproducts could be used as a source of bioactive compounds for developing cosmeceutical and nutricosmetic products.

Genome-Wide Association Study Reveals Novel Candidate Genes Associated with Productivity and Disease Resistance to Moniliophthora spp. in Cacao (Theobroma cacao L.)

Cacao (Theobroma cacao L.), the source of chocolate, is one of the most important commodity products worldwide that helps improve the economic livelihood of farmers. Diseases like frosty pod rot caused by Moniliophthora roreri and witches’ broom caused by Moniliophthora perniciosa limit the cacao productivity, this can be solved by using resistant varieties. In the current study, we sequenced 229 cacao accessions using genotyping-by-sequencing to examine the genetic diversity and population structure employing 9,003 and 8,131 single nucleotide polymorphisms recovered by mapping against two cacao genomes (Criollo B97-61/B2 v2 and Matina 1-6 v1.1). In the phenotypic evaluation, three promising accessions for productivity and 10 with good tolerance to the frosty pod rot and witches’ broom diseases were found. A genome-wide association study was performed on 102 accessions, discovering two genes associated with productivity and seven to disease resistance. The results enriched the knowledge of the genetic regions associated with important cacao traits that can have significant implications for conservation and breeding strategies like marker-assisted selection.

Cocoa Bean Shell-A By-Product with Nutritional Properties and Biofunctional Potential

Cocoa bean shells (CBS) are one of the main by-products from the transformation of cocoa beans, representing 10%‒17% of the total cocoa bean weight. Hence, their disposal could lead to environmental and economic issues. As CBS could be a source of nutrients and interesting compounds, such as fiber (around 50% w/w), cocoa volatile compounds, proteins, minerals, vitamins, and a large spectrum of polyphenols, CBS may be a valuable ingredient/additive for innovative and functional foods. In fact, the valorization of food by-products within the frame of a circular economy is becoming crucial due to economic and environmental reasons. The aim of this review is to look over the chemical and nutritional composition of CBS and to revise the several uses that have been proposed in order to valorize this by-product for food, livestock feed, or industrial usages, but also for different medical applications. A special focus will be directed to studies that have reported the biofunctional potential of CBS for human health, such as antibacterial, antiviral, anticarcinogenic, antidiabetic, or neuroprotective activities, benefits for the cardiovascular system, or an anti-inflammatory capacity.

First-tier detection of intragenomic 16S rRNA gene variation in culturable endophytic bacteria from cacao seeds

Background

Intragenomic variability in 16S rDNA is a limiting factor for taxonomic and diversity characterization of Bacteria, and studies on its occurrence in natural/environmental populations are scarce. In this work, direct DNA amplicon sequencing coupled with frequent-cutter restriction analysis allowed detection of intragenomic 16S rDNA variation in culturable endophytic bacteria from cacao seeds in a fast and attractive manner.

Methods

Total genomic DNA from 65 bacterial strains was extracted and the 16S rDNA hyper variable V5-V9 regions were amplified for enzyme digestion and direct Sanger-type sequencing. The resulting electropherograms were visually inspected and compared to the corresponding AluI-restriction profiles, as well as to complete genome sequences in databases. Restriction analysis were employed to substitute the need of amplicon cloning and re-sequencing. A specifically improved polyacrylamide-gradient electrophoresis allowed to resolve 5-bp differences in restriction fragment sizes. Chi-square analysis on 2 × 2 contingency table tested for the independence between the 'number of AluI bands' and 'type of eletropherogram'.

Results

Two types of electropherograms were obtained: unique template, with single peaks per base (clean chromatograms), and heterogeneous template, with various levels of multiple peaks per base (mixed chromatograms). Statistics revealed significant interaction between number of restriction fragments and type of electropherogram for the same amplicons: clean or mixed ones associated to ≤5 or ≥6 bands, respectively. The mixed-template pattern combined with the AluI-restriction profiles indicated a high proportion of 49% of the culturable endophytes from a tropical environment showing evidence of intragenomic 16S rDNA heterogeneity.

Conclusion

The approach presented here was useful for a rapid, first-tier detection of intragenomic variation in culturable isolates, which can be applied in studies of other natural populations; a preliminary view of intragenomic heterogeneity levels can complement culture-dependent and -independent methods. Consequences of these findings in taxonomic and diversity studies in complex bacterial communities are discussed.

5-(3',4'-Dihydroxyphenyl)-γ-valerolactone, a metabolite of procyanidins in cacao, suppresses MDI-induced adipogenesis by regulating cell cycle progression through direct inhibition of CDK2/cyclin O

Cacao (Theobroma cacao) has a significant polyphenol content and has been reported to elicit anti-obesity effects. Previous studies have focused on the properties of cacao extract and procyanidins, while the potential mechanisms have not been fully elucidated. Here, we investigated the inhibitory effects of procyanidin metabolites on adipogenic cocktail-induced adipogenesis and lipogenesis in 3T3-L1 preadipocytes. It was observed that 5-(3',4'-dihydroxyphenyl)-γ-valerolactone (DHPV), a major procyanidin metabolite, exhibited the greatest inhibitory effects on adipogenesis and lipogenesis. DHPV dose-dependently reduced the expression levels of proteins involved in adipogenesis including peroxisome proliferator-activated receptor γ (PPAR γ) and CCAT/enhancer-binding protein α (C/EBP α), as well as lipogenesis-related factors such as fatty acid synthase and acetyl-CoA carboxylase. These inhibitory effects were primarily due to G1 phase arrest and the suppression of cell proliferation during mitotic clonal expansion, the early stage of adipogenesis. In an extensive kinase array, DHPV directly suppressed activation of the CDK2/cyclin O complex, and inhibited the phosphorylation of C/EBP β, which is responsible for the induction of PPAR γ and C/EBP α. Taken together, these findings suggest that DHPV is a highly biologically active compound with potential anti-obesity effects and works by inhibiting the intracellular lipid content and cell differentiation.

Potential of Yeasts as Biocontrol Agents of the Phytopathogen Causing Cacao Witches' Broom Disease: Is Microbial Warfare a Solution?

Plant diseases caused by fungal pathogens are responsible for major crop losses worldwide, with a significant socio-economic impact on the life of millions of people who depend on agriculture-exclusive economy. This is the case of the Witches’ Broom Disease (WBD) affecting cacao plant and fruit in South and Central America. The severity and extent of this disease is prospected to impact the growing global chocolate market in a few decades. WBD is caused by the basidiomycete fungus Moniliophthora perniciosa. The methods used to contain the fungus mainly rely on chemical fungicides, such as copper-based compounds or azoles. Not only are these highly ineffective, but also their utilization is increasingly restricted by the cacao industry, in part because it promotes fungal resistance, in part related to consumers’ health concerns and environmental awareness. Therefore, the disease is being currently tentatively controlled through phytosanitary pruning, although the full removal of infected plant material is impossible and the fungus maintains persistent inoculum in the soil, or using an endophytic fungal parasite of Moniliophthora perniciosa which production is not sustainable. The growth of Moniliophthora perniciosa was reported as being antagonized in vitro by some yeasts, which suggests that they could be used as biological control agents, suppressing the fungus multiplication and containing its spread. Concurrently, some yeast-based products are used in the protection of fruits from postharvest fungal spoilage, and the extension of diverse food products shelf-life. These successful applications suggest that yeasts can be regarded a serious alternative also in the pre-harvest management of WBD and other fungal plant diseases. Yeasts’ GRAS (Generally Recognized as Safe) nature adds to their appropriateness for field application, not raising major ecological concerns as do the present more aggressive approaches. Importantly, mitigating WBD, in a sustainable manner, would predictably have a high socioeconomic impact, contributing to diminish poverty in the cacao-producing rural communities severely affected by the disease. This review discusses the importance/advantages and the challenges that such a strategy would have for WBD containment, and presents the available information on the molecular and cellular mechanisms underlying fungi antagonism by yeasts.

Chocolate and chocolate constituents influence bone health and osteoporosis risk

Bone loss resulting in increased risk for osteoporosis is a major health issue worldwide. Chocolate is a rich source of antioxidant and antiinflammatory flavonoids and dietary minerals with the potential to benefit bone health. However, other chocolate constituents such as cocoa butter, sugar, and methylxanthines may be detrimental to bone. Human studies investigating the role of chocolate consumption on serum bone markers and bone mineral density (BMD) have been inconsistent. A contributing factor is likely the different composition and thereby the nutrient and bioactive content among chocolate types. White and milk chocolate are high in sugar and low in flavonoids and most minerals. Dark chocolate (45-85% cocoa solids) is high in flavonoids, most minerals, and low in sugar with ≥70% cocoa solids resulting in higher fat and methylxanthine content. The aim of this review was to examine the relationship between chocolate consumption and its constiuents, including flavonoid content, on bone health and osteoporosis risk. Studies showed postmenopausal women had no bone effects at moderate chocolate intakes, whereas adolescents consuming chocolate had greater longitudinal bone growth. Based on flavonoid and mineral content, unsweetened cocoa powder appeared to be the best option followed by dark chocolate with higher cocoa content in terms of supporting and preserving bone health. Determining dietary recommendations for chocolate consumption relative to bone health is important because of the growing popularity of chocolate, particularly dark chocolate, and an expected increase in consumption owing to suggestions of health benefits against various degenerative diseases.

Meiosis Research in Orphan and Non-orphan Tropical Crops

Plant breeding is directly linked to the development of crops that can effectively adapt to challenging conditions such as soil nutrient depletion, water pollution, drought, and anthropogenic climate change. These conditions are extremely relevant in developing countries already burdened with population growth and unchecked urban expansion, especially in the tropical global southern hemisphere. Engineering new crops thus has potential to enhance food security, prevent hunger, and spur sustainable agricultural growth. A major tool for the improvement of plant varieties in this context could be the manipulation of homologous recombination and genome haploidization during meiosis. The isolation or the design of mutations in key meiotic genes may facilitate DNA recombination and transmission of important genes quickly and efficiently. Genome haploidization through centromeric histone mutants could be an option to create new crosses rapidly. This review covers technical approaches to engineer key meiotic genes in tropical crops as a blueprint for future work and examples of tropical crops in which such strategies could be applied are given.

Glucocorticoid receptor-regulated TcLEC2 expression triggers somatic embryogenesis in Theobroma cacao leaf tissue

Theobroma cacao, the source of cocoa, is a crop of particular importance in many developing countries. Availability of elite planting material is a limiting factor for increasing productivity of Theobroma cacao; therefore, the development of new strategies for clonal propagation is essential to improve farmers’ incomes and to meet increasing global demand for cocoa. To develop a more efficient embryogenesis system for cacao, tissue was transformed with a transgene encoding a fusion of Leafy Cotyledon 2 (TcLEC2) to a glucocorticoid receptor domain (GR) to control nuclear localization of the protein. Upon application of the glucocorticoid dexamethasone (dex), downstream targets of LEC2 involved in seed-development were up-regulated and somatic embryos (SEs) were successfully regenerated from TcLEC2-GR transgenic flower and leaf tissue in large numbers. Immature SEs regenerated from TcLEC2-GR leaves were smaller in size than immature SEs from floral tissue, suggesting a different ontogenetic origin. Additionally, exposure of TcLEC2-GR floral explants to dex increased the number of SEs compared to floral explants from control, non-transgenic trees or from TcLEC2-GR floral explants not treated with dex. Testing different durations of exposure to dex indicated that a three-day treatment produced optimal embryo regeneration. Leaf derived SEs were successfully grown to maturity, converted into plants, and established in the greenhouse, demonstrating that these embryos are fully developmentally competent. In summary, we demonstrate that regulating TcLEC2 activity offers a powerful new strategy for optimizing somatic embryogenesis pipelines for cacao.

Analysis of minor low molecular weight carbohydrates in cocoa beans by chromatographic techniques coupled to mass spectrometry

The low molecular weight carbohydrate (LMWC) profile of cocoa beans has recently been studied using hydrophilic interaction liquid chromatography coupled to electrospray ionization-time of flight mass spectrometry (HILIC-ESI-TOF MS) and HILIC-ESI-tandem mass spectrometry (HILIC-ESI-MSⁿ). However, different LMWC could not be unambiguously identified. Thus, as a first approach in this paper, gas chromatography coupled to mass spectrometry (GC-MS) was used as a complementary analytical technique to characterize LMWC of cocoa beans. Different mono-, di-, tri- and tetrasaccharides, as well as myo-inositol, galactinol and a diglycosil glycerol were detected. scyllo-Inositol, 1-kestose and 6-kestose were identified in unfermented cocoa beans for the first time. Moreover, other minor LMWC were tentatively assigned as fructosyl-fructose, fructosyl-glucose and glucosyl-sucrose. As a second step, in order to evaluate new possible indicators of cocoa bean origin or fermentation status, scyllo-inositol, 1-kestose and galactinol were selected as target compounds and a HILIC-ESI-TOF MS method was optimized for their analysis. The optimized conditions, using an acetonitrile:water gradient with 0.05% ammonium hydroxide at 40 °C showed narrow peaks (w_h: 0.3-0.5 min) with good resolution values (R_s: 0.83-2.83). The validated HILIC-ESI-TOF MS method was applied to the analysis of 35 cocoa bean samples from different origins and fermentation status. The content of scyllo-inositol, 1-kestose and galactinol in unfermented beans (n = 21) was in the range of traces-504.9, 36.1-133.5 and traces-1970.4 μg g^-1 cocoa DM respectively. In fermented beans (n = 14), the content of scyllo-inositol and 1-kestose was in the range of 15.5-491.9 and traces-115.5 μg g^-1 cocoa DM respectively. Galactinol was absent in fermented beans, indicating that it could be a potential indicator of fermentation status. The methodology proposed could be used for quality control of natural products and other food ingredients containing inositols and oligosaccharides.