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Mixed production systems play a vital role in the economic sustainability and ecological balance of agroecosystems. Cocoa and plantain are key crops in Ecuador but face phytosanitary challenges, like witches' broom and black sigatoka diseases, especially when cultivated under monocropping systems. Combining habitat manipulation with adaptive pathogen management (APM) strategies can mitigate these challenges, but their efficacy in mixed cropping systems remains unclear. This study investigates disease and pest incidence in mixed cocoa–plantain systems during the establishment phase, focusing on the impact of spatial arrangements. Mixed agroecosystems showed a lower witches' broom incidence in cocoa than monocultures. Whereas, in plantain, there was a consistent black sigatoka incidence across spatial arrangements but a lower infection rate per leaf within mixed systems. We found varied nematode populations with monocultures hosting the highest root damage due to phytoparasitic nematodes. Weevil populations were also influenced by spatial arrangements with monocultures among the highest. Overall, mixed agroecosystems influence disease and pest incidence, potentially hindering pathogen spread. Plantain–cocoa associations reduce disease incidence in cocoa but may not affect the overall incidence of black sigatoka in plantain, at least during the establishment phase. Continued monitoring is crucial for understanding the long-term impacts and microclimatic effects on pest populations that could offer sustainable pest management strategies, reducing the reliance on chemical pesticides. [ABSTRACT FROM AUTHOR]

Ecuador is one of the leading producers of fine aroma cocoa worldwide, involving around 100,000 producer families. On the American continent, the largest producer is Brazil, with 18%, followed by Ecuador and Colombia, and it is estimated that more than 20 million people depend directly on this crop. Moniliophthora roreri, the causal agent of frost pot rot, has been a cause of great concern due to the production losses it has caused, which in 2022 amounted to 80% in different cocoa-producing provinces of Ecuador and worldwide losses of 30% performance they are estimates. This study aimed to determine the biological control potential of microcapsules made with Trichoderma spp spore solution against M. roreri. The In vitro evaluation of the microcapsules did not show significant results in the percentage of inhibition, and this was not the case in the direct evaluation on the farm, where the severity in the 15-day-old fruits showed 0% external and internal affectation with the use of microcapsules in its liquid presentation. Additionally, the evolution of the microcapsules in 28-day-old fruits was observed in severity from 1 to 25% with intercalated applications. Beneficial fungi were applied first, followed by pathogens; though, when the pathogen was applied first, and then the beneficial fungus, the increased severity of external and internal disease was 26-75% and 80-100%, respectively. In conclusion, using microcapsules based on Trichoderma strains at the early ages of the fruits generates protection against M. roreri throughout the vegetative development of the fruit. [ABSTRACT FROM AUTHOR]

Introduction: Theobroma cacao, the cocoa tree, is a target for pathogens, such as fungi from the genera Phytophthora, Moniliophthora, Colletotrichum, Ceratocystis, among others. Some cacao pathogens are restricted to specific regions of the world, such as the Cacao swollen shoot virus (CSSV) in West African countries, while others are expanding geographically, such as Moniliophthora roreri in the Americas. M. roreri is one of the most threatening cacao pathogens since it directly attacks the cacao pods driving a significant reduction in production, and therefore economic losses. Despite its importance, the knowledge about the microenvironment of this pathogen and the cocoa pods is still poorly characterized. Methods: Herein we performed RNA sequencing of spores in differential stages of culture in a medium supplemented with cacao pod extract and mycelium collected of the susceptible variety ICT 7121 naturally infected by the pathogen to evaluate the diversity and transcriptional activity of microorganisms associated with the in vitro sporulation of M. roreri. Results: Our data revealed a great variety of fungi and bacteria associated with M. roreri, with an exceptional diversity of individuals from the genus Trichoderma sp. Interestingly, the dynamics of microorganisms from different kingdoms varied proportionally, suggesting they are somehow affected by M. roreri culture time. We also identified three sequences similar to viral genomes from the Narnaviridae family, posteriorly confirmed by phylogenetic analysis as members of the genus Narnavirus. Screening of M. roreri public datasets indicated the virus sequences circulating in samples from Ecuador, suggesting a wide spread of these elements. Of note, we did not identify traces of the viral sequences in the M. roreri genome or DNA sequencing, restricting the possibility of these sequences representing endogenized elements. Discussion: To the best of our knowledge, this is the first report of viruses infecting the fungus of the genus Moniliophthora and only the third description of viruses that are able to parasite elements from the Marasmiaceae family. [ABSTRACT FROM AUTHOR]

Societal Impact Statement: Recent surveys conducted on Amazonian cocoa trees in their home range are a unique opportunity to assess the aromas, diversity and potential of the Ecuadorian Amazon to create new aromatic cocoa varieties. Our results reveal informations about the diversity and genesis of aromas in Ecuadorian fine cocoa. The great aromatic diversity could enrich cocoa flavour selection programmes and provide Amazonian populations with new income linked to aromatic varieties, which could lead to a 'grand cru' chocolate. Until now, breeding programmes have been mainly focused on improving characteristics for production, but in recent years cocoa quality has been increasingly examined to meet market expectations. Summary: Ecuador is known worldwide for its fine or flavour cocoa from the Nacional variety. Currently, farmers mainly grow the modern Nacional variety of cocoa trees (hybrids between the ancestral Nacional and Trinitario) while the ancestral Nacional variety tends to be neglected. In order to enlarge the genetic resources related to this ancestral variety, several surveys were carried out in its area of origin located in the South Ecuadorian Amazonia.The 202 trees resulting from these surveys were genotyped using GBS (Genotyping By Sequencing) markers and their dried‐fermented beans were characterised for both their aromatic volatile compounds and sensorial quality. A genome wide association study (GWAS) was carried out with the aim to study the genetic and biochemical bases of the aroma traits of this population and to better exploit them in breeding programmes.Some association areas and candidate genes related to spicy and woody aromas were found for the first time in Theobromacacao. Some association areas and candidate genes related to floral and fruity aromas common to other studies were identified.Our results support the hypothesis that aroma formation may be related to a defence reaction to biotic and abiotic stresses generated by the fermentation process. [ABSTRACT FROM AUTHOR]

Copyright of BIOAGRO is the property of Revista BIOAGRO and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Many decades of improvement in cacao have aided to obtain cultivars with characteristics of tolerance to diseases, adaptability to different edaphoclimatic conditions, and higher yields. In Ecuador, as a result of several breeding programs, the cloneCCN51 was obtained, which gradually expanded through the cacao-production regions of Ecuador, Colombia, Brazil and Peru. Recognized for its high yield and adaptability to different regions and environments, it has become one of the most popular clones for breeding programs and cultivation around the world. This review aims to summarize the current evidence on the origin, genetics, morphological, volatile compounds, and organoleptic characteristics of this clone. Physiological evidence, production dynamics, and floral biology are also included to explain the high yield of CCN 51. Thus, characteristics such as osmotic adjustment, long pollen longevity, and fruit formation are further discussed and associated with high production at the end of the dry period. Finally, the impact of this popular clone on the current and future cacao industry will be discussed highlighting the major challenges for flavor enhancement and its relevance as a platform for the identification of novel genetic markers for cultivar improvement in breeding programs. [ABSTRACT FROM AUTHOR]

Copyright of BIOAGRO is the property of Revista BIOAGRO and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract: BACKGROUND: Ecuador exports two major types of cocoa beans, the highly regarded and lucrative National, known for its fine aroma, and the CCN‐51 clone type, used in bulk for mass chocolate products. In order to discourage exportation of National cocoa adulterated with CCN‐51, a fast and objective methodology for distinguishing between the two types of cocoa beans is needed. RESULTS: This study reports a methodology based on computer vision, which makes it possible to recognize these beans and determine the percentage of their mixture. The methodology was challenged with 336 samples of National cocoa and 127 of CCN‐51. By excluding the samples with a low fermentation level and white beans, the model discriminated with a precision higher than 98%. The model was also able to identify and quantify adulterations in 75 export batches of National cocoa and separate out poorly fermented beans. CONCLUSION: A scientifically reliable methodology able to discriminate between Ecuadorian National and CCN‐51 cocoa beans and their mixtures was successfully developed. © 2017 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Cocoa ( Theobroma cacao ) is a crop of economic importance. In Ecuador, there are two predominant cocoa varieties: National and CCN-51. The National variety is the most demanded, since its cocoa beans are used to produce the finest chocolates. Raman measurements of fermented, dried and unpeeled cocoa beans were performed using a handheld spectrometer. Samples of the National and CCN-51 varieties were collected from different provinces and studied in this work. For each sample, 25 cocoa beans were considered and each bean was measured at 4 different spots. The most important Raman features of the spectra were assigned and discussed. The spectroscopic data were processed using chemometrics, resulting in a distinction of varieties with 91.8% of total accuracy. Differences in the average Raman spectra of cocoa beans from different sites but within the same variety can be attributed to environmental factors affecting the cocoa beans during the fermentation and drying processes. [ABSTRACT FROM AUTHOR]

The cocoa cultivated in Ecuador is having greatest aroma, exquisite flavor, fragrance and quality for exportation market; it is a strategic species for the Ecuadorian agribusiness. The present study was aimed at characterizing the associate mycobiota to cocoa fruits with symptoms of Moniliasis based on morphological characters in the Ecuadorian Amazon. Infected plant materials (flowers, and fruits) were collected and processed in the laboratory to prepare humid cameras. Once isolated, using the technique of humid cameras and based on morphological criteria the following genera and species of filamentous fungi associated with cacao fruits were identified: Cylindrocladium (Morgan), Dichobotrys (Hennebert) Moniliophthora roreri (Cif.) HC Evans, Stalpers (Samson & Benny), Colletotrichum (Corda) and Phytophthora palmivora (EJ Butler). The results indicated that the morphological features are very useful to identify and characterize filamentous fungi associated with cacao pods. These microorganisms can cause deterioration of the harvested material. [ABSTRACT FROM AUTHOR]

• 44 yeast strains were tested against Moniliophthora roreri ; Frosty pod rot of cacao. • Six strains totally control M. roreri in vitro. • Seven yeasts were identified by molecular tools and found to belong to two genera. • Antifungal properties involved a combination of mechanisms. • Co-culture and VOCs reduced mycelial growth and spore numbers of M. roreri. Frosty pod rot is the most significant disease of cacao (Theobroma cacao L.) in Tropical America, enormously decreasing cacao production in these regions. The introduction of the disease in Cruzeiro do Sul, Brazil, increased cacao growers' concern. Preventive control measurements are already being studied and established. Therefore, this study aimed to isolate and identify yeasts from cacao tissues with the potential to control Moniliophthora roreri , the causal agent of frosty pod rot disease, and further evaluate some of their possible antagonistic mechanisms of action. The initial screening was conducted through a dual-culture with two M. roreri isolates from Ecuador and forty-four yeast isolates (38 from Ecuador, six from Brazil) from cacao tissues, cultivated separately. Yeast antagonistic activity was verified by co-cultivation, volatile organic compounds, cell-free suspensions, and thermostable compounds. Moreover, the biofilm-forming capacity of yeast isolates was examined. Seven yeast isolates were selected and showed an inhibitory effect of up to 71% in dual-cultures. None of them grew in body temperature. The isolates were identified by primer pairs of the D1/D2 region of the large subunit ribosomal ribonucleic acid (LSU rRNA) of Hannaella pagnoccae (INIAP-YYL 111, INIAP-YYL 112 and INIAP-YML 324), H. luteola (INIAP-YYL 521), Vishniacozyma carnescens (INIAP-YYL 612), Hannaella spp. (INIAP-YYL 123) and Rhodotorula paludigena (LEV 169), the last one already studied against Moniliophthora perniciosa in Brazil. Seven out of the forty-four yeast studied showed high inhibitory potential against M. roreri by different antagonistic mechanisms: co-cultivation in culture medium, volatile organic compounds, cell-free and thermostable compounds, and capacity for biofilm formation, some of these characteristics are promising for further use of yeasts as a biocontrol agent of M. roreri. [ABSTRACT FROM AUTHOR]

The cocoa type "Colección Castro Naranjal 51" (CCN-51) is known for its resistance to specific climate conditions and its high yield, but it shows a weaker flavor profile and therefore is marketed as bulk cocoa. In a previous study, the two cocoa types Arriba and CCN-51 could easily be distinguished, but differences among the CCN-51 samples were observed. This was unexpected, as CCN-51 is reported to be a clone. To confirm whether CCN-51 is a pure clone, 10 simple sequence repeats (SSR) located on the nuclear genome were used to analyze various CCN-51 samples in comparison to the cocoa varieties Arriba and Criollo. As expected, there are differences in the SSR pattern among CCN-51, Arriba, and Criollo, but a variability within the CCN-51 sample set was detected as well. The previously described sequence variation in the chloroplast genome was confirmed by a variability in the microsatellite loci of the nuclear genome for a comprehensive cultivar collection of CCN-51 of both bean and leaf samples. In summary, beneath somaclonal variation, misidentification of plant collections and also sexual reproduction of CCN-51 can be suggested.

Two cocoa types, Arriba and CCN-51, are being cultivated in Ecuador. With regard to the unique aroma, Arriba is considered a fine cocoa type, while CCN-51 is a bulk cocoa because of its weaker aroma. Because it is being assumed that Arriba is mixed with CCN-51, there is an interest in the analytical differentiation of the two types. Two methods to identify CCN-51 adulterations in Arriba cocoa were developed on the basis of differences in the chloroplast DNA. On the one hand, a different repeat of the sequence TAAAG in the inverted repeat region results in a different length of amplicons for the two cocoa types, which can be detected by agarose gel electrophoresis, capillary gel electrophoresis, and denaturing high-performance liquid chromatography. On the other hand, single nucleotide polymorphisms (SNPs) between the CCN-51 and Arriba sequences represent restriction sites, which can be used for restriction fragment length polymorphism analysis. A semi-quantitative analysis based on these SNPs is feasible. A method for an exact quantitation based on these results is not realizable. These sequence variations were confirmed for a comprehensive cultivar collection of Arriba and CCN-51, for both bean and leaf samples.