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Contrasting impacts of Faidherbia albida on maize and cotton production at two sites in the Sudanian zone of Cameroon
No full textCassava cooking properties characterization using NIRS on fresh ground cassava – Updated dataset 2020-2023
No full textThis report, written under the RTB Breeding project, explores the characterization of cassava cooking properties using Near-Infrared Spectroscopy (NIRS). The study, conducted over five years, is based on the analyses of 3049 cassava genotypes (5815 samples) originated from various breeding populations at the CIAT research centre and from experimental fields. The samples were evaluated for their water absorption capacity after 30 minutes of boiling (WA30, a key indicator of cooking quality) and their near infrared fingerprints. Genotypes were classified into 2 classes according to their WA30 values with C1 corresponding to WA30 < 12% and C2 corresponding to WA30 ≥ 12%. The repartition by classes was 3111 samples in C1 and 2704 samples in C2. To classify the genotypes, the study used Principal Components Analysis (PCA) to reduce the dimensionality of the spectral data, followed by Locally Weighted Partial Least Squares Regression Discriminant Analysis (LWPLSRDA) for predicting the genotype classes. The robustness and accuracy of these models were key focuses. The final LWPLSRDA model achieved a classification accuracy of 80% in distinguishing between "low cooking time" and "long cooking time" genotypes. The model was balanced in terms of sensitivity and specificity, which means a high capacity to detect true positives and true negatives genotypes. This study confirms that there is a relationship between the NIR fingerprint of fresh cassava tubers, largely due to chemical composition, and their cooking capacity. By integrating NIRS technology into cassava breeding, researchers can more efficiently identify varieties with optimal cooking properties, thereby supporting the development of superior cassava cultivars
Diversité et abondance des principaux acariens ravageurs sur Solanaceae et de leurs ennemis naturels. Mise en avant de l'influence de l'usage des pesticides et de l'enherbement sur ces variables. Étude exploratoire dans 4 grandes agglomérations de Côte d'Ivoire
No full textLa filière maraichage en Afrique de l'Ouest est fragilisée, depuis plusieurs années, par des attaques de divers ravageurs dont les acariens phytophages. Cependant, un manque de données sur la diversité et l'abondance des acariens et de leurs ennemis naturels en Côte d'Ivoire a été constaté. La réduction des produits phytosanitaires, dont l'usage local est aujourd'hui peu maitrisé, devient également un enjeu sanitaire, économique et écologique face, notamment, à la diminution de la biodiversité au sein des agrosystèmes. Cette étude tente donc de présenter une première image de l'abondance et la répartition des acariens ravageurs et de leurs ennemis naturels en Côte d'ivoire. La mise en relation de ces variables avec les pesticides utilisés et la gestion de la couverture du sol ont également été traités. L'étude exploratoire a été réalisée dans 4 zones maraichères urbaines et périurbaines de Côte d'Ivoire : Abidjan, Yamoussoukro, Bouaké et Korhogo. Les échantillonnages ont été portés sur cultures de tomate (Solanum lycopersicum), aubergine africaine (Solanum aethiopicum) et aubergine (Solanum melongena). Après rinçage et filtrage des feuilles récoltées, les individus (acariens phytophages et prédateurs) ont été comptés et montés entre lames et lamelles. Des enquêtes directives sur les différentes pratiques agricoles dernièrement réalisées sur les parcelles ont été conduites. Les identifications ont confirmé la présence de Tetranychus evansi dans les quatre zones d'études avec une abondance marquée à Korhogo, où le climat sec et chaud, est propice à son développement. La plus grande diversité de Tetranychidae a été observée dans la zone d'Abidjan avec la découverte de deux nouvelles espèces du groupe urticae. Cette étude a aussi permis de mettre en évidence une très faible abondance de Phytoseiidae, même dans les parcelles peu ou pas traitées depuis plusieurs mois. Aucun insecte ennemi naturel n'a été relevé. Au total, 5 espèces de phytoséiides ont été identifiées : Amblyseius swirskii (Athias-Henrio), Neoseiulus barkeri (Hughes), Amblyseius Tamatavensis (Blommers), Paraphytoseius horrifer (Pritchard & Baker) et Neoseiulus teke (Pritchard & Baker). Enfin, l'AFDM a relevé une corrélation positive entre le taux d'enherbement et la diversité et abondance des phytoséiides. Le développement d'élevage de Phytoseiulus longipes pourrait être envisagé dans les zones d'étude afin de lutter contre Tetranychus evansi
Influence of cover crops and their traits on the yield of main annual crops grown in tropical and subtropical environments - A meta-analysis
Get PDFContext or problem: The sustainability of agriculture in tropical regions is threatened by climate change, soil degradation, and food insecurity. Crop diversification through growing cover crops is a promising strategy to mitigate these problems. However, their effects in rotation and as intercrops has not been comprehensibly assessed in the tropics, considering cultural practices, edapho-climatic conditions, and the functional traits of these cover crops. This study aims to conduct a comprehensive meta-analysis to simultaneously analyze, in rotation and intercropping systems, the effect of cover crops and their traits on the yield of main annual crops grown in tropical and subtropical regions. Methods: A meta-analysis was conducted based on 1788 field observations from 191 articles covering 29 tropical and subtropical countries and regions. The analysis accounted for both rotation and intercropping systems, while considering the variability in cultural practices, edapho-climatic conditions, and traits of cover crops. Results: The results showed that the cover crops increased yields of cereals, legumes, and fiber crops by 25 % in rotation and by 7 % in intercrops compared to monocrops. These effects varied greatly depending on the context. In rotation, yield gains were enhanced by crop residue incorporation, nitrogen application, bimodal tropical climates compared to unimodal ones, and altitude. In intercrops, positive effects were associated with the use of Fabaceae as cover crops, staggered sowing, altitude, temperature, and subtropical climates and volcanic soils (Andosols). Yield responses varied depending on the annual crop: in rotation, maize (290 %), soybeans (300 %), and cotton (240 %), relative yield gains were observed in low-yielding environments, while in intercrops only maize (360 %) showed gains under these conditions, and rice (- 30 %) suffered a decline. Analysis of cover crop traits revealed that in rotation systems, aboveground cover crops biomass, root diameter and root density explained part of the relative yield variability and were positively associated with relative yield. In intercrops, cover crops aboveground nitrogen mass was explanatory of annual crop yield. Conclusions: Fabaceae cover crops tend to perform better in intercropping, particularly in subtropical climates and in Andosols. In tropical crop rotations, conserving cover crop residues improves yields, further enhanced by nitrogen fertilization. Cover crops are particularly beneficial in low-yield contexts. Furthermore, the traits of cover crops are insufficiently documented, and their explanatory power remains limited, making the effects of cover crops on annual crop yields unclear. This highlights the importance of conducting further research in this area to gather additional evidence
Bioinformatics solutions for addressing post-processing challenges in Nanopore sequencing data
Get PDFNanopore sequencing (Oxford Nanopore Technology) has rapidly become more accessible and widely adopted in research laboratories, offering a real-time, cost-effective, and portable sequencing technology. This advancement has significantly accelerated scientific discoveries, particularly in metagenomic studies, by enabling comprehensive analyses of diverse microbial and viral communities. However, the inherent characteristics of Nanopore sequencing introduce several challenges. The high error rate, for instance, complicates the assembly of reads, as well as the detection and removal of Nanopore adapters and barcodes. Additionally, the ligation of adapters to DNA fragments (using the Ligation Sequencing Kit) and/or the overloading of DNA in the flowcell, appear to contribute to a substantial number of chimeric and inverted repeated reads, especially when dealing with short DNA fragments. These issues significantly complicate the processing of sequencing data from multiplexed DNA samples, as many reads are either misallocated to incorrect samples (e.g., chimeric reads) or poorly assembled (e.g., inverted repeated reads). Existing bioinformatics tools, such as Dorado, Guppy, and Porechop, do not fully address these challenges. Consequently, we identified the need for specialized, custom-built tools designed to tackle these specific problems. To address this, we are currently developing three computational tools: . DeSIR: a tool for detecting and splitting inverted repeat reads, . Tripatouille: a tool for identifying and removing adapters and barcodes (custom or Nanopore), particularly suited for demultiplexing and cleaning multiplexed amplicon reads, such as those derived from the virion-associated nucleic acid (VANA)-based metagenomics approach, . ChimeraKiller: a tool for detecting and splitting chimeric reads (currently under development). These tools, still in the prototype phase, require further refinement, particularly in terms of execution speed and adjustments to sensitivity and specificity
The American cocoa pod borer, Carmenta foraseminis, an emerging pest of cocoa: A review
Get PDFThis review provides a synthesis of the available knowledge on Carmenta foraseminis, an emerging cocoa pest in northern South America. This moth was first described in 1995 in Panama, and its proliferation across the Amazon basin is currently threatening the production of cocoa in the region and may endanger the sector's sustainability. Hence, it is important to further draw the attention of researchers towards this emerging pest. The larvae of this lepidopteran burrow within the pod and feed on beans and their pulp, causing important losses. We present a critical synthesis of the knowledge on C. foraseminis (biology, geographic distribution, phylogenetic status, ecology), to identify the cause of its emergence and key points for its control. We also describe similarities to another lepidopteran, the Cocoa Pod Borer (CPB) Conopomorpha cramerella, which is the main pest of cocoa in Asia, especially on the way it is controlled and eventual lessons and recommendations that can be drawn from the situation in Asia to better understand and manage cocoa pod infestation in the Amazon basin. Additionally, we propose further research themes to be explored for Carmenta foraseminis that will help in the development of efficient management practices
Navigating the complexity of lipid oxidation and antioxidation: A review of evaluation methods and emerging approaches
Get PDFLipid oxidative degradation contributes to the deterioration of food quality and poses potential health risks. A promising approach to counteract this is the use of plant-based antioxidants. However, accurately evaluating the antioxidant capacity and effectiveness of these compounds remains a challenge. While many rapid in vitro tests are available, they must be categorized according to their specific responses to avoid overinterpreting results. This review opens with an overview of current knowledge on lipid autoxidation and recent findings that high- light the challenges in measuring antioxidant capacity. We then examine various methods, addressing their limitations in accurately anticipating outcomes in complex compartmentalized lipid systems. The aim is to clarify the gap between predictions and real-world efficacy in final products. Additionally, the review compares the strengths and weaknesses of methods used to evaluate antioxidant capacity and assess oxidation degrees in complex environments, such as those found in food and cosmetics. Finally, new analytical techniques for multiproduct detection are introduced, paving the way for a more 'omic' and spatiotemporally defined approach
Exploring the effects of slow pyrolysis temperature and species on the quality of charcoal from Amazonian woody wastes
No full textThe literature lacks information on how the final slow pyrolysis temperature and Amazonian Forest wood species impact charcoal's physical, chemical, and energetical properties. Thus, this study aimed to evaluate the effect of wood species and final slow pyrolysis temperatures on the charcoal quality for the Brazilian steelmaking industry. Wood wastes were sampled from the branches of six tropical hardwoods (Dinizia excelsa, Manikara elata, Caryocar villosum, Couratari oblongifolia, Anacardium giganteum, and Parkia gigantocarpa). Laboratory-scale slow pyrolysis was performed at 400, 500, 600, and 700 ◦C. The variations were significant for wood basic density (0.420–0.990 g cm 3), lignin content (22.78–40.68 %, based on dry mass - db), and total extractives' content (2.45–12.01 % db). Furthermore, a significant effect of the pyrolysis temperature and wood species on the gravimetric yield of charcoals (31.66–39.41 % db) was confirmed. The greatest higher heating values for charcoal (>31.00 MJ kg 1) were observed for pyrolysis performed above 600 ◦ C for all species, except P. gigantocarpa, which provided charcoal with 31.90 MJ kg 1 at 500 ◦C. Balancing all variables studied, temperatures between 400 and 500 ◦C were optimal for charcoal production. For such species, the effect of the raw wood properties overcame the impact of slow pyrolysis temperature
Bayesian joint-regression analysis of unbalanced series of on-farm trials
Get PDFParticipatory plant breeding (PPB) is aimed at developing varieties adapted to agroecologically-based systems. In PPB, selection is decentralized in the target environments, and relies on collaboration between farmers, farmers' organisations and researchers. By doing so, evaluation of new genotypes takes genotype x environment (GxE) interactions into account to select for specific adaptation. In many cases, there is little overlap among genotypes assessed from farm to farm because the farmers participating in a PPB project choose which ones to assess on their farm. In addition, on-farm trials can often generate more extreme observations than trials carried out on research stations. These features make the estimation of genotype, environment and interaction effects more difficult. This challenge is not unique to PPB, as many breeding programs use sparse testing or incomplete block designs to evaluate more genotypes, however in PPB genotypes are not always assigned randomly to environments. To explore methods of overcoming these challenges, this article tests various data analysis scenarios using a Bayesian approach with different models and a real wheat PPB dataset over 11 years. Four morpho-agronomic traits were studied, representing over 1000 GxE combinations from 189 on-farm trials. This dataset was severely unbalanced with more than 90% of GxE combinations missing. We compared various Bayesian Finlay-Wilkinson models and found that placing hierarchical distributions on model parameters and modelling residuals using a Student's t distribution jointly improved the estimates of main effects and interactions. Environment effects were the most important and explained more than 50% of the variance of observations. This statistical framework allowed us to estimate two indicators of genotype stability (one static and one dynamic) despite the high disequilibrium of the data. We found differences in mean and stability between genotype categories, with registred varieties consistently shorter (-30 cm) and containing less protein (-0.3%) than other types of varieties. The methods developed could be used for evaluation and/or selection within networks of various stakeholders such as farmers, gardeners, plant breeders or managers of genetic resource centres