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Cassava brown streak virus disease: Past, present and future.
Cassava has been an important success story in Africa's developing agriculture over the past decade. The crop's inherei'lt capacity to cope with marginal growing conditions and unpredictable rainfall, coupled with determined efforts of a number of countries to move away from over-reliance on maize, have helped establish it as the continent's number one crop in terms of total fresh production. The hope provided by these gains is now threatened, however, by the devastating impact of the virus diseases, cassava mosaic and cassava brown streak. Both have been known for many years, but seem to be becoming increasingly damaging, and pose an ever greater threat to the livelihoods of the millions of Africans who depend on cassava as a food staple. Substantial effort has been directed towards understanding and managing cassava mosaic. By contrast, cassava brown streak disease (CBSD), which has a more limited distribution, and causes most severe damage in the coastal lowlands of Eastern and Southern Africa, has received little attention. In order to address this deficiency, an international workshop was convened at Mombasa, Kenya. This meeting brought together a diverse range of cassava stakeholders with the twin aims of reviewing current research into cassava brown streak and developing a plan to guide future research for development initiatives. The IS papers presented in these proceedings provide a useful and informative summary of the history and current status of CBSD, recent research initiatives and management options for the worst affected countries - Malawi, Tanzania, Kenya and Mozambique. Outputs of the research and on-farm working group sessions are also included. lt is anticipated that this information will serve both as a useful technical resource as well as an essential planning tool for scientists, development workers and others with an interest in the management of CBSD and the development of cassava in Africa
Unravelling the genetic diversity among cassava Bemisia tabaci whiteflies using NextRAD Sequencing
Article purchased; Published online: 31 Oct 2017Bemisia tabaci threatens production of cassava in Africa through vectoring viruses that cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). B. tabaci sampled from cassava in eight countries in Africa were genotyped using NextRAD sequencing, and their phylogeny and population genetics were investigated using the resultant single nucleotide polymorphism (SNP) markers. SNP marker data and short sequences of mitochondrial DNA cytochrome oxidase I (mtCOI) obtained from the same insect were compared. Eight genetically distinct groups were identified based on mtCOI, whereas phylogenetic analysis using SNPs identified six major groups, which were further confirmed by PCA and multidimensional analyses. STRUCTURE analysis identified four ancestral B. tabaci populations that have contributed alleles to the six SNP-based groups. Significant gene flows were detected between several of the six SNP-based groups. Evidence of gene flow was strongest for SNP-based groups occurring in central Africa. Comparison of the mtCOI and SNP identities of sampled insects provided a strong indication that hybrid populations are emerging in parts of Africa recently affected by the severe CMD pandemic. This study reveals that mtCOI is not an effective marker at distinguishing cassava-colonizing B. tabaci haplogroups, and that more robust SNP-based multilocus markers should be developed. Significant gene flows between populations could lead to the emergence of haplogroups that might alter the dynamics of cassava virus spread and disease severity in Africa. Continuous monitoring of genetic compositions of whitefly populations should be an essential component in efforts to combat cassava viruses in Africa
Application of FTA technology for sampling, recovery and molecular characterization of viral pathogens and virus-derived transgenes from plant tissues
BACKGROUND: Plant viral diseases present major constraints to crop production. Effective sampling of the viruses infecting plants is required to facilitate their molecular study and is essential for the development of crop protection and improvement programs. Retaining integrity of viral pathogens within sampled plant tissues is often a limiting factor in this process, most especially when sample sizes are large and when operating in developing counties and regions remote from laboratory facilities. FTA is a paper-based system designed to fix and store nucleic acids directly from fresh tissues pressed into the treated paper. We report here the use of FTA as an effective technology for sampling and retrieval of DNA and RNA viruses from plant tissues and their subsequent molecular analysis. RESULTS: DNA and RNA viruses were successfully recovered from leaf tissues of maize, cassava, tomato and tobacco pressed into FTA(Âź )Classic Cards. Viral nucleic acids eluted from FTA cards were found to be suitable for diagnostic molecular analysis by PCR-based techniques and restriction analysis, and for cloning and nucleotide sequencing in a manner equivalent to that offered by tradition isolation methods. Efficacy of the technology was demonstrated both from sampled greenhouse-grown plants and from leaf presses taken from crop plants growing in farmer's fields in East Africa. In addition, FTA technology was shown to be suitable for recovery of viral-derived transgene sequences integrated into the plant genome. CONCLUSION: Results demonstrate that FTA is a practical, economical and sensitive method for sampling, storage and retrieval of viral pathogens and plant genomic sequences, when working under controlled conditions and in the field. Application of this technology has the potential to significantly increase ability to bring modern analytical techniques to bear on the viral pathogens infecting crop plants
Automated registration of multimodal optic disc images: clinical assessment of alignment accuracy
Purpose: To determine the accuracy of automated alignment algorithms for the registration of optic disc images obtained by 2 different modalities: fundus photography and scanning laser tomography.
Materials and Methods: Images obtained with the Heidelberg Retina Tomograph II and paired photographic optic disc images of 135 eyes were analyzed. Three state-of-the-art automated registration techniques Regional Mutual Information, rigid Feature Neighbourhood Mutual Information (FNMI), and nonrigid FNMI (NRFNMI) were used to align these image pairs. Alignment of each composite picture was assessed on a 5-point grading scale: âFailâ (no alignment of vessels with no vessel contact), âWeakâ (vessels have slight contact), âGoodâ (vessels with 50% contact), and âExcellentâ (complete alignment). Custom software generated an image mosaic in which the modalities were interleaved as a series of alternate 5Ă5-pixel blocks. These were graded independently by 3 clinically experienced observers.
Results: A total of 810 image pairs were assessed. All 3 registration techniques achieved a score of âGoodâ or better in >95% of the image sets. NRFNMI had the highest percentage of âExcellentâ (mean: 99.6%; range, 95.2% to 99.6%), followed by Regional Mutual Information (mean: 81.6%; range, 86.3% to 78.5%) and FNMI (mean: 73.1%; range, 85.2% to 54.4%).
Conclusions: Automated registration of optic disc images by different modalities is a feasible option for clinical application. All 3 methods provided useful levels of alignment, but the NRFNMI technique consistently outperformed the others and is recommended as a practical approach to the automated registration of multimodal disc images
Genetic diversity of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) colonizing sweet potato and cassava in South Sudan
Open Access Journal; Published online: 17 Jan 2020Bemisia tabaci (Gennadius) is a polyphagous, highly destructive pest that is capable of vectoring viruses in most agricultural crops. Currently, information regarding the distribution and genetic diversity of B. tabaci in South Sudan is not available. The objectives of this study were to investigate the genetic variability of B. tabaci infesting sweet potato and cassava in South Sudan. Field surveys were conducted between August 2017 and July and August 2018 in 10 locations in Juba County, Central Equatoria State, South Sudan. The sequences of mitochondrial DNA cytochrome oxidase I (mtCOI) were used to determine the phylogenetic relationships between sampled B. tabaci. Six distinct genetic groups of B. tabaci were identified, including three non-cassava haplotypes (Mediterranean (MED), Indian Ocean (IO), and Uganda) and three cassava haplotypes (Sub-Saharan Africa 1 sub-group 1 (SSA1-SG1), SSA1-SG3, and SSA2). MED predominated on sweet potato and SSA2 on cassava in all of the sampled locations. The Uganda haplotype was also widespread, occurring in five of the sampled locations. This study provides important information on the diversity of B. tabaci species in South Sudan. A comprehensive assessment of the genetic diversity, geographical distribution, population dynamics, and host range of B. tabaci species in South Sudan is vital for its effective management
Efficacy of selected botanical oils against the cassava whitefly ( Bemisia tabaci ) and their effects on its feeding behaviour
The control of the whitefly Bemisia tabaci relies heavily on the use of synthetic insecticides. There is a need to develop alternative control strategies due to concerns about impact of these insecticides on the environmental and human health, and the threat of insecticide resistance. Botanical oil extracts could potentially be used for the management of whiteflies and other pests. The study reported here therefore aimed to evaluate the efficacy of selected botanical oils against the cassava whitefly, B. tabaci and test their effect on its feeding behaviour. Patchouli oil treatment was the most effective at repelling whiteflies in no choice and choice experiments with up to 85% of whiteflies being repelled. Oviposition was also reduced 50â89% in patchouli. Neem was found to be effective at reducing oviposition, nymph and adult emergence by 50%, 70% and 80%, respectively, in a screenhouse no choice experiment. Patchouli significantly reduced the phloem ingestion phase (E2) by 40% and potential drops (pd) by 46% compared to control plants. Neem significantly increased the nonâprobing duration by 48% and reduced pd by 50% compared to the control. Patchouli and neem were found to be the most effective among the selected botanical oils. These two oils should be further evaluated for efficacy under field conditions to determine suitability for recommendation as biopesticides against the cassava B. tabaci whitefly
A Mobile-Based Deep Learning Model for Cassava Disease Diagnosis
Convolutional neural network (CNN) models have the potential to improve plant disease phenotyping where the standard approach is visual diagnostics requiring specialized training. In scenarios where a CNN is deployed on mobile devices, models are presented with new challenges due to lighting and orientation. It is essential for model assessment to be conducted in real world conditions if such models are to be reliably integrated with computer vision products for plant disease phenotyping. We train a CNN object detection model to identify foliar symptoms of diseases in cassava (Manihot esculenta Crantz). We then deploy the model in a mobile app and test its performance on mobile images and video of 720 diseased leaflets in an agricultural field in Tanzania. Within each disease category we test two levels of severity of symptoms-mild and pronounced, to assess the model performance for early detection of symptoms. In both severities we see a decrease in performance for real world images and video as measured with the F-1 score. The F-1 score dropped by 32% for pronounced symptoms in real world images (the closest data to the training data) due to a decrease in model recall. If the potential of mobile CNN models are to be realized our data suggest it is crucial to consider tuning recall in order to achieve the desired performance in real world settings. In addition, the varied performance related to different input data (image or video) is an important consideration for design in real world applications
Improving oceanic overflow representation in climate models : the Gravity Current Entrainment Climate Process Team
Author Posting. © American Meteorological Society, 2009. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Bulletin of the American Meteorological Society 90 (2009): 657-670, doi:10.1175/2008BAMS2667.1.Oceanic overflows are bottom-trapped density currents originating in semienclosed basins, such as the Nordic seas, or on continental shelves, such as the Antarctic shelf. Overflows are the source of most of the abyssal waters, and therefore play an important role in the large-scale ocean circulation, forming a component of the sinking branch of the thermohaline circulation. As they descend the continental slope, overflows mix vigorously with the surrounding oceanic waters, changing their density and transport significantly. These mixing processes occur on spatial scales well below the resolution of ocean climate models, with the result that deep waters and deep western boundary currents are simulated poorly. The Gravity Current Entrainment Climate Process Team was established by the U.S. Climate Variability and Prediction (CLIVAR) Program to accelerate the development and implementation of improved representations of overflows within large-scale climate models, bringing together climate model developers with those conducting observational, numerical, and laboratory process studies of overflows. Here, the organization of the Climate Process Team is described, and a few of the successes and lessons learned during this collaboration are highlighted, with some emphasis on the well-observed Mediterranean overflow. The Climate Process Team has developed several different overflow parameterizations, which are examined in a hierarchy of ocean models, from comparatively well-resolved regional models to the largest-scale global climate models.The Gravity Current
Entrainment Climate Process Team was funded by NSF
grants OCE-0336850 and OCE-0611572 and NOAA as a
contribution to U.S.CLIVAR
Epidemiological analysis of Cassava Mosaic and Brown Streak Diseases, and Bemisia tabaci in the Comoros Islands
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Open AccessArticle
Epidemiological Analysis of Cassava Mosaic and Brown Streak Diseases, and Bemisia tabaci in the Comoros Islands
by Rudolph Rufini Shirima 1,*ORCID,Everlyne Nafula Wosula 1ORCID,Abdou Azali Hamza 2,Nobataine Ali Mohammed 2,Hadji Mouigni 2,Salima Nouhou 2,Naima Mmadi Mchinda 2,Gloria Ceasar 1,Massoud Amour 1,Emmanuel Njukwe 3 andJames Peter Legg 1ORCID
1
International Institute of Tropical Agriculture (IITA-Tanzania), P.O. Box 34441, Dar es Salaam 14112, Tanzania
2
Institut National de Recherche pour LâAgriculture, La PĂȘche et LâEnvironnement (INRAPE), Moroni BP 1406, Comoros
3
West and Central African Council for Agricultural Research and Development (CORAF), Dakar CP 18523, Senegal
*
Author to whom correspondence should be addressed.
Viruses 2022, 14(10), 2165; https://doi.org/10.3390/v14102165
Received: 2 August 2022 / Revised: 15 September 2022 / Accepted: 28 September 2022 / Published: 30 September 2022
(This article belongs to the Special Issue Plant Virus Surveillance and Metagenomics)
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Abstract
A comprehensive assessment of cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) was carried out in Comoros where cassava yield (5.7 t/ha) is significantly below the African average (8.6 t/ha) largely due to virus diseases. Observations from 66 sites across the Comoros Islands of Mwali, Ngazidja, and Ndzwani revealed that 83.3% of cassava fields had foliar symptoms of CBSD compared with 95.5% for CMD. Molecular diagnostics confirmed the presence of both cassava brown streak ipomoviruses (CBSIs) and cassava mosaic begomoviruses (CMBs). Although real-time RT-PCR only detected the presence of one CBSI species (Cassava brown streak virus, CBSV) the second species (Ugandan cassava brown streak virus, UCBSV) was identified using next-generation high-throughput sequencing. Both PCR and HTS detected the presence of East African cassava mosaic virus (EACMV). African cassava mosaic virus was not detected in any of the samples. Four whitefly species were identified from a sample of 131 specimens: Bemisia tabaci, B. afer, Aleurodicus dispersus, and Paraleyrodes bondari. Cassava B. tabaci comprised two mitotypes: SSA1-SG2 (89%) and SSA1-SG3 (11%). KASP SNP genotyping categorized 82% of cassava B. tabaci as haplogroup SSA-ESA. This knowledge will provide an important base for developing and deploying effective management strategies for cassava viruses and their vectors
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