Brown Streak Research Articles

Utility of Ugandan genomic selection cassava breeding populations for prediction of cassava viral disease resistance and yield in West African clones.

Cassava (Manihot esculenta Crantz) is a staple crop for ~800 million people in sub-Saharan Africa. Its production and productivity are being heavily affected by the two viral diseases: cassava brown streak disease (CBSD) and cassava mosaic disease (CMD), impacting greatly on edible root yield. CBSD is currently endemic to central, eastern and southern Africa, if not contained could spread to West Africa the largest cassava producer and consumer in the continent. Genomic selection (GS) has been implemented in Ugandan cassava breeding for accelerated development of virus resistant and high yielding clones. This study leveraged available GS training data in Uganda for pre-emptive CBSD breeding in W. Africa alongside CMD and fresh root yield (FRW). First, we tracked genetic gain through the current three cycles of GS in Uganda. The mean genomic estimated breeding values (GEBVs), indicated general progress from initial cycle zero (C0) to cycle one (C1) and cycle two (C2) for CBSD traits and yield except for CMD. Secondly, we used foliar data of both CBSD and CMD, as well as harvest root necrosis and yield data to perform cross-validation predictions. Cross-validation prediction accuracies of five GS models were tested for each of the three GS cycles and West African (WA) germplasm as a test set. In all cases, cross-validation prediction accuracies were low to moderate, ranging from -0.16 to 0.68 for CBSD traits, -0.27 to 0.57 for CMD and -0.22 to 0.41 for fresh root weight (FRW). Overall, the highest prediction accuracies were recorded in C0 for all traits tested across models and the best performing model in cross-validation was G-BLUP. Lastly, we tested the predictive ability of the Ugandan training sets to predict CBSD in W. African clones. In general, the Ugandan training sets had low prediction accuracies for all traits across models in West African germplasm, varying from -0.18 to 0.1. Based on the findings of this study, the cassava breeding program in Uganda has made progress through application of GS for most target traits, but the utility of the training population for pre-emptive breeding in WA is limiting. In this case, efforts should be devoted to sharing Ugandan germplasm that possess resistance with the W. African breeding programs for hybridization to fully enable deployment of genomic selection as a pre-emptive CBSD breeding strategy in W. Africa.

Epidemic Pressure of Cassava Mosaic and Brown Streak Diseases on Ten Exotic Cassava (Manihot esculenta Crantz) Cultivars in Kisangani, DRC

The crucial obstacle to cassava production in most of African countries is the diseases and pests. The present study assessed in field the epidemic pressure of Cassava mosaic disease (CMD) and Cassava brown streak disease (CBSD) on 10 exotic cassava genotypes in Kisangani. To assess the disease impact, trials were established in two sites in Kisangani, Tshopo Province in DRC. The experiment was laid out in randomized completed block design and thrice replicated. Sixty stem cuttings per variety were planted in a plot of 7 rows each measuring 25 m long. Results showed a relatively important CBSD pressure on all the ten exotic cassava genotypes tested (incidence close 60%, severity score 2 and 3.5 whiteflies/plant) and low CMD pressure (incidence 3.3%, severity score 2 and 3.5 whiteflies/plant). CMD remained relatively negligible depending on low symptom manifestation of the tested genotypes. Whitefly population varied according to the genotype and the crop age. The most abundant population was recorded on cultivar ‘Mayombe’ (17 whiteflies/plant). A negative relationship was statistically established between the abundance of whiteflies and the incidence and severity as well as for CBSD and for CMD. The production in terms of percentage of marketable tubers was (74.9%) for cultivar ‘Mayombe’, (70.3%) for ‘Obama 1’, (69.9%) for ‘Obama 2’ and (65.3%) for ‘Ngandajika’. CBSD resulted in variable yield loss on all cultivars tested. The cultivar ‘Butamu’ (85%) recorded the highest loss rate, followed by the cultivar ‘Mvuama’ (70.8%) and ‘Muzuri’ (64.3%). The yield in cassava tubers was destroyed (˂ 5 t/ha) by large necrotic spots of the brown streak in the pulp. This loss is due to the depressive of viral pandemia pressure on the output of ten exotic cassava cultivars studied in Kisangani. Our study highlighted that the best moment of harvesting cassava in Kisangani is 9 MAP, this moment would be ideal to minimize harvesting losses due to CBSD root necrosis.

Evaluation of the Efficacy of Flupyradifurone against Bemisia tabaci on Cassava in Tanzania.

Simple SummaryCassava-colonizing Bemisia tabaci whitefly negatively impact cassava production in sub-Saharan Africa through transmission of viruses that cause cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). This study evaluated the efficacy of a novel insecticide flupyradifurone against this whitefly pest through standard spraying and cutting dip methods. The results from the laboratory, screenhouse and field experiments consistently showed flupyradifurone is effective at reducing whiteflies compared to control treatments. A single cutting dip using this insecticide was highly effective at reducing whiteflies under field conditions and, therefore, should be considered as an alternative to insecticide spraying in cassava systems. Additionally, whiteflies were least abundant during the long rainy season (Masika) and on cassava variety Mkuranga1.A novel butenolide insecticide—flupyradifurone (Sivanto SL 200)—was evaluated for efficacy against cassava-colonizing Bemisia tabaci whitefly under laboratory, screenhouse and field conditions. LC50 values from leaf disc spray assays were comparable for both flupyradifurone (12.7 g a.i/100 L) and imidacloprid (12.6 g a.i/100 L). Both insecticides caused high levels of adult whitefly mortality in leaf disc and leaf dip assays when compared to untreated controls. In screenhouse-based trials, longer soaking (60 min) with flupyradifurone or imidacloprid was more effective than shorter soaking durations (15 or 30 min). In field spraying experiments, flupyradifurone significantly reduced whiteflies, and both insecticides demonstrated powerful knockdown effects on whitefly adult abundances over a period up to 24 h. Single cutting dip application of flupyradifurone reduced whitefly adult abundance by 2 to 6 times, and nymphs by 2 to 13 times. Lower whitefly abundances resulting from insecticide application reduced the incidence of CMD or CBSD. In addition, in field experiments, whiteflies were fewer during the long rainy season (Masika) and on cassava variety Mkuranga1. The findings from this study demonstrate that cutting dips with flupyradifurone could be incorporated as a management tactic against cassava whiteflies. This would ideally be combined in an IPM strategy with other cassava virus and virus vector management tactics including host-plant resistance, phytosanitation and the use of clean seed.

Epidemiological Analysis of Cassava Mosaic and Brown Streak Diseases, and Bemisia tabaci in the Comoros Islands.

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.

Diversity and Distribution of Whiteflies Colonizing Cassava in Eastern Democratic Republic of Congo.

Simple SummaryWe report here the first detailed characterization of Bemisia whiteflies on cassava in eastern Democratic Republic of Congo (DRC). Bemisia tabaci transmits viruses responsible for devastating epidemics of cassava mosaic and brown streak diseases. KASP SNP genotyping of B. tabaci specimens collected from cassava in revealed the existence of four haplogroups, while phylogenetic analysis of mitochondrial COI sequences showed the presence of two major clusters of B. afer. This study provides important information on the genetic diversity of B. tabaci and B. afer in eastern DRC and emphasizes the need for continuous monitoring of whitefly populations on cassava to guide the strategic application of management practices that reduce the impact of cassava virus diseases throughout DRC and the wider Central Africa region.The present study characterizes Bemisia tabaci and Bemisia afer from cassava in eastern Democratic Republic of Congo (DRC). The Mitochondrial COI sequencing revealed the occurrence of six cassava B. tabaci mitotypes, which were designated into four haplogroups (SSA-ECA, SSA-CA, SSA2, and SSA-ESA) using KASP SNP genotyping. SSA-ECA (72%) was the most prevalent and occurred in the northern part of the surveyed area, in the Ituri and Nord/Sud-Kivu provinces, whilst SSA-CA (21%) was present in the south, primarily in Haut-Katanga. SSA-ECA was predominant in the areas of north-eastern DRC most severely affected by cassava brown streak disease and was also reported in the new outbreak area in Pweto territory, Haut-Katanga, in the south. Bemisia afer comprised two major clusters with 85.5% of samples in cluster one, while the rest were in cluster two, which has no reference sequence in GenBank. This study provides important information on the genetic diversity of B. tabaci and B. afer in eastern DRC. This knowledge will be used as a basis for further studies to understand and to identify the role of whitefly haplogroups, their population densities and consequences for virus epidemics and spread as well as leading to improved vector and virus management strategies.

Screening of cultivars against cassava brown streak disease and molecular identification of the phytopathogenic infection-associated viruses

Cassava brown streak disease (CBSD) has been reported as a serious and significant constraint on the cassava crop in Democratic Republic of the Congo (DRC), especially in its eastern part, South Kivu, where cassava has exceedingly high socio-economic value in small-holder farming systems. The recent rapid spread and damage of CBSD are alarming. Compared to cassava mosaic disease (CMD) which causes yield losses of up to 70% in very susceptible cassava cultivars, CBSD destroys whole the field causing 100% crop loss, including immediate and direct losses of tuberous roots, planting material, and quality of leaves. The study gathered information on the circulation of viral species present in the region, and screening of cassava cultivars against CBSD. Here we evaluated the disease incidence (DI) and severity (DS), whitefly vector Bemisia tabaci parameters including number of nymphs and adults. Thereat, the work consisted of quantifying the pressure of the disease to find performing cassava cultivars, which may still be recommendable for farmers. Thirty-one improved and local Congolese cassava cultivars were selected. Disease assessment focused more specifically on morphological, epidemiologic studies, and advanced molecular diagnostic techniques for virus detection. The mean extreme values of disease incidence and severity ranged respectively from 0.0 to 59.44%, and 1 to 2.86, root infection up to 100%, whiteflies up to 2 adults, and 68 nymphs per plant. Accordingly, the viral species identified in circulation are Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV) (picornalike (+) ssRNA viruses, Ipomovirus, Potyviridae). Varieties like Cibongoyoka, Dorothea, Kamegere, Korengo, Liyayi, M’Bailo, Nabana, Rav, and Siri showed no symptoms of necrosis on the roots. Some cultivars are even less susceptible or not to the disease and may be recommended in this time of the lack of planting material for farmers.

How growers make decisions impacts plant disease control.

While the spread of plant disease depends strongly on biological factors driving transmission, it also has a human dimension. Disease control depends on decisions made by individual growers, who are in turn influenced by a broad range of factors. Despite this, human behaviour has rarely been included in plant epidemic models. Considering Cassava Brown Streak Disease, we model how the perceived increase in profit due to disease management influences participation in clean seed systems (CSS). Our models are rooted in game theory, with growers making strategic decisions based on the expected profitability of different control strategies. We find that both the information used by growers to assess profitability and the perception of economic and epidemiological parameters influence long-term participation in the CSS. Over-estimation of infection risk leads to lower participation in the CSS, as growers perceive that paying for the CSS will be futile. Additionally, even though good disease management can be achieved through the implementation of CSS, and a scenario where all controllers use the CSS is achievable when growers base their decision on the average of their entire strategy, CBSD is rarely eliminated from the system. These results are robust to stochastic and spatial effects. Our work highlights the importance of including human behaviour in plant disease models, but also the significance of how that behaviour is included.

The first uses of colour: what do we know?

Colour strongly shapes our perception of the world and plays a main role in the emergence of language and in the transmission of information. It has been shown that systematic use of ochre, along with other cultural traits that reflect cognitive complexity, disappear and reappear from the archaeological record, suggesting that cultural transmission follows discontinuous trajectories that to this day are unknown to us. Understanding when humans started using colour and how this feature evolved may therefore be instrumental to understand the evolutionary paths followed by members of our lineage towards cultural complexity. The earliest secure evidence for ochre use is found at 300.000-year-old archaeological sites from Africa and Europe. It usually consists of iron-rich rocks characterized by a red, orange, yellow or brown colour and/or streak, modified by grinding, scraping and knapping to produce red or yellow powder, ochre residues adhering to different types of artefacts or sediment stained with ochre or rich in ochre microfragments. Around 160 ka, ochre use becomes a recurrent feature. Although analyses of ochre collections have become increasingly frequent, there is still very little information on the first instances of ochre use and on how this cultural feature evolved through time. Most cases of early evidence for colour use by different human fossil species were recovered during excavations conducted several decades ago, when ochre was not documented systematically. Excluding a few recently studied cases, there is often a lack of evidence to support the anthropogenic nature of these findings. The aim of this paper is to summarise what we know on ochre use during the Lower Palaeolithic / Early Stone Age (ESA) and Middle Palaeolithic / Middle Stone Age (MSA), review techniques currently used for the analysis of this material and highlight analytical and theoretical issues surrounding this complex cultural feature.

Risk factors associated with cassava brown streak disease dissemination through seed pathways in Eastern D.R. Congo.

Vegetatively propagated crops are particularly prone to disease dissemination through their seed systems. Strict phytosanitary measures are important to limit the impact of diseases as illustrated by the potato seed system in Europe. Cassava brown streak disease (CBSD) is a devastating disease caused by two viral species collectively named cassava brown streak viruses (CBSVs). CBSD can cause substantial root yield losses of up to 100% in the worst affected areas and is easily transmitted through stem cuttings. In Eastern and Central Africa, the epidemiology of CBSVs in the local socio-economical context of production remains poorly known while a better understanding would be an asset to properly manage the disease. This lack of information explains partially the limited efficiency of current regulatory schemes in increasing the availability of quality seed to smallholders and mitigating the spread of pests and diseases. This study surveyed the epidemiology of CBSVs in Uvira territory, Eastern D.R. Congo, and its drivers using a multivariate approach combining farmer’s interview, field observation, sampling and molecular detection of CBSVs. Investigation on the epidemiology of CBSD revealed that three clusters in the study area could be identified using five most significant factors: (i) symptoms incidence, (ii) number of whiteflies, (iii) types of foliar symptoms, (iv) cutting’s pathways and (v) plant age. Among the three clusters identified, one proved to be potentially interesting for seed multiplication activities since the disease pressure was the lowest. Through risk assessment, we also identified several key socio-economic determinants on disease epidemy: (i) factors related to farmer’s knowledge and awareness (knowledge of cassava pests and diseases, knowledge of management practices, support from extension services and management strategies applied), (ii) factors related to the geographical location of farmer’s fields (proximity to borders, proximity to town, distance to acquire cuttings), as well as (iii) the pathways used to acquire cuttings.

Identification and Distribution of Viruses Associated with Cassava Brown Streak Disease in North Kivu, DR Congo

Identification and Distribution of Viruses Associated with Cassava Brown Streak Disease in North Kivu, DR Congo

African cassava whitefly and viral disease management through timed application of imidacloprid

Cassava whitefly are a group of cryptic species within the Bemisia tabaci sensu lato complex that causes significant damage to cassava in Africa. B. tabaci Sub-Saharan Africa 1 (SSA1) is the major species in the study region which transmits plant-virus diseases to cassava and causes direct feeding damage. Benefits from management of cassava viral diseases through deployment of resistant varieties are being undermined by their susceptibility to B. tabaci SSA1 and the problem is exacerbated by high populations of B. tabaci in cassava fields. To develop a clean seed system that is disease-free, the judicious use of insecticides is required to manage this pest and vector. This study evaluated the effect of timing of insecticide application on controlling B. tabaci SSA1 population abundance and damage to cassava. Field trials were carried out between 2017 and 2018 in Kamuli and Wakiso districts of Uganda using the widely available insecticide Imidacloprid. Three cassava cultivars (NAROCASS1, SAUTI, KBH/2002/026) were planted in a randomized complete block trial design replicated three times. The insecticide was applied in split-plots designated as: (i) no protection (NP), no insecticide applied (control), (ii) early protection (EP), insecticide applied 2 times between 0 and 4 months after planting, (iii) long protection (LP), insecticide applied 3 times between 0 and 8 months after planting, and (iv) total protection (TP), insecticide applied 4 times between 0 and 12 months after planting. Except for control plots, stem cuttings were first dipped into a diluted solution of Imidacloprid prior to planting. Bi-monthly data were collected on the B. tabaci population, feeding damage, cassava mosaic disease and cassava brown streak disease. Stem cuttings and root yields were determined at harvest. The marginal rate of return for each treatment was calculated to determine cost effectiveness. Insecticide application effectively reduced B. tabaci populations, feeding damage and disease spread. Cassava yield differed significantly with insecticide treatment and amongst cultivars. Root and stem yield losses of >60% was recorded in unprotected control plots. The marginal rate of return of the early protection (0–4 MAP) program was 163%. We discuss these findings and the implication for judicious use of insecticides as part of a cassava clean seed system.

High-Throughput Virus Screening in Crosses of South American and African Cassava Germplasm Reveals Broad-Spectrum Resistance against Viruses Causing Cassava Brown Streak Disease and Cassava Mosaic Virus Disease

Screening cassava lines for resistance against viruses causing cassava brown streak disease (CBSD) is cumbersome because of the unpredictable and erratic virus infections in the slow plant infection processes that are frequently not associated with distinct leaf symptoms and because of the reliance on the assessment of root necrosis as an indicator of plant resistance/tolerance. The selection of resistant candidates thus extends over several growing cycles and is still associated with uncertainties about the stage of virus infection. To reduce the time for selection of resistant crosses and the uncertainties associated with field screening, we have developed a fast-forward virus screening workflow to assess cassava seedlings from crosses of cassava brown streak- and cassava mosaic virus-resistant parents. After passing through an intensive and precise virus infection routine, cassava seedlings that carried resistance against cassava brown streak and mosaic viruses were identified. Taking the results of 195 seedlings from 18 crossing families together, it became evident that resistance against the viruses causing CBSD is a dominant trait. The protocol developed for virus resistance screening in cassava can be readily adopted. It shifts resistance evaluation from the field to the nursery and replaces the erroneous and lengthy virus infection and screening process with a method of precision and speed.

Agronomic Performance and Carotenoid Content of Kenyan Yellow-Fleshed Cassava Clones

Vitamin A deficiency is common in Kenya; it has been reported among populations that depend on cassava as their main staple. Clonal evaluation of 324 locally developed yellow-fleshed cassava clones was carried out in two sites, Thika and Kiboko located in central and eastern Kenya respectively. Data was collected on agronomic performance, yield quality and reaction to biotic constraints. The clones rated well for the evaluated traits. The overall performance was better in Kiboko than Thika. Cassava Mosaic Disease, Cassava Brown Streak Disease (CBSD) and Cassava Green Mite (CGM) severity was scored on a scale of 1-5. The mean CBSD score was 1.17 in Kiboko and 1.46 in Thika, CMD severity was 1.15 in Kiboko but the disease was not observed at Thika. The CGM damage severity was 1.63 in Kiboko and 1.97 in Thika. The weight of roots per plant was 3.49 and 2.25 kg at Kiboko and Thika respectively. The dry, matter content of the roots was 49.86% at Kiboko and 29.06 at Thika. The cyanogenic potential was assessed using the pictrate test and rated on a scale of 1-9 and Kiboko had a score of 2.79 compared to 4.14 in Thika. A total of 91 samples were analyzed for carotenoid content using the spectrophotometry method. The Kiboko site had a higher mean carotenoid content (1736.96 µg/100 g) compared to Thika (1105.85 µg/100 g). Most of the samples (71%) analyzed had recorded a higher carotenoid content in Kiboko than Thika. The beta-carotene content was higher in Thika (374.16 µg/100 g) than Kiboko (291.30 µg/100 g). Promising clones adaptable to the two sites were identified.

Farmer-Cultivated Landraces and Improved Cassava Genotypes Exhibit Varied Response to Cassava Brown Streak Disease Under Natural Infections in Kenya

Cassava brown streak disease (CBSD) affects cassava growth and production with resultant foliar symptoms and storage root necrosis causing significant economic losses to farmers. The disease is caused by either Cassava brown streak virus (CBSV) or Uganda cassava brown streak virus (UCBSV), both vectored by whitefly, Bemisia tabaci. Cultivation of CBSD-free or resistant cassava genotypes offers the most long term sustainable CBSD management.

Cassava Brown Streak Viruses express second 6-kilodalton (6K2) protein with varied polarity and three dimensional (3D) structures: Basis for trait discrepancy between the virus species.

Cassava Brown Streak Virus (CBSV) and Ugandan Cassava Brown Streak Virus (UCBSV) are the two among six virus species speculated to cause the most catastrophic Brown Streak Disease of Cassava (CBSD) in Africa and Asia. Cassava Brown Streak Virus (CBSV) is hard to breed resistance for compared to Ugandan Cassava Brown Streak Virus (UCBSV) species. This is exemplified by incidences of CBSV species rather than UCBSV species in elite breeding line, KBH 2006/0026 at Bagamoyo, Tanzania. It is not yet understood as to why CBSV species could breakdown CBSD-resistance in the KBH 2006/0026 unlike the UCBSV species. This marks the first in silico study conducted to understand molecular basis for the trait discrepancy between CBSV and UCBSV species from structural biology view point. Following ab initio modelling and analysis of physical-chemical properties of second 6-kilodalton (6K2) protein encoded by CBSV and UCBSV species, using ROBETTA server and Protein Parameters tool, respectively we report that; three dimensional (3D) structures and polarity of the protein differs significantly between the two virus species. (95% and 5%) and (85% and 15%) strains of 20 CBSV and 20 UCBSV species respectively, expressed the protein in homo-trimeric and homo-tetrameric forms, correspondingly. 95% and 85% of studied strain population of the two virus species expressed hydrophilic and hydrophobic 6K2, respectively. Based on findings of the curent study, we hypothesize that; (i) The hydrophilic 6K2 expressed by the CBSV species, favour its faster systemic movement via vascular tissues of cassava host and hence result into higher tissue titres than the UCBSV species encoding hydrophobic form of the protein. t and (ii) The hydrophilic 6K2 expressed byCBSV species have additional interaction advantage with Nuclear Inclusion b protease domain (NIb) and Viral genome-linked protein (VPg), components of Virus Replication Complex (VRC) and hence contributing to faster replication of viral genome than the hydrophobic 6K2 expressed by the UCBSV species. Experimental studies are needed to resolve the 3D structures of the 6K2, VPg and NIb and comprehend complex molecular interactions between them. We suggest that, the 6K2 gene should be targeted for improvement of RNA interference (RNAi)-directed transgenesis of virus-resistant cassava as a more effective way to control the CBSD besides breeding.

Early detection of plant virus infection using multispectral imaging and spatial\u2013spectral machine learning

Cassava brown streak disease (CBSD) is an emerging viral disease that can greatly reduce cassava productivity, while causing only mild aerial symptoms that develop late in infection. Early detection of CBSD enables better crop management and intervention. Current techniques require laboratory equipment and are labour intensive and often inaccurate. We have developed a handheld active multispectral imaging (A-MSI) device combined with machine learning for early detection of CBSD in real-time. The principal benefits of A-MSI over passive MSI and conventional camera systems are improved spectral signal-to-noise ratio and temporal repeatability. Information fusion techniques further combine spectral and spatial information to reliably identify features that distinguish healthy cassava from plants with CBSD as early as 28 days post inoculation on a susceptible and a tolerant cultivar. Application of the device has the potential to increase farmers’ access to healthy planting materials and reduce losses due to CBSD in Africa. It can also be adapted for sensing other biotic and abiotic stresses in real-world situations where plants are exposed to multiple pest, pathogen and environmental stresses.

Maf/ham1-like pyrophosphatases of non-canonical nucleotides are host-specific partners of viral RNA-dependent RNA polymerases.

Cassava brown streak disease (CBSD), dubbed the "Ebola of plants", is a serious threat to food security in Africa caused by two viruses of the family Potyviridae: cassava brown streak virus (CBSV) and Ugandan (U)CBSV. Intriguingly, U/CBSV, along with another member of this family and one secoviridae, are the only known RNA viruses encoding a protein of the Maf/ham1-like family, a group of widespread pyrophosphatase of non-canonical nucleotides (ITPase) expressed by all living organisms. Despite the socio-economic impact of CDSD, the relevance and role of this atypical viral factor has not been yet established. Here, using an infectious cDNA clone and reverse genetics, we demonstrate that UCBSV requires the ITPase activity for infectivity in cassava, but not in the model plant Nicotiana benthamiana. HPLC-MS/MS experiments showed that, quite likely, this host-specific constraint is due to an unexpected high concentration of non-canonical nucleotides in cassava. Finally, protein analyses and experimental evolution of mutant viruses indicated that keeping a fraction of the yielded UCBSV ITPase covalently bound to the viral RNA-dependent RNA polymerase (RdRP) optimizes viral fitness, and this seems to be a feature shared by the other members of the Potyviridae family expressing Maf/ham1-like proteins. All in all, our work (i) reveals that the over-accumulation of non-canonical nucleotides in the host might have a key role in antiviral defense, and (ii) provides the first example of an RdRP-ITPase partnership, reinforcing the idea that RNA viruses are incredibly versatile at adaptation to different host setups.

Enhanced Convolutional Neural Network Model for Cassava Leaf Disease Identification and Classification

Cassava is a crucial food and nutrition security crop cultivated by small-scale farmers and it can survive in a brutal environment. It is a significant source of carbohydrates in African countries. Sometimes, Cassava crops can be infected by leaf diseases, affecting the overall production and reducing farmers’ income. The existing Cassava disease research encounters several challenges, such as poor detection rate, higher processing time, and poor accuracy. This research provides a comprehensive learning strategy for real-time Cassava leaf disease identification based on enhanced CNN models (ECNN). The existing Standard CNN model utilizes extensive data processing features, increasing the computational overhead. A depth-wise separable convolution layer is utilized to resolve CNN issues in the proposed ECNN model. This feature minimizes the feature count and computational overhead. The proposed ECNN model utilizes a distinct block processing feature to process the imbalanced images. To resolve the color segregation issue, the proposed ECNN model uses a Gamma correction feature. To decrease the variable selection process and increase the computational efficiency, the proposed ECNN model uses global average election polling with batch normalization. An experimental analysis is performed over an online Cassava image dataset containing 6256 images of Cassava leaves with five disease classes. The dataset classes are as follows: class 0: “Cassava Bacterial Blight (CBB)”; class 1: “Cassava Brown Streak Disease (CBSD)”; class 2: “Cassava Green Mottle (CGM)”; class 3: “Cassava Mosaic Disease (CMD)”; and class 4: “Healthy”. Various performance measuring parameters, i.e., precision, recall, measure, and accuracy, are calculated for existing Standard CNN and the proposed ECNN model. The proposed ECNN classifier significantly outperforms and achieves 99.3% accuracy for the balanced dataset. The test findings prove that applying a balanced database of images improves classification performance.

Genetic diversity of local and introduced cassava germplasm in Burundi using DArTseq molecular analyses

In Burundi most small-scale farmers still grow traditional cassava landraces that are adapted to local conditions and have been selected for consumer preferred attributes. They tend to be susceptible, in varying degrees, to devastating cassava viral diseases such as Cassava Brown Streak Disease (CBSD) and Cassava Mosaic Disease (CMD) with annual production losses of US$1 billion. For long term resistance to the disease, several breeding strategies have been proposed. A sound basis for a breeding program is to understand the genetic diversity of both landraces and elite introduced breeding cultivars. This will also assist in efforts to conserve landraces ahead of the broad distribution of improved varieties which have the possibility of replacing landraces. Our study aimed at determining the genetic diversity and relationships within and between local landraces and introduced elite germplasm using morphological and single nucleotide polymorphism (SNP) markers. A total of 118 cultivars were characterized for morphological trait variation based on leaf, stem and root traits, and genetic variation using SNP markers. Results of morphological characterization based on Ward's Method revealed three main clusters and five accessions sharing similar characteristics. Molecular characterization identified over 18,000 SNPs and six main clusters and three pairs of duplicates which should be pooled together as one cultivar to avoid redundancy. Results of population genetic analysis showed low genetic distance between populations and between local landraces and elite germplasm. Accessions that shared similar morphological traits were divergent at the molecular level indicating that clustering using morphological traits was inconsistent. Despite the variabilities found within the collection, it was observed that cassava germplasm in Burundi have a narrow genetic base.

Garpenbergite, Mn6□As5+Sb5+O10(OH)2, a new mineral related to manganostibite, from the Garpenberg Zn–Pb–Ag deposit, Sweden

AbstractGarpenbergite is a new mineral (IMA2020-099) from the Garpenberg Norra mine, Hedemora, Dalarna, Sweden. It occurs with carlfrancisite and minor stibarsen, paradocrasite and filipstadite in a fractured skarn matrix of granular jacobsite, alleghanyite, kutnohorite and dolomite. Crystals are short-prismatic, up to 1.5 mm in length. They have a blackish to greyish brown colour, and are lustrous semi-opaque, with brown streak. Garpenbergite is brittle, with an uneven to subconchoidal fracture. Cleavage is distinct on {010}. Hardness ≈ 5 (Mohs) and VHN100 = 650(40). Dcalc = 4.47(1) g⋅cm−3, overall ncalc = 1.85. Maximum specular reflectance values (%) obtained are 9.2 (470 nm), 9.1 (546 nm), 9.0 (589 nm) and 8.9 (650 nm). The empirical chemical formula of garpenbergite, based on electron microprobe data, is (Mn2+3.97Mg1.48Mn3+0.26Zn0.29)Σ6.00(As0.89Fe3+0.04Mn3+0.06Si0.01)Σ1.00(Sb0.98Fe0.02)Σ1O10[(OH)1.99Cl0.01]Σ2.00. The five strongest Bragg peaks in the powder X-ray diffraction pattern [d, Å (I, %) (hkl)] are 3.05 (30) (002), 2.665 (100) (161), 2.616 (40) (301), 2.586 (25) (251) and 1.545 (45) (462). The orthorhombic unit-cell dimensions (in Å) are a = 8.6790(9), b = 18.9057(19) and c = 6.1066(6), with V = 1001.99(18) Å3 for Z = 4. The crystal structure was refined from single-crystal X-ray diffraction data in the space-group Ibmm to R1 = 3.7% for 957 reflections. Garpenbergite, ideally Mn6As5+Sb5+O10(OH)2, is isostructural with manganostibite, Mn7AsSbO12, but possesses a cation vacancy (□) at an octahedrally coordinated structural site; the two minerals are thus related by the exchange Mn2+ + 2O2– → □ + 2(OH)–. The presence of hydroxyl groups is supported by vibration bands at 3647 and 3622 cm−1 in the Raman spectrum of garpenbergite and by bond-valence considerations.