Cassava Mosaic Disease Research Articles

A Comparison of Deterministic and Stochastic Plant-Vector-Virus Models Based on Probability of Disease Extinction and Outbreak

In this investigation, we formulate and analyse a stochastic epidemic model using the continuous-time Markov chain model for the propagation of a vector-borne cassava mosaic disease in a single population. The stochastic model is based upon a pre-existing deterministic plant-vector-virus model. To see how demographic stochasticity affects the vector-borne cassava mosaic disease dynamics, we compare the disease dynamics of both deterministic and stochastic models through disease extinction process. The probability of disease extinction and therefore the major outbreak are estimated analytically using the multitype Galton-Watson branching process (GWbp) approximation. Also, we have found the approximate probabilities of disease extinction numerically based on 30000 sample paths, and it is shown to be good estimate with the calculated probabilities from GWbp approximation. In particular, it is observed that there is a very high probability of disease extinction when the disease is introduced via the infected vectors rather than through infected plants.

Selection for resistance to cassava mosaic disease in African cassava germplasm using single nucleotide polymorphism markers

Cassava mosaic disease (CMD) is one of the main constraints that hamper cassava production. Breeding for varieties that are CMD resistant is a major aim in cassava breeding programmes. However, the use of the conventional approach has its limitations, including a lengthy growth cycle and a low multiplication rate of planting materials. To increase breeding efficiency as well as genetic gain of traits, SNP markers can be used to screen and identify resistant genotypes. The objective of this study was to predict the performance of 145 cassava genotypes from open-pollinated crosses for CMD resistance using molecular markers. Two SNP markers (S12_7926132 and S14_4626854), previously converted into Kompetitive allele-specific PCR (KASP) assays, as well as CMD incidence and severity scores, were used for selection. About 76% of the genotypes were revealed to be resistant to CMD based on phenotypic scores, while over 24% of the total population were found to be susceptible. Significant effects were observed for alleles associated with marker S12_7926132 while the other marker had non-significant effects. The predictive accuracy (true positives and true negatives) of the major CMD2 locus on chromosome 12 was 77% in the population used in this study. Our study provides insight into the potential use of marker-assisted selection for CMD resistance in cassava breeding programmes.Significance: With an aim towards reducing the food insecurity rate in Africa, we report on the use of genetic tools for a fast and efficient release of new cassava varieties to benefit breeders, farmers and consumers, given the food and industrial importance of this staple crop. This study adds tremendous knowledge to phenotypic and molecular screening for CMD resistance. The outcome will encourage breeders in various cassava breeding programmes to accelerate genetic gains as well as increase breeding accuracy and efficiency for CMD resistance.

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.

Evaluation of Different Industrial End Uses of Improved Cassava Varieties Grown in South-Eastern Africa

This work characterized two local and seven improved Cassava Mosaic Disease [CMD]-tolerant cassava varieties for their biochemical composition and viscoelastic (pasting) properties. The biochemical composition and starch pasting properties were evaluated respectively using standard analytical methods and Brabender Viscoamylograph. Cluster dendogram and principal component analyses compared similarities in the nine cassava varieties, thus predicting their varied food and industrial end uses. The different cassava varieties had starch, total sugars and reducing sugars content ranging from 53-69%, 6.5-9.2% and 0.9-2.5%, respectively. The starch content of the cassava varieties on dry weight basis (DW) varied from 54.0% to 69.0% with Nalumino having the lowest and Mweru having the highest respectively. Tanganyika, Mweulu, and Banguerlu also recorded relatively higher starch content of 62.7%, 63.6% and 63.6% respectively. Mweru, Tangayoka, Mweulu, and Bangweulu had fairly high starch content (>60%) and thus could be used for many commercial products such as starches, alcohols and glucose. The viscoelastic properties of the different varieties had pasting temperature (63.5–67.6oC), peak viscosity (402–595 BU), viscosity at 95oC (394–592 BU), viscosity at 50oC (126–254), breakdown viscosity (236–352 BU) and setback (-100–4 BU). Tanganyika recorded the highest pasting temperature (67.6oC), peak viscosity (595 BU), viscosity at 95oC (592 BU) and viscosity at 95oC-hold (317 BU). Bangweulu, Mweulu, Mweru, Manyokola, Nalumino, Kampolombo and Chila A were clustered differently from Chila B and Tanganyika on the basis of their biochemical qualities and pasting properties. These characterizations showed that Tanganyika would be suitable for products requiring high elasticity and gel strength, easier to cook and also more stable during cooking/preparation such as fufu (pounded cassava) and banku or Nshima. Chila A would also be suitable for use as fillers and binders in the baking, confectionery industries as substitutes of wheat flour. The low viscosities of Chila B make it suitable for household food uses such as snacks where the roots are boiled, roasted or toasted and consumed.

East African cassava mosaic virus

East African cassava mosaic virus

Cassava mosaic disease (African cassava mosaic)

Cassava mosaic disease (African cassava mosaic)

Indian cassava mosaic virus (Indian cassava mosaic)

Indian cassava mosaic virus (Indian cassava mosaic)

South African cassava mosaic virus

This datasheet on South African cassava mosaic virus covers Identity, Distribution, Hosts/Species Affected, Vectors & Intermediate Hosts, Further Information.

African cassava mosaic virus (African cassava mosaic)

African cassava mosaic virus (African cassava mosaic)

Sri Lankan cassava mosaic virus

This datasheet on Sri Lankan cassava mosaic virus covers Identity, Distribution, Hosts/Species Affected, Vectors & Intermediate Hosts, Further Information.

Identification and Characterization of Cassava Mosaic Begomoviruses in Non-crop Plants from Unguja and Pemba Islands

Cassava mosaic disease caused by cassava mosaic begomoviruses (CMBs) remains one of the major constraints to cassava production since it causes yield losses up to 100%. Researches showed that some of CMBs infecting cassava plants may be coming from non-crop plants. This study intended to identify and characterize CMBs isolated from non-crop plant species in Unguja and Pemba Islands. A total of 108 viral symptomatic and asymptomatic non-crop leaf samples were collected using stratified sampling. DNA was extracted by using CTAB protocol followed by polymerase chain reaction using universal and specific primers for cassava mosaic begomoviruses identification. Results showed that, among eleven samples that were amplified, four were African cassava mosaic viruses (ACMV) and seven were East African cassava mosaic viruses (EACMV). DNA sequencing by Sanger method showed 97–99% similarities with isolates of ACMV and EACMV reported elsewhere in Africa. Using RbcL and MatK plant barcode genes, Datura stramonium, Solanum melongena and Solanum incanum were found associated with ACMV, while Senna occidentalis, Sida acuta and Ricinus communis harboured EACMV. These findings are a key in understanding the epidemiology of cassava mosaic disease and are potential in the development of sustainable management strategies for this disease.
 Keywords: Begomoviruses, Cassava mosaic disease, East African cassava mosaic virus, Non crop plants.

Modelling the dynamics of Cassava Mosaic Disease with non-cassava host plants

Cassava Mosaic Disease (CMD) is the prominent cassava disease which compromises cassava production in Africa, both qualitatively and quantitatively for many years. In this study, the mathematical model for the dynamics of CMD with Non-cassava host plant population is formulated and analysed. The analysis of basic model properties confirmed the positive boundedness of the model solution for all time t≥0. Utilizing the next generation matrix the basic reproduction number R0 is derived and stability of disease-free equilibrium point (DFE) is analysed. Analytical results confirmed that, the disease-free equilibrium point (DFE) is locally asymptotically stable whenever R0<1 and unstable otherwise. The sensitivity index analysis identified mortality rate and the carrying capacity of whiteflies as the most sensitive parameters of model. This implies that, any deliberate efforts towards controlling CMD should be directed into reducing the number of whiteflies. This can be implemented by either increasing the mortality rate of whiteflies or reducing their carrying capacity. In view of this, it is clear that deliberate measures such as the use of pesticides and entomopathogenic fungi which increases the parameter value of ω, and removing non-cassava host plants which will eventually decrease the parameter value of κw may bring significant results in combating CMD compared to the control of other model parameters. The decision regarding the best approach out of the two requires optimal control and cost-effective analysis of available control strategies. Furthermore, the numerical simulation results suggested that Cassava Mosaic Disease (CMD) can be controlled by increasing mortality rate of whiteflies, and the decreasing in the carrying capacity of whiteflies.

Experimental Study of Extension Impact on Farmers’ KAP towards Sri Lankan Cassava Mosaic Disease Prevention in Cambodia

Experimental Study of Extension Impact on Farmers’ KAP towards Sri Lankan Cassava Mosaic Disease Prevention in Cambodia

Molecular Characterization of Cassava Mosaic Viruses and Current Mosaic Disease Concern in Three Major Cassava Production Areas in Côte D’ivoire

Molecular Characterization of Cassava Mosaic Viruses and Current Mosaic Disease Concern in Three Major Cassava Production Areas in Côte D’ivoire

An experimental strategy for preparing circular ssDNA virus genomes for next-generation sequencing

The ability of begomoviruses to evolve rapidly threatens many crops and underscores the importance of detecting these viruses quickly and to understand their genome diversity. This study presents an improved protocol for the enhanced amplification and enrichment of begomovirus DNA for use in next generation sequencing of the viral genomes. An enhanced rolling circle amplification (RCA) method using EquiPhi29 polymerase was combined with size selection to generate a cost-effective, short-read sequencing method. This improved short-read sequencing produced at least 50 % of the reads mapping to the target viral reference genomes, African cassava mosaic virus and East African cassava mosaic virus. This study provided other insights into common misconceptions about RCA and lessons that could be learned from the sequencing of single-stranded DNA virus genomes. This protocol can be used to examine the viral DNA as it moves from host to vector, thus producing valuable information for viral DNA population studies, and would likely work well with other circular Rep-encoding ssDNA viruses (CRESS) DNA viruses.

A population based expression atlas provides insights into disease resistance and other physiological traits in cassava (Manihot esculenta Crantz)

Cassava, a food security crop in Africa, is grown throughout the tropics and subtropics. Although cassava can provide high productivity in suboptimal conditions, the yield in Africa is substantially lower than in other geographies. The yield gap is attributable to many challenges faced by cassava in Africa, including susceptibility to diseases and poor soil conditions. In this study, we carried out 3’RNA sequencing on 150 accessions from the National Crops Resources Research Institute, Uganda for 5 tissue types, providing population-based transcriptomics resources to the research community in a web-based queryable cassava expression atlas. Differential expression and weighted gene co-expression network analysis were performed to detect 8820 significantly differentially expressed genes (DEGs), revealing similarity in expression patterns between tissue types and the clustering of detected DEGs into 18 gene modules. As a confirmation of data quality, differential expression and pathway analysis targeting cassava mosaic disease (CMD) identified 27 genes observed in the plant–pathogen interaction pathway, several previously identified CMD resistance genes, and two peroxidase family proteins different from the CMD2 gene. Present research work represents a novel resource towards understanding complex traits at expression and molecular levels for the development of resistant and high-yielding cassava varieties, as exemplified with CMD.

Evaluation of Ten Cassava Varieties for Resistance to Cassava Mosaic Disease in Burkina Faso

The whitefly-transmitted cassava mosaic disease (CMD) caused by cassava mosaic geminiviruses (CMGs) is the most important disease threatening the production of cassava (Manihot esculenta Crantz). Among the main measures for controlling CMD, the use of resistant varieties seems to be among the best methods. This study was conducted in 2017/2018 cassava growing season at three locations to evaluate the level of resistance to CMD of 7 elite cassava varieties widely used by farmers and 3 local cassava varieties cultivated in Burkina Faso. Both morphological and molecular markers were used to screen these varieties against CMGs infection. Morphological markers revealed 8 varieties as highly resistant (TMS 91/02312, TMS 92/0067, TMS 92/0325, TMS 92/0427, TMS 4(2)1425, TMS 94/0270, TMS 30572 and Boborola) whilst the two others (Nouhao and Santidougou) were resistant. The molecular markers linked to CMD1 and CMD2 genes were detected in all varieties. The molecular marker associated with CMD3 gene was detected only in the 8 highly resistant varieties. However, whitefly number per plant and disease pressure were low during this study. It was, therefore, concluded that a better assessment of resistance of cassava varieties to CMD in Burkina Faso could be obtained by combining agro-inoculation and molecular screening.

Cassava Brown Streak Disease Response and Association With Agronomic Traits in Elite Nigerian Cassava Cultivars.

Cassava mosaic geminiviruses (CMGs) and cassava brown streak viruses (CBSVs) cause the highest yield losses in cassava production in Africa. In particular, cassava brown streak disease (CBSD) is and continues to be a significant constraint to optimal cassava production in Eastern and Southern Africa. While CBSD has not been reported in West Africa, its recent rapid spread and damage to cassava productivity in Eastern, and Southern Africa is alarming. The aim of this study was to evaluate Nigerian cassava genotypes in order to determine their responses to CBSD, in the event that it invades Nigeria, the world’s largest cassava producer. The study gathered information on whether useful CBSD resistance alleles are present in the elite Nigerian cassava accessions. A total of 1,980 full-sib cassava seedlings from 106 families were assessed in the field at the seedling stage for a year. A subset of 569 clones were selected and assessed for another year at the clonal stage in Namulonge, central Uganda, a known hotspot for CBSD screening. Results indicated that foliar and root incidences and severities varied significantly (p ≤ 0.01, p ≤ 0.001) except for CBSD foliar incidence at 6 months (CBSD6i). Highest and lowest plot-based heritability estimates for CBSD were registered for CBSD root severity (CBSDrs) (0.71) and CBSD6i (0.5). Positive and highly significant correlations were noted between CBSD root incidence (CBSDri) and CBSDrs (r = 0.90***). Significant positive correlations were also noted between CBSD foliar severity at 3 months (CBSD3s) and CBSD foliar incidence at 6 months (CBSD6i) (r = 0.77***), CBSD3s and CBSDrs (r = 0.35***). Fresh root weight (FreshRW) negatively correlated with CBSDri and CBSDrs, respectively (r = −0.21*** and r = −0.22***). Similarly, CBSD3s correlated negatively with cassava mosaic disease severity at 3 (CMD3s) and 6 months (CMD6s), respectively (r = −0.25*** and r = −0.21***). Fifteen clones were selected using a non-weighted summation selection index for further screening. In conclusion, results revealed that the elite Nigerian accessions exhibited significant susceptibility to CBSD within 2 years of evaluation period. It is expected that this information will aid future breeding decisions for the improvement of CBSD resistance among the Nigerian cassava varieties.

Smallholder Cassava Planting Material Movement and Grower Behavior in Zambia: Implications for the Management of Cassava Virus Diseases.

Cassava (Manihot esculenta) is an important food crop across sub-Saharan Africa, where production is severely inhibited by two viral diseases, cassava mosaic disease (CMD) and cassava brown streak disease (CBSD), both propagated by a whitefly vector and via human-mediated movement of infected cassava stems. There is limited information on growers' behavior related to movement of planting material, as well as growers' perception and awareness of cassava diseases, despite the importance of these factors for disease control. This study surveyed a total of 96 cassava subsistence growers and their fields across five provinces in Zambia between 2015 and 2017 to address these knowledge gaps. CMD symptoms were observed in 81.6% of the fields, with an average incidence of 52% across the infected fields. No CBSD symptoms were observed. Most growers used planting materials from their own (94%) or nearby (<10 km) fields of family and friends, although several large transactions over longer distances (10 to 350 km) occurred with friends (15 transactions), markets (1), middlemen (5), and nongovernmental organizations (6). Information related to cassava diseases and certified clean (disease-free) seed reached only 48% of growers. The most frequent sources of information related to cassava diseases included nearby friends, family, and neighbors, while extension workers were the most highly preferred source of information. These data provide a benchmark on which to plan management approaches to controlling CMD and CBSD, which should include clean propagation material, increasing growers' awareness of the diseases, and increasing information provided to farmers (specifically disease symptom recognition and disease management options).[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Contribution of historical herbarium small RNAs to the reconstruction of a cassava mosaic geminivirus evolutionary history

Emerging viral diseases of plants are recognised as a growing threat to global food security. However, little is known about the evolutionary processes and ecological factors underlying the emergence and success of viruses that have caused past epidemics. With technological advances in the field of ancient genomics, it is now possible to sequence historical genomes to provide a better understanding of viral plant disease emergence and pathogen evolutionary history. In this context, herbarium specimens represent a valuable source of dated and preserved material. We report here the first historical genome of a crop pathogen DNA virus, a 90-year-old African cassava mosaic virus (ACMV), reconstructed from small RNA sequences bearing hallmarks of small interfering RNAs. Relative to tip-calibrated dating inferences using only modern data, those performed with the historical genome yielded both molecular evolution rate estimates that were significantly lower, and lineage divergence times that were significantly older. Crucially, divergence times estimated without the historical genome appeared in discordance with both historical disease reports and the existence of the historical genome itself. In conclusion, our study reports an updated time-frame for the history and evolution of ACMV and illustrates how the study of crop viral diseases could benefit from natural history collections.