Nucleotide sequence evidence for the occurrence of three distinct whitefly-transmitted geminiviruses in cassava

The Role of Extensive Recombination in the Evolution of Geminiviruses

Mutation, recombination and pseudo-recombination are the major forces driving the evolution of viruses by the generation of variants upon which natural selection, genetic drift and gene flow can act to shape the genetic structure of viral populations. Recombination between related virus genomes co-infecting the same cell usually occurs via template swapping during the replication process and produces a chimeric genome. The family Geminiviridae shows the highest evolutionary success among plant virus families, and the common presence of recombination signatures in their genomes reveals a key role in their evolution. This review describes the general characteristics of members of the family Geminiviridae and associated DNA satellites, as well as the extensive occurrence of recombination at all taxonomic levels, from strain to family. The review also presents an overview of the recombination patterns observed in nature that provide some clues regarding the mechanisms involved in the generation and emergence of recombinant genomes. Moreover, the results of experimental evolution studies that support some of the conclusions obtained in descriptive or in silico works are summarized. Finally, the review uses a number of case studies to illustrate those recombination events with evolutionary and pathological implications as well as recombination events in which DNA satellites are involved.

Advances in Genetic Analysis and Breeding of Cassava (Manihot esculenta Crantz): A Review

Cassava (Manihot esculenta Crantz) is the sixth most important food crop and consumed by 800 million people worldwide. In Africa, cassava is the second most important food crop after maize and Africa is the worlds' largest producer. Though cassava is not one of the main commodity crops in South Africa, it is becoming a popular crop among farming communities in frost-free areas, due to its climate-resilient nature. This necessitated the establishment of a multi-disciplinary research program at the Agricultural Research Council of South Africa. The objective of this review is to highlight progress made in cassava breeding and genetic analysis. This review highlights the progress of cassava research worldwide and discusses research findings on yield, quality, and adaptability traits in cassava. It also discusses the limitations and the prospects of the cassava R&D program towards development of the cassava industry in South Africa.

Cassava mosaic disease and its management in Southeast Asia

Key message

Status of the current outbreak of cassava mosaic disease (CMD) in Southeast Asia was reviewed. Healthy cassava seed production and dissemination systems have been established in Vietnam and Cambodia, along with integrated disease and pest management systems, to combat the outbreak.

Abstract

Cassava (Manihot esculenta Crantz) is one of the most important edible crops in tropical and subtropical regions. Recently, invasive insect pests and diseases have resulted in serious losses to cassava in Southeast Asia. In this review we discuss the current outbreak of cassava mosaic disease (CMD) caused by the Sri Lankan cassava mosaic virus (SLCMV) in Southeast Asia, and summarize similarities between SLCMV and other cassava mosaic begomoviruses. A SATREPS (Science and Technology Research Partnership for Sustainable Development) project “Development and dissemination of sustainable production systems based on invasive pest management of cassava in Vietnam, Cambodia and Thailand”, was launched in 2016, which has been funded by The Japan International Cooperation Agency (JICA) and The Japan Science and Technology Agency (JST), Japan. The objectives of SATREPS were to establish healthy seed production and dissemination systems for cassava in south Vietnam and Cambodia, and to develop management systems for plant diseases and insect pests of cassava. To achieve these goals, model systems of healthy seed production in Vietnam and Cambodia have been developed incorporating CMD-resistant planting materials through international networks with The International Center for Tropical Agriculture (CIAT) and The International Institute of Tropical Agriculture (IITA).

Supplementary Information

The online version contains supplementary material available at 10.1007/s11103-021-01168-2.

Development of a triple antibody sandwich enzyme-linked immunosorbent assay for cassava mosaic disease detection using a monoclonal antibody to Sri Lankan cassava mosaic virus

Background

Cassava mosaic disease (CMD) is one of the most devastating viral diseases for cassava production in Africa and Asia. Accurate yet affordable diagnostics are one of the fundamental tools supporting successful CMD management, especially in developing countries. This study aimed to develop an antibody-based immunoassay for the detection of Sri Lankan cassava mosaic virus (SLCMV), the only cassava mosaic begomovirus currently causing CMD outbreaks in Southeast Asia (SEA).

Methods

Monoclonal antibodies (MAbs) against the recombinant coat protein of SLCMV were generated using hybridoma technology. MAbs were characterized and used to develop a triple antibody sandwich enzyme-linked immunosorbent assay (TAS-ELISA) for SLCMV detection in cassava leaves and stems. Assay specificity, sensitivity and efficiency for SLCMV detection was investigated and compared to those of a commercial ELISA test kit and PCR, the gold standard.

Results

A TAS-ELISA for SLCMV detection was successfully developed using the newly established MAb 29B3 and an in-house polyclonal antibody (PAb) against begomoviruses, PAb PK. The assay was able to detect SLCMV in leaves, green bark from cassava stem tips, and young leaf sprouts from stem cuttings of SLCMV-infected cassava plants without cross-reactivity to those derived from healthy cassava controls. Sensitivity comparison using serial dilutions of SLCMV-infected cassava sap extracts revealed that the assay was 256-fold more sensitive than a commercial TAS-ELISA kit and 64-fold less sensitive than PCR using previously published SLCMV-specific primers. In terms of DNA content, our assay demonstrated a limit of detection of 2.21 to 4.08 × 10⁶ virus copies as determined by quantitative real-time PCR (qPCR). When applied to field samples (n = 490), the TAS-ELISA showed high accuracy (99.6%), specificity (100%), and sensitivity (98.2%) relative to the results obtained by the reference PCR. SLCMV infecting chaya (Cnidoscolus aconitifolius) and coral plant (Jatropha multifida) was also reported for the first time in SEA.

Conclusions

Our findings suggest that the TAS-ELISA for SLCMV detection developed in this study can serve as an attractive tool for efficient, inexpensive and high-throughput detection of SLCMV and can be applied to CMD screening of cassava stem cuttings, large-scale surveillance, and screening for resistance.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-021-01572-6.

Accuracy of a Smartphone-Based Object Detection Model, PlantVillage Nuru, in Identifying the Foliar Symptoms of the Viral Diseases of Cassava-CMD and CBSD

Nuru is a deep learning object detection model for diagnosing plant diseases and pests developed as a public good by PlantVillage (Penn State University), FAO, IITA, CIMMYT, and others. It provides a simple, inexpensive and robust means of conducting in-field diagnosis without requiring an internet connection. Diagnostic tools that do not require the internet are critical for rural settings, especially in Africa where internet penetration is very low. An investigation was conducted in East Africa to evaluate the effectiveness of Nuru as a diagnostic tool by comparing the ability of Nuru, cassava experts (researchers trained on cassava pests and diseases), agricultural extension officers and farmers to correctly identify symptoms of cassava mosaic disease (CMD), cassava brown streak disease (CBSD) and the damage caused by cassava green mites (CGM). The diagnosis capability of Nuru and that of the assessed individuals was determined by inspecting cassava plants and by using the cassava symptom recognition assessment tool (CaSRAT) to score images of cassava leaves, based on the symptoms present. Nuru could diagnose symptoms of cassava diseases at a higher accuracy (65% in 2020) than the agricultural extension agents (40-58%) and farmers (18-31%). Nuru's accuracy in diagnosing cassava disease and pest symptoms, in the field, was enhanced significantly by increasing the number of leaves assessed to six leaves per plant (74-88%). Two weeks of Nuru practical use provided a slight increase in the diagnostic skill of extension workers, suggesting that a longer duration of field experience with Nuru might result in significant improvements. Overall, these findings suggest that Nuru can be an effective tool for in-field diagnosis of cassava diseases and has the potential to be a quick and cost-effective means of disseminating knowledge from researchers to agricultural extension agents and farmers, particularly on the identification of disease symptoms and their management practices.

Genetic Diversity of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) Colonizing Sweet Potato and Cassava in South Sudan

Bemisia 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.

A 7-Amino-Acid Motif of Rep Protein Essential for Virulence Is Critical for Triggering Host Defense Against Sri Lankan Cassava Mosaic Virus

Geminiviruses cause severe damage to agriculture worldwide. The replication (Rep) protein is the indispensable viral protein for viral replication. Although various functional domains of Rep protein in Geminivirus spp. have been characterized, the most carboxyl terminus of Rep protein was not available. We have reported the first cassava-infecting geminivirus, Sri Lankan cassava mosaic virus (SLCMV-HN7 strain), in China. In this study, we reported the second Chinese SLCMV strain, SLCMV-Col, and conducted comparative genomic analysis between these two SLCMV strains. The virulence of SLCMV-Col is much stronger than SLCMV-HN7, indicated by the higher virus titer, more severe symptoms, and more extent host defense. We functionally characterized that Rep protein, a 7-amino-acid motif at the most carboxyl terminus, is essential for Rep protein accumulation and virulence of SLCMV. We also provided evidence suggesting that the motif could also enhance triggering of salicylic acid (SA) defense against SLCMV infection in Nicotiana benthamiana. The significance of the balance between virulence and host SA defense responses in expanding invasions of SLCMV is also discussed.

What has changed in the outbreaking populations of the severe crop pest whitefly species in cassava in two decades?

High populations of African cassava whitefly (Bemisia tabaci) have been associated with epidemics of two viral diseases in Eastern Africa. We investigated population dynamics and genetic patterns by comparing whiteflies collected on cassava in 1997, during the first whitefly upsurges in Uganda, with collections made in 2017 from the same locations. Nuclear markers and mtCOI barcoding sequences were used on 662 samples. The composition of the SSA1 population changed significantly over the 20-year period with the SSA1-SG2 percentage increasing from 0.9 to 48.6%. SSA1-SG1 and SSA1-SG2 clearly interbreed, confirming that they are a single biological species called SSA1. The whitefly species composition changed: in 1997, SSA1, SSA2 and B. afer were present; in 2017, no SSA2 was found. These data and those of other publications do not support the 'invader' hypothesis. Our evidence shows that no new species or new population were found in 20 years, instead, the distribution of already present genetic clusters composing SSA1 species have changed over time and that this may be in response to several factors including the introduction of new cassava varieties or climate changes. The practical implications are that cassava genotypes possessing both whitefly and disease resistances are needed urgently.

Cassava mosaic disease: a review of a threat to cassava production in Zambia

Cassava (Manihot esculenta Crantz) is one of the most important root staple crops in Zambia. An estimated 30% of Zambians, over 4 million people, consume cassava as part of their daily diet. Cassava is mostly grown by subsistence farmers on fields of less than 1 ha. Cultivation of cassava is hampered by several biotic constraints, of which cassava mosaic disease (CMD) is currently the most important factor limiting cassava production in Zambia. CMD occurs in all the cassava-growing provinces and accounts for 50% to 70% of yield losses countrywide. Strategies to counter CMD were initiated in the early 1990s and included the release of CMD-resistant cassava cultivars. However, efforts to control CMD are limited because few growers plant these cultivars. More recently, to address the CMD problem, regular disease monitoring and diagnostic capabilities have been strengthened, and there is increased support for screening breeders materials. CMD is a rising threat to cassava production in Zambia. This review of CMD research on disease surveillance, CMD spread, yield losses, awareness campaigns and control options in Zambia over the past 25 years informs future control efforts and management strategies.

Unravelling the Genetic Diversity among Cassava Bemisia tabaci Whiteflies Using NextRAD Sequencing

Bemisia 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.

Rolling circle amplification-based analysis of Sri Lankan cassava mosaic virus isolates from Tamil Nadu, India, suggests a low level of genetic variability

Cassava mosaic disease is a widespread disease of cassava in south Asia and the African continent. In India, CMD is known to be caused by two single-stranded DNA viruses (geminiviruses), Indian cassava mosaic virus (ICMV) and Sri Lankan cassava mosdaic virus (SLCMV). Previously, the diversity of ICMV and SLCMV in India has been studied using PCR, a sequence-dependent method. To have a more in-depth study of the variability of the above viruses and to detect any novel geminiviruses associated with CMD, sequence-independent amplification using rolling circle amplification (RCA)-based methods were used. CMD affected cassava plants were sampled across eighty locations in nine districts of the southern Indian state of Tamil Nadu. Twelve complete sequence of coat protein genes of the resident geminiviruses, comprising 256 amino acid residues were generated from the above samples, which indicated changes at only six positions. RCA followed by RFLP of the 80 samples indicated that most samples (47) contained only SLCMV, followed by 8, which were infected jointly with ICMV and SLCMV. In 11 samples, the pattern did not match the expected patterns from either of the two viruses and hence, were variants. Sequence analysis of an average of 700 nucleotides from 31 RCA-generated fragments of the variants indicated identities of 97-99% with the sequence of a previously reported infectious clone of SLCMV. The evidence suggests low levels of genetic variability in the begomoviruses infecting cassava, mainly in the form of scattered single nucleotide changes.

The Search for Resistance to Cassava Mosaic Geminiviruses: How Much We Have Accomplished, and What Lies Ahead

The cassava mosaic disease (CMD), which occurs in all cassava growing regions of Africa and the Indian subcontinent, is caused by cassava mosaic geminiviruses (CMGs). CMGs are considered to be the most damaging vector-borne plant pathogens. So far, the most successful approach used to control these viruses has been the transfer of a polygenic recessive resistance locus, designated CMD1, from wild cassava to cassava cultivars. Further progress in harnessing natural resistance to contain CMGs has come from the discovery of the dominant monogenic resistance locus, CMD2, in some West African cassava cultivars. CMD2 has been combined with CMD1 through genetic crosses. Because of the limitations of the cassava breeding approach, especially with regard to time required to produce a variety and the loss of preferred agronomic attributes, efforts have been directed toward the deployment of genetic engineering approaches. Most of these approaches have been centered on RNA silencing strategies, developed mainly in the model plant Nicotiana benthamiana. Early RNA silencing platforms assessed for CMG resistance have been use of viral genes for co-suppression, antisense suppression or for hairpin RNAs-mediated gene silencing. Here, progress and challenges in the deployment of these approaches in the control of CMGs are discussed. Novel functional genomics approaches with potential to overcome some of the drawbacks of the current strategies are also discussed.

Emergence of a Latent Indian Cassava Mosaic Virus from Cassava Which Recovered from Infection by a Non-Persistent Sri Lankan Cassava Mosaic Virus

The major threat for cassava cultivation on the Indian subcontinent is cassava mosaic disease (CMD) caused by cassava mosaic geminiviruses which are bipartite begomoviruses with DNA A and DNA B components. Indian cassava mosaic virus (ICMV) and Sri Lankan cassava mosaic virus (SLCMV) cause CMD in India. Two isolates of SLCMV infected the cassava cultivar Sengutchi in the fields near Malappuram and Thiruvananthapuram cities of Kerala State, India. The Malappuram isolate was persistent when maintained in the Madurai Kamaraj University (MKU, Madurai, Tamil Nadu, India) greenhouse, whereas the Thiruvananthapuram isolate did not persist. The recovered cassava plants with the non-persistent SLCMV, which were maintained vegetative in quarantine in the University of Basel (Basel, Switzerland) greenhouse, displayed re-emergence of CMD after a six-month period. Interestingly, these plants did not carry SLCMV but carried ICMV. It is interpreted that the field-collected, SLCMV-infected cassava plants were co-infected with low levels of ICMV. The loss of SLCMV in recovered cassava plants, under greenhouse conditions, then facilitated the re-emergence of ICMV. The partial dimer clones of the persistent and non-persistent isolates of SLCMV and the re-emerged isolate of ICMV were infective in Nicotiana benthamiana upon agroinoculation. Studies on pseudo-recombination between SLCMV and ICMV in N. benthamiana provided evidence for trans-replication of ICMV DNA B by SLCMV DNA A.

Survey, Molecular Detection, and Characterization of Geminiviruses Associated with Cassava Mosaic Disease in Zambia

A survey was conducted from April to May 2014 in 214 farmers' fields located across six major cassava-producing provinces (Western, Northwestern, Northern, Luapula, Lusaka, and Eastern) of Zambia to determine the status of cassava mosaic disease (CMD) and the species diversity of associated cassava mosaic geminiviruses (CMG). Mean CMD incidence varied across all six provinces but was greatest in Lusaka Province (81%) and least in Northern Province (44%). Mean CMD severity varied slightly between provinces, ranging from 2.78 in Eastern Province to 3.00 in Northwestern Province. Polymerase chain reaction discrimination of 226 survey samples, coupled with complete DNA-A genome sequence analysis, revealed the presence of African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), and East African cassava mosaic Malawi virus (EACMMV) as single or mixed infections of different proportions. Single-virus infections were predominant, occurring in 62.8% (ACMV), 5.8% (EACMMV), and 2.2% (EACMV) of samples relative to mixed-virus infections, which occurred in 19.5% (ACMV + EACMMV), 0.4% (ACMV + EACMV), and 0.9% (ACMV + EACMV + EACMMV) of samples. Phylogenetic analysis revealed the segregation of virus isolates from Zambia into clades specific to ACMV, EACMV, and EACMMV, further confirming the presence of all three viruses in Zambia. The results point to a greater diversity of CMG across major cassava-growing provinces of Zambia and implicate contaminated cassava cuttings in disease spread.

Cassava brown streak disease: a threat to food security in Africa

Cassava brown streak disease (CBSD) has emerged as the most important viral disease of cassava (Manihot esculenta) in Africa and is a major threat to food security. CBSD is caused by two distinct species of ipomoviruses, Cassava brown streak virus and Ugandan cassava brown streak virus, belonging to the family Potyviridae. Previously, CBSD was reported only from the coastal lowlands of East Africa, but recently it has begun to spread as an epidemic throughout the Great Lakes region of East and Central Africa. This new spread represents a major threat to the cassava-growing regions of West Africa. CBSD-resistant cassava cultivars are being developed through breeding, and transgenic RNA interference-derived field resistance to CBSD has also been demonstrated. This review aims to provide a summary of the most important studies on the aetiology, epidemiology and control of CBSD and to highlight key research areas that need prioritization.

The Agrobacterium tumefaciens Ti Plasmid Virulence Gene virE2 Reduces Sri Lankan Cassava Mosaic Virus Infection in Transgenic Nicotiana benthamiana Plants

Cassava mosaic disease is a major constraint to cassava cultivation worldwide. In India, the disease is caused by Indian cassava mosaic virus (ICMV) and Sri Lankan cassava mosaic virus (SLCMV). The Agrobacterium Ti plasmid virulence gene virE2, encoding a nuclear-localized, single-stranded DNA binding protein, was introduced into Nicotiana benthamiana to develop tolerance against SLCMV. Leaf discs of transgenic N. benthamiana plants, harboring the virE2 gene, complemented a virE2 mutation in A. tumefaciens and produced tumours. Three tested virE2 transgenic plants displayed reduction in disease symptoms upon agroinoculation with SLCMV DNA A and DNA B partial dimers. A pronounced reduction in viral DNA accumulation was observed in all three virE2 transgenic plants. Thus, virE2 is an effective candidate gene to develop tolerance against the cassava mosaic disease and possibly other DNA virus diseases.

Resistance to Sri Lankan cassava mosaic virus (SLCMV) in genetically engineered cassava cv. KU50 through RNA silencing

Cassava ranks fifth among the starch producing crops of the world, its annual bioethanol yield is higher than for any other crop. Cassava cultivar KU50, the most widely grown cultivar for non-food purposes is susceptible to Sri Lankan cassava mosaic virus (SLCMV). The objective of this work was to engineer resistance to SLCMV by RNA interference (RNAi) in order to increase biomass yield, an important aspect for bioethanol production. Here, we produced transgenic KU50 lines expressing dsRNA homologous to the region between the AV2 and AV1 of DNA A of SLCMV. High level expression of dsRNA of SLCMV did not induce any growth abnormality in the transgenic plants. Transgenic lines displayed high levels of resistance to SLCMV compared to the wild-type plants and no virus load could be detected in uninoculated new leaves of the infected resistant lines after PCR amplification and RT-PCR analysis. The agronomic performance of the transgenic lines was unimpaired after inoculation with the virus as the plants presented similar growth when compared to the mock inoculated control plants and revealed no apparent reduction in the amount and weight of tubers produced. We show that the resistance is correlated with post-transcriptional gene silencing because of the production of transgene specific siRNA. The results demonstrate that transgenic lines exhibited high levels of resistance to SLCMV. This resistance coupled with the desirable yield components in the transgenic lines makes them better candidates for exploitation in the production of biomass as well as bioethanol.

Cassava virus diseases: biology, epidemiology, and management

Cassava (Manihot esculenta Crantz.) is the most important vegetatively propagated food staple in Africa and a prominent industrial crop in Latin America and Asia. Its vegetative propagation through stem cuttings has many advantages, but deleteriously it means that pathogens are passed from one generation to the next and can easily accumulate, threatening cassava production. Cassava-growing continents are characterized by specific suites of viruses that affect cassava and pose particular threats. Of major concern, causing large and increasing economic impact in Africa and Asia are the cassava mosaic geminiviruses that cause cassava mosaic disease in Africa and Asia and cassava brown streak viruses causing cassava brown streak disease in Africa. Latin America, the center of origin and domestication of the crop, hosts a diverse set of virus species, of which the most economically important give rise to cassava frog skin disease syndrome. Here, we review current knowledge on the biology, epidemiology, and control of the most economically important groups of viruses in relation to both farming and cultural practices. Components of virus control strategies examined include: diagnostics and surveillance, prevention and control of infection using phytosanitation, and control of disease through the breeding and promotion of varieties that inhibit virus replication and/or movement. We highlight areas that need further research attention and conclude by examining the likely future global outlook for virus disease management in cassava.

Biology and management of Bemisia whitefly vectors of cassava virus pandemics in Africa

Cassava mosaic disease and cassava brown streak disease are caused by viruses transmitted by Bemisia tabaci and affect approximately half of all cassava plants in Africa, resulting in annual production losses of more than $US 1 billion. A historical and current bias towards virus rather than vector control means that these diseases continue to spread, and high Bemisia populations threaten future virus spread even if the extant strains and species are controlled. Progress has been made in parts of Africa in replicating some of the successes of integrated Bemisia control programmes in the south-western United States. However, these management efforts, which utilise chemical insecticides that conserve the Bemisia natural enemy fauna, are only suitable for commercial agriculture, which presently excludes most cassava cultivation in Africa. Initiatives to strengthen the control of B. tabaci on cassava in Africa need to be aware of this limitation, and to focus primarily on control methods that are cheap, effective, sustainable and readily disseminated, such as host-plant resistance and biological control. A framework based on the application of force multipliers is proposed as a means of prioritising elements of future Bemisia control strategies for cassava in Africa.

Spatio-temporal patterns of genetic change amongst populations of cassava Bemisia tabaci whiteflies driving virus pandemics in East and Central Africa

The greatest current threat to cassava in sub-Saharan Africa, is the continued expansion of plant virus pandemics being driven by super-abundant populations of the whitefly vector, Bemisia tabaci. To track the association of putatively genetically distinct populations of B. tabaci with pandemics of cassava mosaic disease (CMD) and cassava brown streak disease (CBSD), a comprehensive region-wide analysis examined the phylogenetic relationships and population genetics of 642 B. tabaci adults sampled from cassava in six countries of East and Central Africa, between 1997 and 2010, using a mitochondrial DNA cytochrome oxidase I marker (780 bases). Eight phylogenetically distinct groups were identified, including one, designated herein as 'East Africa 1' (EA1), not previously described. The three most frequently occurring groups comprised >95% of all samples. Among these, the Sub-Saharan Africa 2 (SSA2) group diverged by c. 8% from two SSA1 sub-groups (SSA1-SG1 and SSA1-SG2), which themselves were 1.9% divergent. During the 14-year study period, the group associated with the CMD pandemic expansion shifted from SSA2 to SSA1-SG1. Population genetics analyses of SSA1, using Tajima's D, Fu's Fs and Rojas' R2 statistics confirmed a temporal transition in SSA1 populations from neutrally evolving at the outset, to rapidly expanding from 2000 to 2003, then back to populations more at equilibrium after 2004. Based on available evidence, hybrid introgression appears to be the most parsimonious explanation for the switch from SSA2 to SSA1-SG1 in whitefly populations driving cassava virus pandemics in East and Central Africa.

Begomovirus research in India: a critical appraisal and the way ahead

Begomoviruses are a large group of whitefly-transmitted plant viruses containing single-stranded circular DNA encapsidated in geminate particles. They are responsible for significant yield losses in a wide variety of crops in India. Research on begomoviruses has focussed on the molecular characterization of the viruses, their phylogenetic analyses, infectivities on host plants, DNA replication, transgenic resistance, promoter analysis and development of virus-based gene silencing vectors. There have been a number of reports of satellite molecules associated with begomoviruses. This article aims to summarize the major developments in begomoviral research in India in the last approximately 15 years and identifies future areas that need more attention.

PCR-RFLP analysis indicates that recombination might be a common occurrence among the cassava infecting begomoviruses in India

Cassava mosaic disease (CMD) is caused in India by two bipartite begomoviruses, Indian cassava mosaic virus (ICMV), and Sri Lankan cassava mosaic virus (SLCMV). Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used as a rapid means of investigating the molecular diversity of ICMV and SLCMV in 38 samples of CMD-affected cassava plants under field conditions in new areas of cassava cultivation, along with traditional areas in southern India. A very large proportion of the samples showed SLCMV, based on a discriminatory PCR between SLCMV and ICMV, reported earlier. PCR-RFLP analysis of three regions of viral DNA indicated that in most samples, although the AC1 and the AV1 resembled SLCMV, as expected, the intergenic regions (binding site for host replication machinery) resembled ICMV more closely, indicating recombination events between ICMV and SLCMV. Results also indicate that the AC1 is more conserved within SLCMV compared to the AV1 gene.

Dominance of resistance-breaking cotton leaf curl Burewala virus (CLCuBuV) in northwestern India

Cotton leaf curl disease (CLCuD) is a major limitation to cotton production on the Indian subcontinent. A survey for viruses causing CLCuD was conducted during the 2009 and 2010 cropping seasons in the northwestern Indian cotton-growing belt in the states of Punjab, Haryana and Rajasthan. Partial sequences of 258 and full-length sequences of 22 virus genomes were determined. This study shows that the resistance-breaking cotton leaf curl Burewala virus (CLCuBuV) is now the dominant virus in many fields. The spread and establishment of the mutant CLCuBuV in northwestern India, the variation in its genomic sequence, its virulence and infectivity, and the implications for cotton breeding are discussed.

Biotechnological approaches to determine the impact of viruses in the energy crop plant Jatropha curcas

BACKGROUND

Geminiviruses infect a wide range of plant species including Jatropha and cassava both belonging to family Euphorbiaceae. Cassava is traditionally an important food crop in Sub - Saharan countries, while Jatropha is considered as valuable biofuel plant with great perspectives in the future.

RESULTS

A total of 127 Jatropha samples from Ethiopia and Kenya and 124 cassava samples from Kenya were tested by Enzyme-Linked Immunosorbent Assay (ELISA) for RNA viruses and polymerase chain reaction for geminiviruses. Jatropha samples from 4 different districts in Kenya and Ethiopia (analyzed by ELISA) were negative for all three RNA viruses tested: Cassava brown streak virus (CBSV), Cassava common mosaic virus, Cucumber mosaic virus, Three cassava samples from Busia district (Kenya) contained CBSV. Efforts to develop diagnostic approaches allowing reliable pathogen detection in Jatropha, involved the amplification and sequencing of the entire DNA A molecules of 40 Kenyan isolates belonging to African cassava mosaic virus (ACMV) and East African cassava mosaic virus - Uganda. This information enabled the design of novel primers to address different questions: a) primers amplifying longer sequences led to a phylogenetic tree of isolates, allowing some predictions on the evolutionary aspects of Begomoviruses in Jatrophia; b) primers amplifying shorter sequences represent a reliable diagnostic tool. This is the first report of the two Begomoviruses in J. curcas. Two cassava samples were co - infected with cassava mosaic geminivirus and CBSV. A Defective DNA A of ACMV was found for the first time in Jatropha.

CONCLUSION

Cassava geminiviruses occurring in Jatropha might be spread wider than anticipated. If not taken care of, this virus infection might negatively impact large scale plantations for biofuel production. Being hosts for similar pathogens, the planting vicinity of the two crop plants needs to be handled carefully.

Genetic variability of East African cassava mosaic Cameroon virus under field and controlled environment conditions

Cassava geminiviruses occur in all cassava growing areas of Africa and are considered to be the most damaging vector-borne plant pathogens. At least seven species of these viruses have been identified. We investigated genetic variation in East African cassava mosaic cassava Cameroon virus (EACMCV) from naturally infected cassava and from experimentally infected Nicotiana benthamiana. Results showed that the populations of EACMCV in cassava and in N. benthamiana were genetically heterogeneous. Mutation frequencies in the order of 10(-4), comparable to that reported for plant RNA viruses, were observed in both hosts. We also produced an EACMCV mutant that induces reversion and second site mutations, thus suggesting that a high mutation frequency facilitates the maintenance of genome structure and function. This is direct experimental evidence showing that cassava geminiviruses exhibit a high mutation frequency and that a single clone quickly transforms into a collection of mutant sequences upon introduction into the host.

Cassava: constraints to production and the transfer of biotechnology to African laboratories

Knowledge and technology transfer to African institutes is an important objective to help achieve the United Nations Millennium Development Goals. Plant biotechnology in particular enables innovative advances in agriculture and industry, offering new prospects to promote the integration and dissemination of improved crops and their derivatives from developing countries into local markets and the global economy. There is also the need to broaden our knowledge and understanding of cassava as a staple food crop. Cassava (Manihot esculenta Crantz) is a vital source of calories for approximately 500 million people living in developing countries. Unfortunately, it is subject to numerous biotic and abiotic stresses that impact on production, consumption, marketability and also local and country economics. To date, improvements to cassava have been led via conventional plant breeding programmes, but with advances in molecular-assisted breeding and plant biotechnology new tools are being developed to hasten the generation of improved farmer-preferred cultivars. In this review, we report on the current constraints to cassava production and knowledge acquisition in Africa, including a case study discussing the opportunities and challenges of a technology transfer programme established between the Mikocheni Agricultural Research Institute in Tanzania and Europe-based researchers. The establishment of cassava biotechnology platform(s) should promote research capabilities in African institutions and allow scientists autonomy to adapt cassava to suit local agro-ecosystems, ultimately serving to develop a sustainable biotechnology infrastructure in African countries.

Comparing the regional epidemiology of the cassava mosaic and cassava brown streak virus pandemics in Africa

The rapid geographical expansion of the cassava mosaic disease (CMD) pandemic, caused by cassava mosaic geminiviruses, has devastated cassava crops in 12 countries of East and Central Africa since the late 1980s. Region-level surveys have revealed a continuing pattern of annual spread westward and southward along a contiguous 'front'. More recently, outbreaks of cassava brown streak disease (CBSD) were reported from Uganda and other parts of East Africa that had been hitherto unaffected by the disease. Recent survey data reveal several significant contrasts between the regional epidemiology of these two pandemics: (i) severe CMD radiates out from an initial centre of origin, whilst CBSD seems to be spreading from independent 'hot-spots'; (ii) the severe CMD pandemic has arisen from recombination and synergy between virus species, whilst the CBSD pandemic seems to be a 'new encounter' situation between host and pathogen; (iii) CMD pandemic spread has been tightly linked with the appearance of super-abundant Bemisia tabaci whitefly vector populations, in contrast to CBSD, where outbreaks have occurred 3-12 years after whitefly population increases; (iv) the CMGs causing CMD are transmitted in a persistent manner, whilst the two cassava brown streak viruses appear to be semi-persistently transmitted; and (v) different patterns of symptom expression mean that phytosanitary measures could be implemented easily for CMD but have limited effectiveness, whereas similar measures are difficult to apply for CBSD but are potentially very effective. An important similarity between the pandemics is that the viruses occurring in pandemic-affected areas are also found elsewhere, indicating that contrary to earlier published conclusions, the viruses per se are unlikely to be the key factors driving the two pandemics. A diagrammatic representation illustrates the temporal relationship between B. tabaci abundance and changing incidences of both CMD and CBSD in the Great Lakes region. This emphasizes the pivotal role played by the vector in both pandemics and the urgent need to identify effective and sustainable strategies for controlling whiteflies on cassava.

Emerging virus diseases transmitted by whiteflies

Virus diseases that have emerged in the past two decades limit the production of important vegetable crops in tropical, subtropical, and temperate regions worldwide, and many of the causal viruses are transmitted by whiteflies (order Hemiptera, family Aleyrodidae). Most of these whitefly-transmitted viruses are begomoviruses (family Geminiviridae), although whiteflies are also vectors of criniviruses, ipomoviruses, torradoviruses, and some carlaviruses. Factors driving the emergence and establishment of whitefly-transmitted diseases include genetic changes in the virus through mutation and recombination, changes in the vector populations coupled with polyphagy of the main vector, Bemisia tabaci, and long distance traffic of plant material or vector insects due to trade of vegetables and ornamental plants. The role of humans in increasing the emergence of virus diseases is obvious, and the effect that climate change may have in the future is unclear.

Genetically engineered virus-resistant plants in developing countries: current status and future prospects

Plant viruses cause severe crop losses worldwide. Conventional control strategies, such as cultural methods and biocide applications against arthropod, nematode, and plasmodiophorid vectors, have limited success at mitigating the impact of plant viruses. Planting resistant cultivars is the most effective and economical way to control plant virus diseases. Natural sources of resistance have been exploited extensively to develop virus-resistant plants by conventional breeding. Non-conventional methods have also been used successfully to confer virus resistance by transferring primarily virus-derived genes, including viral coat protein, replicase, movement protein, defective interfering RNA, non-coding RNA sequences, and protease, into susceptible plants. Non-viral genes (R genes, microRNAs, ribosome-inactivating proteins, protease inhibitors, dsRNAse, RNA modifying enzymes, and scFvs) have also been used successfully to engineer resistance to viruses in plants. Very few genetically engineered (GE) virus resistant (VR) crops have been released for cultivation and none is available yet in developing countries. However, a number of economically important GEVR crops, transformed with viral genes are of great interest in developing countries. The major issues confronting the production and deregulation of GEVR crops in developing countries are primarily socio-economic and related to intellectual property rights, biosafety regulatory frameworks, expenditure to generate GE crops and opposition by non-governmental activists. Suggestions for satisfactory resolution of these factors, presumably leading to field tests and deregulation of GEVR crops in developing countries, are given.

Cassava mosaic geminiviruses: actual knowledge and perspectives

SUMMARY Cassava mosaic disease (CMD) caused by cassava mosaic geminiviruses (CMGs) is one of the most devastating crop diseases and a major constraint for cassava cultivation. CMD has been reported only from the African continent and Indian subcontinent despite the large-scale cultivation of cassava in Latin America and several South-East Asian countries. Seven CMG species have been reported from Africa and two from the Indian subcontinent and, in addition, several strains have been recognized. Recombination and pseudo-recombination between CMGs give rise not only to different strains, but also to members of novel virus species with increased virulence and a new source of biodiversity, causing severe disease epidemics. CMGs are known to trigger gene silencing in plants and, in order to counteract this natural host defence, geminiviruses have evolved suppressor proteins. Temperature and other environmental factors can affect silencing and suppression, and thus modulate the symptoms. In the case of mixed infections of two or more CMGs, there is a possibility for a synergistic interaction as a result of the presence of differential and combinatorial suppressor proteins. In this article, we provide the status of recent research findings with regard to the CMD complex, present the molecular biology knowledge of CMGs with reference to other geminiviruses, and highlight the mechanisms by which CMGs have exploited nature to their advantage.

Tissue and cell tropism of Indian cassava mosaic virus (ICMV) and its AV2 (precoat) gene product

In order to establish defined viruses for challenging plants in resistance breeding programmes, Indian cassava mosaic virus (ICMV; family Geminiviridae) DNA clones were modified to monitor viral spread in plants by replacing the coat protein gene with the green fluorescent protein (GFP) reporter gene. Comparative in situ hybridization experiments showed that ICMV was restricted to the phloem in cassava and tobacco. GFP-tagged virus spread similarly, resulting in homogeneous fluorescence within nuclei and cytoplasm of infected cells. To analyze viral intercellular transport in further detail, GFP was fused to AV2, a protein that has been implicated in viral movement. Expressed from replicating viruses or from plasmids, AV2:GFP became associated with the cell periphery in punctate spots, formed cytoplasmic as well as nuclear inclusion bodies, the latter as conspicuous paired globules. Upon particle bombardment of expression plasmids, AV2:GFP was transported into neighboring cells of epidermal tissues showing that the intercellular transport of the AV2 protein is not restricted to the phloem. The results are consistent with a redundant function of ICMV AV2 acting as a movement protein, presumably as an evolutionary relic of a monopartite geminivirus that may still increase virus fitness but is no longer necessary in a bipartite genome. The fusion of ICMV ORF AV2 to the GFP gene is the first example of a reporter construct that follows the whole track of viral DNA from inside the nucleus to the cell periphery and to the next cell.

Deletion and recombination events between the DNA-A and DNA-B components of Indian cassava-infecting geminiviruses generate defective molecules in Nicotiana benthamiana

Cloned DNA-B components, belonging to the bipartite begomoviruses Indian cassava mosaic virus (ICMV) and Sri Lankan cassava mosaic virus (SLCMV), family Geminiviridae, when co-inoculated along with previously cloned DNA-A components of the respective viruses onto the experimental host Nicotiana benthamiana, generated defective DNAs (def-DNA) ranging in size from 549 to 1555 nucleotides. All the cloned def-DNAs contained the common region (CR) as well as portions of either DNA-A or DNA-B and, in a few cases, both DNA-A and DNA-B, representing recombinant products, the junction points of which correspond to repeats of 2-11 bases found in the parental molecules. The DNA-B-derived def-DNAs were, in some cases, associated with a decrease in levels of DNA-B, with a concomitant change in the symptoms from downward leaf curling in the older leaves to upward leaf-rolling in newly emerging leaves, more typical of monopartite begomoviruses.

Genetic diversity and phylogeography of cassava mosaic viruses in Kenya

Cassava is a major factor in food security across sub-Saharan Africa. However, the crop is susceptible to losses due to biotic stresses, in particular to viruses of the genus Begomovirus (family Geminiviridae) that cause cassava mosaic disease (CMD). During the 1990s, an epidemic of CMD severely hindered cassava production across eastern and central Africa. A significant influence on the appearance of virus epidemics is virus diversity. Here, a survey of the genetic diversity of CMD-associated begomoviruses across the major cassava-growing areas of Kenya is described. Because an initial PCR-restriction fragment-length polymorphism analysis identified a much greater diversity of viruses than assumed previously, representative members of the population were characterized by sequence analysis. The full-length sequences of 109 components (68 DNA-A and 41 DNA-B) were determined, representing isolates of East African cassava mosaic virus and East African cassava mosaic Zanzibar virus, as well as a novel begomovirus species for which the name East African cassava mosaic Kenya virus is proposed. The DNA-B components were much less diverse than their corresponding DNA-A components, but nonetheless segregated into western and eastern (coastal) groups. All virus species and strains encountered showed distinct geographical distributions, highlighting the importance of preventing both the movement of viruses between these regions and the importation of the disease from adjacent countries and islands in the Indian Ocean that would undoubtedly encourage further diversification.

Status of Cassava Begomoviruses and Their New Natural Hosts in Nigeria

A diagnostic survey was conducted in 2002-03 to determine the status of cassava mosaic begomoviruses in Nigeria and to ascertain if the virulent Ugandan variant of East African cassava mosaic virus (EACMV-Ug2) was present. Of the 418 farms visited, 48% had cassava with moderately severe or severe symptoms, whereas 52% had cassava with mild symptoms. These distributions were at random. Of the 1,397 cassava leaf samples examined, 1,106 had symptoms. In polymerase chain reaction tests, 74.1% of the symptom-bearing samples tested positive for African cassava mosaic virus (ACMV) alone, 0.3% for EACMV alone, 24.4% for mixed infections by the two viruses, and 1.2% did not react with any of the primers used. The two viruses also were detected in 32% of the 291 symptomless plants and in the whitefly vector samples. EACMV-Ug2, Indian cassava mosaic virus, and South African cassava mosaic virus were not detected in any of the whitefly or leaf samples. Most farms had ACMV in single infection as well as in mixed infections with EACMV. Most doubly infected plants showed severe symptoms. Two biological variants of ACMV were identified based on symptom expression on cassava in the field. ACMV and EACMV were detected in the leguminous plant Senna occidentalis (L.) Link and the weed Combretum confertum Lams.; these are new natural hosts of the viruses. Although the virulent EACMV-Ug2 was not detected, the occurrence of variants of ACMV and a high proportion of mixed infections by ACMV and EACMV, which could result in recombination events such as the one that produced EACMV-Ug2, demands appropriate measures to safeguard cassava production in Nigeria.

Molecular ecology and emergence of tropical plant viruses

An appreciation of the risks caused by emergent plant viruses is critical in tropical areas that rely heavily on agriculture for subsistence and rural livelihood. Molecular ecology, within 10 years, has unraveled the factors responsible for the emergence of several of the economically most important tropical plant viruses: Rice yellow mottle virus (RYMV), Cassava mosaic geminiviruses (CMGs), Maize streak virus (MSV), and Banana streak virus (BSV). A large range of mechanisms--most unsuspected until recently--were involved: recombination and synergism between virus species, new vector biotypes, genome integration of the virus, host adaptation, and long-distance dispersal. A complex chain of molecular and ecological events resulted in novel virus-vector-plant-environment interactions that led to virus emergence. It invariably involved a major agricultural change: crop introduction, cultural intensification, germplasm movement, and new genotypes. A current challenge is now to complement the analysis of the causes by an assessment of the risks of emergence. Recent attempts to assess the risks of emergence of virulent virus strains are described.

Identification of a second begomovirus, Sri Lankan cassava mosaic virus, causing cassava mosaic disease in India

The DNA A and DNA B components of a begomovirus associated with cassava mosaic disease (CMD) originating from Kerala, India, were cloned. Biolistically inoculated clones induced symptoms typical of CMD in cassava. Sequence comparisons showed the virus to be an isolate of Sri Lankan cassava mosaic virus (SLCMV). This is the first time this begomovirus species has been identified in India and only the second species shown to cause CMD in the country. The implication of these findings on our understanding of the diversity and geographic distribution of CMD-associated begomoviruses in the region and on efforts to obtain resistance to CMD are discussed.

Molecular biodiversity of cassava begomoviruses in Tanzania: evolution of cassava geminiviruses in Africa and evidence for East Africa being a center of diversity of cassava geminiviruses

Cassava is infected by numerous geminiviruses in Africa and India that cause devastating losses to poor farmers. We here describe the molecular diversity of seven representative cassava mosaic geminiviruses (CMGs) infecting cassava from multiple locations in Tanzania. We report for the first time the presence of two isolates in East Africa: (EACMCV-[TZ1] and EACMCV-[TZ7]) of the species East African cassava mosaic Cameroon virus, originally described in West Africa. The complete nucleotide sequence of EACMCV-[TZ1] DNA-A and DNA-B components shared a high overall sequence identity to EACMCV-[CM] components (92% and 84%). The EACMCV-[TZ1] and -[TZ7] genomic components have recombinations in the same genome regions reported in EACMCV-[CM], but they also have additional recombinations in both components. Evidence from sequence analysis suggests that the two strains have the same ancient origin and are not recent introductions. EACMCV-[TZ1] occurred widely in the southern part of the country. Four other CMG isolates were identified: two were close to the EACMV-Kenya strain (named EACMV-[KE/TZT] and EACMV-[KE/TZM] with 96% sequence identity); one isolate, TZ10, had 98% homology to EACMV-UG2Svr and was named EACMV-UG2 [TZ10]; and finally one isolate was 95% identical to EACMV-[TZ] and named EACMV-[TZ/YV]. One isolate of African cassava mosaic virus with 97% sequence identity with other isolates of ACMV was named ACMV-[TZ]. It represents the first ACMV isolate from Tanzania to be sequenced. The molecular variability of CMGs was also evaluated using partial B component nucleotide sequences of 13 EACMV isolates from Tanzania. Using the sequences of all CMGs currently available, we have shown the presence of a number of putative recombination fragments that are more prominent in all components of EACMV than in ACMV. This new knowledge about the molecular CMG diversity in East Africa, and in Tanzania in particular, has led us to hypothesize about the probable importance of this part of Africa as a source of diversity and evolutionary change both during the early stages of the relationship between CMGs and cassava and in more recent times. The existence of multiple CMG isolates with high DNA genome diversity in Tanzania and the molecular forces behind this diversity pose a threat to cassava production throughout the African continent.

Molecular Cloning of Coat Protein Gene of an Indian Cotton Leaf Curl Virus (CLCuV-HS2) Isolate and its Phylogenetic Relationship with others Members of Geminiviridae

Cotton leaf curl geminivirus is a whitefly (Bemisia tabaci Genn.) transmitted Begomovirus (Family Geminiviridae) causing a serious disease of cotton in northern India. The very typical symptoms of present isolate (CLCuV-HS2) showed thickened veins, dark green discoloration of the leaves with upward curling and leaf like structure known as enation (one in number), which develops into cup-shaped on the reverse side of leaves. The polymerase chain reaction (PCR) based technique can detect the viral DNA in samples stored upto 3 days after the collection and have wide application for the field diagnosis. The complete nucleotide sequence of the Indian isolate of cotton leaf curl geminivirus (CLCuV-HS2) coat protein (CP) gene component was determined using CP specific primers through PCR amplification from field infected cotton plants growing in Haryana, India. Comparison of the amino acid sequence of the putative CP with some other mono and bipartite geminiviruses revealed a maximum of 97.3% identity with Pakistan cotton leaf curl virus (CLCuV-62). A nuclear localization signal located close to the N-terminal of CP gene was determined.

Cassava mosaic geminiviruses in Africa

Cassava mosaic disease (CMD) caused by cassava mosaic geminiviruses (CMGs) (Geminiviridae:Begomovirus) is undoubtedly the most important constraint to the production of cassava in Africa at the outset of the 21st century. Although the disease was recorded for the first time in the latter part of the 19th century, for much of the intervening period it has been relatively benign in most of the areas where it occurs and has generally been considered to be of minor economic significance. Towards the end of the 20th century, however, the inherent dynamism of the causal viruses was demonstrated, as a recombinant hybrid of the two principal species was identified, initially from Uganda, and shown to be associated with an unusually severe and rapidly spreading epidemic of CMD. Subsequent spread throughout East and Central Africa, the consequent devastation of production of the cassava crop, a key staple in much of this region, and the observation of similar recombination events elsewhere, has once again demonstrated the inherent danger posed to man by the capacity of these viruses to adapt to their environment and optimally exploit their relationships with the whitefly vector, plant host and human cultivator. In this review of cassava mosaic geminiviruses in Africa, we examine each of these relationships, and highlight the ways in which the CMGs have exploited them to their own advantage.

Variants of East African cassava mosaic virus and Its Distribution in Double Infections with African cassava mosaic virus in Nigeria

In a survey for cassava mosaic begomoviruses conducted in 1997 and 1998 in Nigeria, East African cassava mosaic virus (EACMV) was detected by the polymerase chain reaction together with African cassava mosaic virus (ACMV) in 27 out of 290 cassava leaf samples of infected plants from 254 farmers' fields in five agroecological zones. One plant was infected with EACMV only. Five variant isolates of EACMV were observed based on their reactions to primers that could detect Cameroonian and East African strains of EACMV. Isolates of variants 1 and 3 occurred mostly in the derived or coastal and southern Guinea savannahs, while variants 4 and 5 predominated in the humid forest region. Isolates of variant 2 were widely distributed across the three agroecologies. EACMV was not detected in the northern Guinea savannah and arid and semiarid zones. Most doubly infected plants showed more severe symptoms than plants with single infection. Occurrence of EACMV variants together with ACMV detection and information about their distribution in Nigeria could be used for the selection of cassava clones in cassava mosaic disease resistance programs.

Co-adaptation between cassava mosaic geminiviruses and their local vector populations

Four cassava mosaic geminivirus (CMG) isolates; African cassava mosaic virus from Namulonge, Uganda (ACMV-[Nam]), East African cassava mosaic virus from Mtwara, Tanzania (EACMV-[Mtw]), EACMV-Uganda from Namulonge (EACMV-UG[Nam]) and Indian cassava mosaic virus from Trivandrum, India (ICMV-[Tri]) were compared for their ability to be transmitted by four colonies of cassava whitefly, Bemisia tabaci (Gennadius), collected from Namulonge (NAM), Mtwara (MTW), Kumasi (KUM) and Trivandrum (TRI). With 20 adult whiteflies per test plant, the CMGs from Africa were transmitted by all three of the African B. tabaci populations to 60-79% of the target plants. Indian cassava B. tabaci transmitted ICMV-[Tri] to 89% of the target plants. In contrast, Indian cassava B. tabaci transmitted EACMV-[Mtw] and Tanzanian cassava B. tabaci transmitted ICMV-[Tri] less than a tenth as often, even when using 50 adults per plant and with increased acquisition and inoculation access periods. The complete coat protein genes of the CMGs had sequences typical of their source viruses, the major differences occurring between those originating from India and Africa. Symptom severity of the CMGs was quantified precisely by both visual assessment and image analysis techniques. EACMV-[Mtw] and ACMV-[Nam] were the most and least damaging isolates with 15.4 and 10.0% of the leaf area diseased, respectively. In these tests the transmission frequency was not linked to symptom severity in the source plants. These data support the hypothesis that virus-vector co-adaptation exists in the cassava mosaic disease (CMD) pathosystem and the results are discussed in relation to CMD epidemiology.

Characterisation of Sri Lankan cassava mosaic virus and Indian cassava mosaic virus: evidence for acquisition of a DNA B component by a monopartite begomovirus

Two bipartite begomoviruses, Indian cassava mosaic virus (ICMV) and Sri Lankan cassava mosaic virus (SLCMV), have been isolated from mosaic-diseased cassava originating from central India and Sri Lanka, respectively. ICMV was transmitted with low efficiency from cassava to Nicotiana benthamiana by sap inoculation to give leaf curl symptoms. SLCMV was much more virulent in this host, producing severe stunting, leaf curl, and chlorosis. These symptoms were reproduced when their cloned genomic components (DNAs A and B) were introduced into N. benthamiana by either mechanical or Agrobacterium-mediated inoculation (agroinoculation). SLCMV is more closely related to ICMV (DNA A, 84%; DNA B, 94% nucleotide identity) than African cassava mosaic virus (ACMV) (DNA A, 74%; DNA B, 47% nucleotide identity). Sequence comparisons suggest that SLCMV DNA B originated from ICMV DNA B by a recombination event involving the SLCMV DNA A intergenic region. Pseudorecombinants produced by reassortment of the cloned components of ICMV and ACMV were not infectious in N. benthamiana, emphasising their status as distinct virus species. In contrast, a pseudorecombinant between ACMV DNA A and SLCMV DNA B was infectious. Consistent with these observations, iteron motifs located within the intergenic region that may be involved in the initiation of viral DNA replication are conserved between SLCMV and ACMV but not ICMV. When introduced into N. benthamiana by agroinoculation, SLCMV DNA A alone produced a severe upward leaf roll symptom, reminiscent of the phenotype associated with some monopartite begomoviruses. Furthermore, coinoculation of SLCMV DNA A and the satellite DNA beta associated with ageratum yellow vein virus (AYVV) produced severe downward leaf curl in N. glutinosa and yellow vein symptoms in Ageratum conyzoides, resembling the phenotypes associated with AYVV DNA A and DNA beta infection in these hosts. Thus, SLCMV DNA A has biological characteristics of a monopartite begomovirus, and the virus probably evolved by acquisition of a DNA B component from ICMV.

Tomato yellow leaf curl China virus: monopartite genome organization and agroinfection of plants

The complete DNA sequence (2734 nucleotides) of the monopartite genome of tomato yellow leaf curl China virus (TYLCCNV), a begomovirus transmitted by the whitefly Bemisia tabaci, was determined. The circular genomic DNA contains six open reading frames (ORFs) encoding proteins of molecular weights >10 kDa, of which two (V1 and V2) are located on the virion-sense strand and four (C1, C2, C3 and C4) on the complementary-sense strand. The ORFs are comparable to those of other whitefly-transmitted begomoviruses with a monopartite genome and to those encoded by DNA-A of bipartite begomoviruses. Sequence comparisons with other geminiviruses showed that TYLCCNV belongs to Begomovirus from the Old World. No putative DNA-B genome was found. Nicotiana species and tomato plants agroinoculated with the TYLCCNV monopartite genome developed typical yellowing and leaf-curling symptoms. The cloned molecule carried all the information needed for virus replication and systemic infection of plants.

Differentiation of cassava-infecting begomoviruses using heteroduplex mobility assays

Cassava mosaic disease is an enormous problem affecting the viability and productivity of cassava in all the developing regions in Africa. The disease is now known to be caused by a number of cassava-infecting begomoviruses. New viruses and viral strains continue to be discovered and due to the lack of cloning and sequencing facilities in many African laboratories, a simple, rapid and sensitive technique is needed for screening of cassava plantations. Here we report on the development of a heteroduplex mobility assay (HMA) which could be used for the testing of viral-infected cassava. The assay involves amplifying the highly conserved core region of the coat protein gene of field isolates followed by denaturing and annealing with a number of reference strains. The HMA profiles in this study were able to differentiate four different viral species and 11 different virus strains, and showed a good correlation with sequencing results and phylogenetic comparisons with other sequenced cassava viruses. This technique is sensitive and rapid and has the added advantage of being able to detect mixtures of viruses in field-grown cassava.

Sensitive detection of the Egyptian species of sugarcane streak virus by PCR-probe capture hybridization (PCR-ELISA) and its complete nucleotide sequence

A rapid and sensitive assay for the specific detection of Sugarcane streak virus (SSV) using PCR-probe capture hybridization (PCR-ELISA) was developed. Nucleic acids suitable for PCR were extracted from SSV-infected tissue using organic solvents or Fast DNA kit. SSV cDNA was amplified using viral specific primers and the amplified SSV cDNA (amplicon) was DIG-labelled during the amplification process. The amplicon was then detected in a colorimetric hybridization system by a microtiter plate using a biotinylated cDNA (22 nt), cDNA (789 nt) or cRNA (789 nt) capture probe. This system combines the specificity of molecular hybridization, the ease of the colorimetric protocol, and is 10-100 fold more sensitive than agarose gel electrophoretic analysis in detecting the amplified product. Long cDNA or cRNA capture probe was 2-7 fold more sensitive than the oligo cDNA probe for the detection. Complete nucleotide sequence of SSV from Naga Hammady, Egypt, revealed that SSV-EG is a new species of SSV that shares 66% nucleotide identity with the virus species from Natal, South Africa.

Recombination, pseudorecombination and synergism of geminiviruses are determinant keys to the epidemic of severe cassava mosaic disease in Uganda

The molecular variability of cassava geminiviruses occurring in Uganda was investigated in this study. Infected cassava plants and whiteflies were collected from cassava plantings in different geographical areas of the country and PCR was used for molecular characterization of the viruses. Two complete sequences of DNA-A and -B from African cassava mosaic virus (ACMV), two DNA-A sequences from East African cassava mosaic virus (EACMV), two DNA-B sequences of EACMV and the partial DNA-A nucleotide sequence of a new virus strain isolated in Uganda, EACMV-UG3, are reported here. Analysis of naturally infected cassava plants showed various assortments of DNA-A and DNA-B of the Ugandan viruses, suggesting the occurrence of natural inter- and intraspecies pseudorecombinations and a pattern of cassava mosaic disease (CMD) more complex than previously reported. EACMV-UG2 DNA-A, which contains a recombinant fragment between ACMV and EACMV-UG1 in the coat protein gene that resembles virus from Tanzania, was widespread in the country and always associated with EACMV-UG3 DNA-B, which probably resulted from another natural recombination event. Mixed infections of ACMV-UG and EACMV-UG in cassava and whiteflies were detected in most of the regions where both viruses occurred. These mixed-infected samples always showed extremely severe CMD symptoms, suggesting a synergistic interaction between ACMV-UG and EACMV-UG2. The first demonstration is provided of infectivity of EACMV clones to cassava, proving conclusively that the pseudorecombinant EACMV-UG2 DNA-A+EACMV-UG3 DNA-B is a causal agent of CMD in Uganda.