The effect of cassava mosaic geminiviruses on symptom severity, growth and root yield of a cassava mosaic virus disease-susceptible cultivar in Uganda

A study was carried out to assess the effect of different cassava mosaic geminiviruses (CMGs) occurring in Uganda on the growth and yield of the susceptible local cultivar ‘Ebwanateraka’. Plants infected with African cassava mosaic virus (ACMV), ‘mild’ and ‘severe’ strains of East African cassava mosaic virus‐Uganda (EACMV‐UG2) and both ACMV and EACMV‐UG2 were grown in two experiments in Kabula, Lyantonde in western Uganda. The most severe disease developed in plants co‐infected with ACMV and EACMV‐UG2 and in those infected with the ‘severe’ form of EACMV‐UG2 alone; disease was least severe in plants infected with the ‘mild’ strain of EACMV‐UG2. ACMV‐infected plants and those infected with the ‘mild’ strain of EACMV‐UG2 were tallest in the 1999–2000 and 2000–2001 trials, respectively; plants dually infected with ACMV and EACMV‐UG2 were shortest in both trials. Plants infected with ‘mild’ EACMV‐UG2 yielded the largest number and the heaviest tuberous roots followed by ACMV and EACMV‐UG2 ‘severe’, respectively, whilst plants dually infected with ACMV and EACMV‐UG2 yielded the least considering the two trials together. Reduction in tuberous root weight was greatest in plants dually infected with ACMV and EACMV‐UG2, averaging 82%. Losses attributed to ACMV alone, EACMV‐UG2 ‘mild’ and EACMV‐UG2 ‘severe’ were 42%, 12% and 68%, respectively. Fifty percent and 48% of the plants infected with both ACMV and EACMV‐UG2 gave no root yield in 1999–2000 and 2000–2001, respectively. These results indicate that CMGs, whether in single or mixed infections, reduce root yield and numbers of tuberous roots produced and that losses are substantially increased following mixed infection.     

Eradication of cassava mosaic disease from Nigerian cassava clones by meristem-tip culture

Methods previously established for the propagation of cassava plants free from cassava mosaic disease have been applied to Nigerian clones. Meristem tips from diseased plants subjected to heat treatment for not less than 30 days at 35°–38°C were cultured on modified Murashige-Skoog medium. Concentration ranges of benzyladenine in combination with α-naphthalene acetic acid and gibberellic acid were investigated and, at optimal levels, 36% of the meristems regenerated. Regenerants, with callus and shoots only, were rooted with 80% efficiency by sub-culturing following a dip in a hormone rooting powder. All plants raised from heat-treated meristems were free of the disease as judged by visual inspection of the leaves, rooted explants and assay for the suspected pathogenic agent of the disease.     

Role of a novel type of double infection in the geminivirus-induced epidemic of severe cassava mosaic in Uganda

To study the cause of the current epidemic of severe mosaic in Ugandan cassava, PCR analysis was used to detect and identify African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV) and the recently reported recombinant geminivirus (UgV), which is derived from ACMV and EACMV, in leaf extracts from cassava plants grown from cuttings in the glasshouse at Dundee. The cuttings were collected from plants showing symptoms of different severities and growing at different sites in Uganda inside, at the periphery of, and outside, the area affected by the epidemic. ACMV occurred throughout the nine districts sampled but UgV was detected only in the area affected by the epidemic. EACMV was not found in Uganda. Most plants containing ACMV alone expressed mild or moderate mosaic, whereas very severe mosaic developed in most plants containing UgV plus ACMV and a few of those containing UgV only. Very severe mosaic in cassava from southern Sudan was likewise associated with co-infection by UgV and ACMV. The very severe disease was reproduced by graft-inoculating geminivirus-free cassava with UgV plus ACMV; plants inoculated with either UgV or ACMV developed severe or moderate symptoms, respectively. Unlike ACMV, Malawian EACMV did not enhance the severity of symptoms induced by UgV. However, a very severely affected plant from Ukerewe Island, Tanzania, contained ACMV and EACMV but not UgV. UgV attained a much greater concentration in cassava than did ACMV but the opposite occurred in Nicotiana benthamiana. In neither host was total virus antigen concentration affected by co-infection. Factors affecting the genesis, selection and spread of UgV are discussed. The evidence indicates that UgV is probably of relatively recent origin, that such variants do not appear often, and that the current epidemic has resulted from the rapid spread of UgV to infect plants and to invade regions in which ACMV already occurred. The novel type of virus complex so produced, consisting of an interspecific recombinant virus (UgV) and one of its parents (ACMV), typically has even more severe effects than UgV alone.     

Occurrence and distribution of cassava begomoviruses in Kenya

A survey for cassava mosaic disease (CMD) was conducted in Kenya, to investigate the factors contributing to the generally increased incidence and severity of CMD in the cassava growing regions and to study the distribution of the disease's causal begomoviruses, African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV) and their strains. Special emphasis was given to the occurrence of the destructive recombinant Uganda variant strain of EACMV (EACMV-UG2). Samples from 91 farmers' fields in the main cassava-growing areas of coastal and western Kenya were collected and subjected to ELISA and PCR for detection and typing of the begomoviruses present. CMD incidence was highest in western Kenya (80–100%) and lowest in the Coast province (25–50%). In Western and Nyanza provinces, 52% of the samples tested contained EACMV-UG2, 22% ACMV and 17% contained both ACMV and EACMV-UG2. EACMV was found in four cases at different sites. In cassava samples from the coast province, only EACMV with DNA-A sequences similar to EACMV strains present in Kenya and Tanzania was found. East African cassava mosaic Zanzibar virus (EACMZV) was present in several farms in the Kilifi district. In 15% of all cassava samples with CMD symptoms, flexuous, filamentous virus-like particles were also found, providing evidence for a more complex virus situation in cassava grown at the Kenyan coast. In western Kenya, where intense cassava cultivation takes place, CMD is rampant and EACMV-UG2 was found in mixed virus infections with ACMV driving the epidemics. In coastal areas, where farms are scattered and in isolation, EACMV is endemic, however, with a lower disease incidence and with a limited impact to cassava production.     

Serological studies on cassava latent virus

Particles of cassava latent virus (CLV) were purified by a method that yielded up to 3 mg per 100 g of systemically infected Nicotiana benthamiana leaf. Specific antiserum was prepared and used for enzyme-linked immunosorbent assay (ELISA), which detected purified virus at 5 ng/ml. As estimated by ELISA, CLV antigen reached a greater concentration in leaves of N. benthamiana plants kept at 20–25 °C than in those at 15 °C or 30 °C. CLV was also detected in leaf extracts of naturally infected cassava plants kept at 25 C but its concentration was only 1–7% of that in comparable extracts from N. benthamiana. Staining sections of N. benthamiana leaves with fluorescent antibody indicated that CLV particle antigen accumulates in the nuclei of many phloem cells and of some cells in other tissues. In tests on mosaic-affected cassava plants of Angolan origin, three plants were found in which CLV could not be detected by either ELISA or immunosorbent electron microscopy, or by transmission to indicator plants. This suggests that the mosaic symptoms were caused by a pathogen other than CLV, but no such agent was detected by electron microscopy of leaf extracts. Three kinds of serological test indicated that CLV is related to bean golden mosaic virus. Evidence was also obtained of a distant relationship to beet curly top virus but none was detected to four other geminiviruses.     

Viruses Associated with Cassava Mosaic Disease in Senegal and Guinea Conakry

A survey in Senegal and Guinea Conakry established the presence and incidence of cassava mosaic virus disease (CMD) in both countries. CMD occurred in all the fields surveyed, although its incidence was higher in Senegal (83%) than in Guinea (64%). Populations of the whitefly vector, Bemisia tabaci, were low in both countries averaging 1.7 adults per shoot in Guinea and 3.2 in Senegal. Most infections were attributed to the use of infected cuttings, 86 and 83% in Senegal and Guinea, respectively, and there was no evidence of rapid current‐season, whitefly‐borne infection at any of the sampled locations. Disease severity was generally low in the two countries and averaged 2.5 in Guinea and 2.3 in Senegal. No plants with unusually severe CMD symptoms characteristic of the CMD pandemic in East and Central Africa were observed. Restriction fragment length polymorphism (RFLP)‐based diagnostics revealed that African cassava mosaic virus (ACMV) is exclusively associated with CMD in both the countries. Neither East African cassava mosaic virus (EACMV), nor the recombinant Uganda variant (EACMV‐UG2) was detected in any sample. These survey data indicate that CMD could be effectively controlled in both countries by phytosanitation, involving the use of CMD‐free planting material and the removal of diseased plants.     

Evaluation of Tip Culture, Thermotherapy and Chemotherapy for Elimination of Peanut Mottle Virus from Arachis hypogaea

Peanut (Arachis hypogaea L.) plants (cvs Florunner and Pronto) were inoculated at the two-leaf stage with peanut mottle virus (PMV) to obtain PMV-infected plants. Shoot-tips from plants grown in the glasshouse (27°C) or from plants maintained at 35°C were used for tip culture. In some experiments ribavirin was added to the culture medium at 5 mg/1, 10 mg/1, 15 mg/1 or 20 mg/1. Plants regenerated from meristems or shoot-tips taken from virus-infected plants were not virus-free. After 45 days at 35°C, foliar tissue of 93 % of Florunner and 95 % of Pronto plants tested negative for PMV by enzyme-linked immunosorbent assay (ELISA). When shoot-tips from the plant that tested negative by ELISA were used for tip culture, no virus-free plants were obtained. No virus-free plants were obtained from tips cultured on medium supplemnted with ribavirin. However, when tip culture, thermotherapy and chemotherapy were combined; 80 % of Florunner and 100 % of Pronto plants were found negative for PMV.     

Virus Free Garlic (Allium Sativum L.) Plants Obtained by Thermotherapy and Meristem Tip Culture

Virus infection in garlic considerably reduces yield and quality in Argentina. The production of virus free “seed” was attempted by means of thermotherapy and meristem tip culture. A hot water treatment was employed to determine the lethal temperature/time combination for clonal type (c.t.) Blanco cloves. It was established that 50°C × 20 min, 50°C × 15 min and 55°C × 5 min were the limit thermal/time combinations which garlic could withstand. Those treatments were employed followed by meristem tip culture, however, none of the successfully developed plants after culture (only 13 %) were virus-free. Hot air treatments in a growth chamber at 36°C lasting for 30, 40 and 60 days, and at 25°–32° for 30 days in a greenhouse were tested on c.t. Blanco. Cloves kept at room temperature throughout the experiment were employed as controls. In the 25°–32°C treatment, 73% of meristems produced plants and, of these, 33 % were virus free. After 30 and 40 days at 36 °C, 62 % and 67 % of the meristems developed into plantlets, of which respectively 51 % and 50 % were virus-free. Very few meristems (10 %) developed into plants when cloves had been kept at 36°C for 60 days but the resulting plantlets were all virus free. Controls produced 78 % of plants, of which 14 % were virus free. Results of hot air treatments of 36 °C for 40 days performed on c.t. Colorado, Rosado, Paraguayo, Espaol and Hilario Ascasubi were similar to those obtained with c.t. Blanco. In Espaol and Hilario Ascasubi, no virus-free plants were detected among control specimens (no thermotherapy treatment). The only virus (from up to 3 that infected the plants) that persisted in some plants after themotherapy and meristem tip culture was garlic yellow streak.     

Detection of strains of African cassava mosaic virus by nucleic acid hybridisation and some effects of temperature on their multiplication

DNA probes, made by cloning double-stranded forms of each of the genome parts (DNA-1 and DNA-2) of the Kenyan type isolate of African cassava mosaic virus (ACMV-T), reacted strongly with extracts from Nicotiana benthamiana plants infected with ACMV-T, or with Angolan or Nigerian isolates that are closely serologically related to the type isolate. However, only the DNA-1 probes reacted with extracts of TV. benthamiana infected with a Kenyan coast isolate (ACMV-C), which is serologically less closely related to ACMV-T. DNA-1 and DNA-2 probes also reacted with extracts of mosaic-affected Angolan cassava plants, including some which have not yielded ACMV particles detectable by immunosorbent electron microscopy and from which virus isolates have not been transmitted to TV. benthamiana. These anomalous plants, unlike other naturally infected cassava plants, showed mosaic symptoms on all their leaves which, however, contained only traces of virus particle antigen detectable by enzyme-linked immunosorbent assay. They contain isolates of ACMV that are probably defective for particle production. ACMV-T particles accumulated optimally in N. benthamiana at 20–25°C. At 30°C fewer particles, which apparently had a slightly greater specific infectivity, were produced. At 15°C, considerable quantities of virus particle antigen, virus DNA and virus particles were produced but the particles were poorly infective, and the few that could be purified contained an abnormally large proportion of polydisperse linear DNA molecules, and fewer circular molecules than usual. Angolan isolates, whether particle-producing or not, likewise replicated better in cassava plants at 23 °C than at 30 °C. In contrast, ACMV-C attained only very low concentrations in N. benthamiana, but these were greater at 30 °C than at 23°C.     

Biological Characterization and Complete Genome Sequence of a Possible Strain of Indian cassava mosaic virus from Jatropha curcas in India

The outbreak of a severe mosaic disease with a significant incidence was noticed on Jatropha curcas plants growing in Lucknow, Northern India. The causal virus was successfully transmitted by whiteflies (Bemisia tabaci) and grafting from naturally infected to healthy J. curcas plants. The association of Begomovirus with the mosaic disease of J. curcas was detected by PCR using primers specific to DNA‐A of Begomoviruses. Further, full‐length DNA‐A genome of ～2.7 kb was amplified by RCA followed by digestion with Bam HI restriction enzyme. Cloning and sequencing of obtained amplicons resulted in 2740 nucleotides of complete DNA‐A consisting of six ORFs and IR region (GenBank Accession HM230683 ). The sequence analysis revealed highest 85% similarities with Jatropha curcas mosaic virus, 77–84% with Indian cassava mosaic virus and 73–76% with Sri Lankan cassava mosaic virus isolates. Phylogenetic analysis of the Begomovirus isolate also showed a clear‐cut distinct relationship with earlier reported Begomoviruses from Jatropha curcas and other Begomoviruses. On the basis of the guidelines of the International Committee on Taxonomy of Viruses (ICTV‐2008), our virus isolate was identified as a possible strain of Indian cassava mosaic virus, and its name Jatropha mosaic India virus (JMIV) is proposed.     

In vitro production of Indian citrus ringspot virus (ICRSV) free Kinnow plants employing thermotherapy coupled with shoot tip grafting

Indian citrus ringspot virus (ICRSV) is known to cause serious disease problem in Kinnow (Citrus nobilis Lour × C. deliciosa Tenora) plants. This work reports the elimination of ICRSV by using thermotherapy coupled with shoot tip grafting in vitro. Nodal segments from infected mother plants (indexed by indirect ELISA and RT-PCR) were treated both in water bath and moist hot air at different temperatures viz. 40, 45 and 50°C for 30, 60 and 120 min and cultured on MS medium containing 2-iP (1 mg/l) and malt extract (800 mg/l). Shoot tips were excised from the nodal sprouts and grafted on to rough lemon (C. jambhiri) rootstock under aseptic conditions. Water bath treatment was found to be more effective as compared to moist hot air treatment as maximum number of ICRSV free plants (36.84%) were obtained by grafting the tips (0.7 mm) taken from the nodal segments treated at 50°C in water bath for 2 h. In an alternate treatment regime, 1-year-old infected plants were kept at various temperatures viz.36, 38 and 40°C in a thermotherapy chamber. Maximum of 60% ICRSV free plants were obtained by grafting the tips (0.7 mm) from the plants placed at 40°C followed by the plants placed at 38°C (59.09%) and the least was observed in case of the plants placed at 36°C (40.74%). Only those plants/plantlets were considered virus free, which showed negative reaction both in Indirect ELISA and RT-PCR.     

Molecular Variability and Distribution of Cassava Mosaic Begomoviruses in Nigeria

Several begomovirus species and strains causing Cassava mosaic disease (CMD) have been reported from cassava in Africa. In Nigeria, African cassava mosaic virus (ACMV) was the predominant virus in this important crop, and East African cassava mosaic virus (EACMV), first reported from eastern Nigeria in 1999, was also found occasionally. A survey was conducted in 2002 to resolve the diversity of the virus types present in cassava in Nigeria and to further understand the increasing complexity of the viruses contributing to CMD. A total of 234 leaf samples from cassava with conspicuous CMD symptoms were collected in farmers’ fields across different agroecological zones of Nigeria and subjected to polymerase chain reaction (PCR) with type‐specific primers. In addition and, to provide a full characterization of the viruses present, DNA‐A genome components of several viruses and informative genome fragments were sequenced. In Nigeria, ACMV proved to be the dominant virus with 80% of all samples being positive for ACMV. The East African cassava mosaic Cameroon virus (EACMCV) prevalent in Cameroon and Ivory Coast was detected in single infections (2%) and in mixed infections (18%) with ACMV. There was no indication for other virus strains of EACMV present in the country. The EACMCV samples collected showed a high nucleotide sequence identity >98% and resembled the described sequence of a Cameroon isolate (EACMCV‐CM) more than an Ivory Coast isolate, EACMCV‐CM[CI]. Evidence is provided that the EACMCV has reached epidemiological significance in Nigeria.     

Field Studies of Cross Protection with Cassava Mosaic Geminiviruses in Uganda

The effect of cassava mosaic virus disease (CMD) was compared on plants grown from cuttings that were initially virus‐free at planting and those infected with a mild strain of East African cassava mosaic virus‐Uganda (EACMV‐UG). All initially healthy plants developed CMD symptoms within 5 months of planting (MAP) at both trial sites in Uganda, although spread was more rapid at Kamuli than at Serere. Significantly (P < 0.001) higher symptom severity scores were recorded in initially healthy plants, which had average scores of 3.6 and 3.5 at Kamuli and Serere, respectively, compared with 2.8 for mildly diseased plants at each location. Severity scores of 4 and 5 were more frequent in initially healthy plants, accounting for 77 and 39% of the total infections recorded in comparison with 47 and 11% in mildly diseased plants at Kamuli and Serere, respectively. Mildly diseased plants were significantly taller than initially healthy plants 8 and 12 MAP at both locations. However, the converse was true 4 MAP although differences were significant at Serere but not at Kamuli. Mildly diseased plants yielded significantly more tuberous roots than initially healthy plants at Kamuli but not at Serere. Average total weights of tuberous roots per plant were 2.48 and 1.63 kg for mildly diseased and initially healthy plants at Kamuli and 4.46 and 4.61 kg at Serere, respectively. These results may help to explain the increased prevalence in recent years of mildly diseased plants of local CMD‐susceptible cultivars in eastern Uganda, from where these varieties virtually disappeared following the severe CMD epidemic in the 1990s. The results also provide the first field evidence of a cross protective effect of mild strains of a cassava mosaic geminivirus.     

Dose-dependent RNAi-mediated geminivirus resistance in the tropical root crop cassava

Cassava mosaic disease is a major constraint for cassava production in Africa, resulting in significant economic losses. We have engineered transgenic cassava with resistance to African cassava mosaic virus (ACMV), by expressing ACMV AC1-homologous hairpin double-strand RNAs. Transgenic cassava lines with high levels of AC1-homologous small RNAs have ACMV immunity with increasing viral load and different inoculation methods. We report a correlation between the expression of the AC1-homologous small RNAs and the ACMV resistance of the transgenic cassava lines. Characterization of the small RNAs revealed that only some of the hairpin-derived small RNAs fall into currently known small interfering RNA classes in plants. The method is scalable to stacking by targeting multiple virus isolates with additional hairpins. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Distribution, host range, properties and purification of cassava latent virus, a geminivirus

Cassava latent virus (CLV) is almost entirely confined in East Africa to upland cassava-growing areas west of the Rift Valley, where it is often associated with cassava mosaic disease (it was isolated from 27 of 38 cassava plants with mosaic, but not from 24 without mosaic). However, it is not the causal agent, because it was not recovered from any of 31 mosaic-diseased plants in coastal districts. All attempts to return CLV to cassava failed. The host range of CLV appears to be limited to Euphorbiaceae (Manihot) and Solanaceae (Nicotiana, Datura, Nicandra, Solanum). N. clevelandii proved the most useful assay and propagation host. The dilution end-point of CLV was about 10^-3, thermal inactivation point about 55°C, and longevity in vitro about 3 days. CLV was purified by clarification of leaf extracts with butanol/chloroform mixtures. Purified preparations (A 260/A 280 ratio c. 16) contained numerous 30 20 nm paired particles with a sedimentation coefficient (s₂₀w) of 76 S. Treatment with RNase and DNase showed that the viral nucleic acid is DNA; CLV closely resembles maize streak virus but is not related to it serologically. The cryptogram for CLV is D/1: 0.8/*: S/S: S/*, geminivirus group.     

Particle purification and properties of cassava Ivorian bacilliform virus

A virus found in cassava from the north-west of the Ivory Coast was transmitted by inoculation with sap extracts to herbaceous species in six plant families. Chenopodium quinoa was used as a propagation host and C. murale was used for local lesion assays. The virus particles are bacilliform, c. 18 nm in diameter, with predominant lengths of 42,49 and 76 nm and a structure apparently similar to that found in alfalfa mosaic virus. Purified preparations of virus particles had A₂₆₀/A₂₈₀ of 1.7 ±0.05, contained one protein of M_rc. 22 000, and yielded three species of RNA with M_r (× 10^-6) of c. 0.7, 0.8 and 1.2. Although the virus particles were poorly immunogenic, an antiserum was produced and the virus was detected by enzyme-linked immunosorbent assay (DAS-ELISA) in leaf extracts at concentrations down to c. 6 ng/ml. Four other field isolates were also detected, including a strain which caused only mild systemic symptoms in C. quinoa instead of necrosis. The naturally infected cassava source plants were also infected with African cassava mosaic virus (ACMV) but when the new virus was cultured in Nicotiana benthamiana, either separately or together with ACMV, its concentration was the same. The new virus did not react with antisera to several plant viruses with small bacilliform or quasi-bacilliform particles, and alfalfa mosaic virus reacted only weakly and inconsistently with antiserum to the cassava virus. The new virus, for which the name cassava Ivorian bacilliform virus is proposed, is tentatively classified as the second member of the alfalfa mosaic virus group.     

Disease resistance characterisation of improved cassava genotypes to cassava mosaic disease at different ecozones

Twenty-two cassava genotypes and eight controls were evaluated in two cropping seasons for resistance to cassava mosaic disease (CMD) at the International Institute of Tropical Agriculture (IITA) fields, located at different ecozones of Nigeria. Disease incidence (DI) and index of symptom severity data were obtained monthly at each location and genotype. Symptomatic leaves were also collected during evaluation at each location, and virus was indexed by amplification in polymerase chain reaction. Significant differences within and across locations were observed in the reactions of cassava genotypes to CMD. DI across cassava genotypes was significantly (p = 0.05) highest in the Ibadan (22.6%), followed by Onne (19.3%). Generally, plants of clones 96/0860, 96/1439, 96/0160, 96/1089A, 96/1632, 96/1613, 96/1708, 96/0191, 96/0249 and 96/1565 had significantly lower values of DI in each location. African cassava mosaic virus in single infection was the predominant causal agent of CMD in IITA experimental fields under study.     

Allele exchange at the EPSPS locus confers glyphosate tolerance in cassava

Effective weed control can protect yields of cassava (Manihot esculenta) storage roots. Farmers could benefit from using herbicide with a tolerant cultivar. We applied traditional transgenesis and gene editing to generate robust glyphosate tolerance in cassava. By comparing promoters regulating expression of transformed 5‐enolpyruvylshikimate‐3‐phosphate synthase (EPSPS) genes with various paired amino acid substitutions, we found that strong constitutive expression is required to achieve glyphosate tolerance during in vitro selection and in whole cassava plants. Using strategies that exploit homologous recombination (HR) and nonhomologous end‐joining (NHEJ) DNA repair pathways, we precisely introduced the best‐performing allele into the cassava genome, simultaneously creating a promoter swap and dual amino acid substitutions at the endogenous EPSPS locus. Primary EPSPS‐edited plants were phenotypically normal, tolerant to high doses of glyphosate, with some free of detectable T‐DNA integrations. Our methods demonstrate an editing strategy for creating glyphosate tolerance in crop plants and demonstrate the potential of gene editing for further improvement of cassava.     

Occurrence of three distinct begomoviruses in cassava in Madagascar

The presence of East African cassava mosaic virus in association with cassava mosaic disease in Madagascar has previously been reported. We now describe virus isolates from mosaic‐affected Madagascan cassava with epitope profiles typical of African cassava mosaic virus, and an isolate with a nucleotide sequence similar to that of South African cassava mosaic virus. Thus, three distinct begomoviruses occur in cassava in Madagascar.     

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.