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.     

A geminivirus-induced gene silencing system for gene function validation in cassava

We have constructed an African cassava mosaic virus (ACMV) based gene-silencing vector as a reverse genetics tool for gene function analysis in cassava. The vector carrying a fragment from the Nicotiana tabacumsulfur gene (su), encoding one unit of the chloroplast enzyme magnesium chelatase, was used to induce the silencing of the cassava orthologous gene resulting in yellow–white spots characteristic of the inhibition of su expression. This result suggests that well developed sequence databases from model plants like Arabidopsis thaliana, Nicotiana benthamiana, N. tabacum, Lycopersicon esculentum and others could be used as a major source of information and sequences for functional genomics in cassava. Furthermore, a fragment of the cassava CYP79D2endogenous gene, sharing 89% homology with CYP79D1endogenous gene was inserted into the ACMV vector. The resultant vector was inducing the down regulation of the expression of these two genes which catalyze the first-dedicated step in the synthesis of linamarin, the major cyanogenic glycoside in cassava. At 21 days post-inoculation (dpi), a 76% reduction of linamarin content was observed in silenced leaves. Using transgenic plants expressing antisense RNA of CYP79D1and CYP79D2, Siritunga and Sayre (2003) obtained several lines with a reduction level varying from 60% to 94%. This result provides the first example of direct comparison of the efficiency of a virus-induced gene silencing (VIGS) system and the transgenic approach for suppression of a biosynthetic pathway. The ACMV VIGS system will certainly be a complement and in some cases an alternative to the transgenic approach, for gene discovery and gene function analysis in cassava.     

The use of African cassava mosaic virus as a vector system for plants

This paper describes the development of a gene-displacement vector based on DNA1, one of two single stranded circular genomic components of a bipartite geminivirus, African cassava mosaic virus (ACMV). The DNA1 molecules of ACMV were cloned as dimers into a plant transformation vector and the constructs have been integrated into tobacco protoplasts by PEG-mediated DNA transfer. In transgenic plants extrachromosomal copies of DNA1 monomers could be detected. Deletion of the coat protein-encoding gene in chimeric constructs resulted in free DNA1 copies of reduced size, and extrachromosomal recombinant molecules were detected after displacement of the coat protein-encoding region by foreign DNA fragments of comparable size. Due to the absence of the second component of ACMV, DNA2, the transgenic plants are free from viral infection symptoms which allows the establishment of healthy transformants that carry a recombinant construct in an extrachromosomal form.     

The cassava mosaic geminiviruses occurring in Uganda following the 1990s epidemic of severe cassava mosaic disease

The cassava mosaic geminiviruses (CMGs) isolated from cassava plants expressing mild and severe symptoms of cassava mosaic disease (CMD) in 2002 in Uganda were investigated using the polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) molecular techniques and DNA sequencing. Two previously described cassava mosaic geminiviruses: African cassava mosaic virus (ACMV) said East African cassava mosaic virus - Uganda variant (EACMV-UG2) were detected in Uganda. The RFLP technique distinguished two polymorphic variants of ACMV (ACMV-UG1 and ACMV-UG2) and three of EACMV-UG2 (EACMV-UG2[1], EACMV-UG2[2] and EACMV-UG2[3]). ACMV-UG1 produced the fragments predicted for the published sequences of ACMV-[KE]/UGMld/ UGSvr, while ACMV-UG2, which produced the RFLP fragments predicted for the West African ACMV isolates ACMV-[NG], ACMV-[CM], ACMV-[CM/DO2] and ACMV-[CI], was shown to be ACMV-UGMld/UGSvr after DNA sequencing. EACMV-UG2[1] produced the RFLP fragments predicted for the published sequences of EACMV-UG2/UG2Mld/UG2Svr. However, both EACMV-UG2[2] and EACMV-UG2[3], which produced East African cassava mosaic vzras-[Tanzania]-like polymorphic fragments with RFLP analysis, were confirmed to be isolates of EACMV-UG2 after DNA sequencing. Thus, this study emphasises the importance of DNA sequence analysis for the identification of CMG isolates. EACMV-UG2 was the predominant virus and occurred in all the surveyed regions. It was detected in 73% of the severely and 53% of the mildly diseased plants, while ACMV was less widespread and occurred most frequently in the mildly diseased plants (in 27% of these plants). Mixed infections of ACMV and EACMV-UG2 were detected in only 18% of the field samples. Unlike previously reported results the mixed infection occurred almost equally in plants exhibiting mild or severe disease symptoms (21% and 16%, respectively). The increasing frequency of mild forms of EACMV-UG2 together with the continued occurrence of severe forms in the field warrants further studies of virus-virus and virus-host interactions.     

Resistance to African cassava mosaic virus conferred by a mutant of the putative NTP-binding domain of the Rep gene (AC1) in Nicotiana benthamiana

We constructed a mutation in DNA A of African cassava mosaic virus (ACMV) to alter the putative NTP-binding site in the replication- associated protein gene (AC1). When transgenic Nicotiana benthamiana plants expressing the mutated AC1 gene were infected with ACMV, the plants exhibited tolerance to infection consisting in a delay in symptom appearance and/or the presence of mild symptoms. In addition, the resistant plants accumulated less viral DNA than non-transgenic plants. As judged by northern blot analysis and symptom development of segregating progeny from different lines, a high level of expression of the mutated AC1 gene is essential for the development of resistance. Issues related to the use of different versions of AC1 for the control of ACMV are discussed. This revised version was published online in June 2006 with corrections to the Cover Date.     

Engineering broad-spectrum resistance against RNA viruses in potato

RNA silencing technology has become the tool of choice for inducing resistance against viruses in plants. A significant discovery of this technology is that double-stranded RNA (dsRNA), which is diced into small interfering RNAs (siRNAs), is a potent trigger for RNA silencing. By exploiting this phenomenon in transgenic plants, it is possible to confer high level of virus resistance by specific targeting of cognate viral RNA. In order to maximize the efficiency and versatility of the vector-based siRNA approach, we have constructed a chimeric expression vector containing three partial gene sequences derived from the ORF2 gene of Potato virus X, Helper Component Protease gene of Potato virus Y and Coat protein gene of Potato leaf roll virus. Solanum tuberosum cv. Desiree and Kuroda were transformed with this chimeric gene cassette via Agrobacterium tumefaciens-mediated transformation and transgenic status was confirmed by PCR, Southern and double antibody sandwich ELISA detection. Due to simultaneous RNA silencing, as demonstrated by accumulation of specific siRNAs, the expression of partial triple-gene sequence cassette depicted 20% of the transgenic plants are immune against all three viruses. Thus, expression of a single transgene construct can effectively confer resistance to multiple viruses in transgenic plants.     

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.     

Accumulation of 24 nucleotide transgene‐derived siRNAs is associated with crinivirus immunity in transgenic plants

RNA silencing is a conserved antiviral defence mechanism that has been used to develop robust resistance against plant virus infections. Previous efforts have been made to develop RNA silencing‐mediated resistance to criniviruses, yet none have given immunity. In this study, transgenic Nicotiana benthamiana plants harbouring a hairpin construct of the Lettuce infectious yellows virus (LIYV) RNA‐dependent RNA polymerase (RdRp) sequence exhibited immunity to systemic LIYV infection. Deep sequencing analysis was performed to characterize virus‐derived small interfering RNAs (vsiRNAs) generated on systemic LIYV infection in non‐transgenic N. benthamiana plants as well as transgene‐derived siRNAs (t‐siRNAs) derived from the immune‐transgenic plants before and after LIYV inoculation. Interestingly, a similar sequence distribution pattern was obtained with t‐siRNAs and vsiRNAs mapped to the transgene region in both immune and susceptible plants, except for a significant increase in t‐siRNAs of 24 nucleotides in length, which was consistent with small RNA northern blot results that showed the abundance of t‐siRNAs of 21, 22 and 24 nucleotides in length. The accumulated 24‐nucleotide sequences have not yet been reported in transgenic plants partially resistant to criniviruses, and thus may indicate their correlation with crinivirus immunity. To further test this hypothesis, we developed transgenic melon (Cucumis melo) plants immune to systemic infection of another crinivirus, Cucurbit yellow stunting disorder virus (CYSDV). As predicted, the accumulation of 24‐nucleotide t‐siRNAs was detected in transgenic melon plants by northern blot. Together with our findings and previous studies on crinivirus resistance, we propose that the accumulation of 24‐nucleotide t‐siRNAs is associated with crinivirus immunity in transgenic plants.     

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.     

Virus content of leaves of cassava infected by African cassava mosaic virus

African cassava mosaic virus (ACMV) was detected in cassava leaves by ELISA. Some normal constituents of cassava leaves interfered with virus detection but leaf extracts of Nicotiana benthamiana did not. The symptom pattern was determined early in the growth of a leaf and subsequently changed little. ACMV was found only in the yellow or yellow green areas of the mosaic pattern. Virus content of the leaves increased with increasing symptom intensity, but decreased with leaf age and ACMV was not detected in mature leaves. Most whiteflies were found on young growing cassava leaves and the number decreased progressively with leaf age. This distribution will aid both the acquisition and inoculation of the virus.     

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.