Yellow Mottle Virus Research Articles

Target prediction of candidate miRNAs from Oryza sativa for silencing the RYMV genome

In order to maintain a consistent supply of rice globally, control of pathogens affecting crop production is a matter of due concern. Rice yellow mottle virus(RYMV) is known to cause a variety of symptoms which can result in reduced yield. Four ORFs can be identified in the genome of RYMV encoding for P1 (ORF1), Polyprotein (processed to produce VPg, protease, helicase, RdRp4) (ORF2), putative RdRp (ORF3) and capsid/coat protein (ORF4). This research was aimed at identifying genome encoded miRNAs of O. sativa that are targeted to the genome of Rice Yellow Mottle Virus (RYMV). A consensus of four miRNA target prediction algorithms (RNA22, miRanda, TargetFinder and psRNATarget) was computed, followed by calculation of free energies of miRNA-mRNA duplex formation. A phylogenetic tree was constructed to portray the evolutionary relationships between RYMV strains isolated to date. From the consensus of algorithms used, a total of seven O. sativa miRNAs were predicted and conservation of target site was finally evaluated. Predicted miRNAs can be further evaluated by experiments involving the testing of the success of in vitro gene silencing of RYMV genome; this can pave the way for development of RYMV resistant rice varieties in the future.

Complete Genome Sequences of Rice Yellow Mottle Virus Isolates from the Federal Democratic Republic of Ethiopia.

The full-length genomes of two isolates of Rice yellow mottle virus from Ethiopia were sequenced. A comparison with 28 sequences from East Africa showed that they clustered within a new strain named S4et, related to the S4mg and S4ug strains found in the Lake Victoria Basin and Madagascar, respectively.

NMR chemical shift backbone assignment of the viral protein P1 encoded by the African Rice Yellow Mottle Virus.

RNA silencing describes a pan-eukaryotic pathway of gene regulation where doubled stranded RNA are processed by the RNAse III enzyme Dicer or homologs. In particular, plants use it as a way to defend themselves against pathogen invasions. In turn, to evade the plant immune response, viruses have developed anti-RNA silencing mechanisms. They may indeed code for proteins called "viral suppressor of RNA silencing" which block the degrading of viral genomic or messenger RNA by the plant. The Rice Mottle Virus is an African virus of the sobemovirus family, which attacks the most productive rice varieties cultivated on this continent. It encodes P1, a cysteine-rich protein described as a potential RNA silencing suppressor. P1 is a 157 amino-acid long protein, characterized by a high propensity to aggregate concomitant with a limited stability with time in the conditions used in structural studies. To overcome this problem, shorter fragments were also studied. This strategy enabled the assignment of more than 90% backbone resonances of P1. This assignment should set the base of future NMR investigation of the protein structure and of its interactions with rice cellular partners.

Application of Eco-Engineering Approach for Management of Rice Yellow Mottle Virus (RYMV) in Lowland Rice Ecology

Application of Eco-Engineering Approach for Management of Rice Yellow Mottle Virus (RYMV) in Lowland Rice Ecology

Comparing patterns and scales of plant virus phylogeography: Rice yellow mottle virus in Madagascar and in continental Africa.

Rice yellow mottle virus (RYMV) in Madagascar Island provides an opportunity to study the spread of a plant virus disease after a relatively recent introduction in a large and isolated country with a heterogeneous host landscape ecology. Here, we take advantage of field survey data on the occurrence of RYMV disease throughout Madagascar dating back to the 1970s, and of virus genetic data from ninety-four isolates collected since 1989 in most regions of the country to reconstruct the epidemic history. We find that the Malagasy isolates belong to a unique recombinant strain that most likely entered Madagascar through a long-distance introduction from the most eastern part of mainland Africa. We infer the spread of RYMV as a continuous process using a Bayesian statistical framework. In order to calibrate the time scale in calendar time units in this analysis, we pool the information about the RYMV evolutionary rate from several geographical partitions. Whereas the field surveys and the phylogeographic reconstructions both point to a rapid southward invasion across hundreds of kilometers throughout Madagascar within three to four decades, they differ on the inferred origin location and time of the epidemic. The phylogeographic reconstructions suggest a lineage displacement and unveil a re-invasion of the northern regions that may have remained unnoticed otherwise. Despite ecological differences that could affect the transmission potential of RYMV in Madagascar and in mainland Africa, we estimate similar invasion and dispersal rates. We could not identify environmental factors that have a relevant impact on the lineage dispersal velocity of RYMV in Madagascar. This study highlights the value and complementarity of (historical) nongenetic and (more contemporaneous) genetic surveillance data for reconstructing the history of spread of plant viruses.

Survey of potential insect vectors of Rice Yellow Mottle Virus in the Southern and Central rice basin of Benin

Objectives : Insects are considered as the main vectors of Rice Yellow Mottle Virus (RYMV) in Africa. However, in Benin, little is known about the abundance and diversity of potential insect vectors of RYMV in rice fields to prevent and manage disease impact on rice production. Methodology and Results : The inventory of the potential insect vectors of this disease was carried out in the rice basin of the Southern and Central of Benin where three sites namely Africa Rice station, Koussin and Ouedeme, were prospected. The sweep net technique, visual observation and yellow plates trap were used to conduct the surveys. Eighty insect species belonging to 28 families and 8 orders were recorded at rice tillering, booting, heading and maturation stages. Variation of insect diversity was low among the sites. The shorthorned grasshopper Oxya hyla (Serville) , the ladybird beetle Chnootriba similis (Mulsant) , the rice white leafhopper Cofana spectra (Distant) and the stalk-eyed fly Diopsis thoracica (Westwood) were the most important species considering their relative abundance (10.62%, 5.19%, 7.99% and 7.01%, respectively) and frequency of occurrence (90%, 80%, 73.33% and 80%, respectively). These insects were mostly present at tillering and booting stages. Conclusion and application of results : Seventy-five (75 %) of the recorded species were not identified as RYMV vectors before. Special attention must be paid to the distribution and importance of these insects in the fields. Studies on their ability to transmit RYMV according ecological conditions should be done to know high-risk production areas and to prevent large epidemics of RYMV. Keywords : Rice-feeding insects, West Africa, virus transmission, relative abundance, occurrence, rice ecology

Effect of Rice yellow mottle virus, Sobemovirus on the Contents of N P K Ca and Mg in Leaves of Infected Rice

Effect of Rice yellow mottle virus, Sobemovirus on the Contents of N P K Ca and Mg in Leaves of Infected Rice

Resistance of selected Oryza glaberrima landraces and their intra-specific breeding lines to Beninese Rice yellow mottle virus isolates

Rice yellow mottle virus (RYMV) is a widespread and damaging pathogen, endemic to Africa and affecting rice in lowland, irrigated and upland ecologies. Yield losses of 10–100% have been recorded, depending on rice genotypes, time of infection, cropping system, vector abundance and isolate pathogenicity. Control measures for this disease are based mainly on cultural practices and the use of varietal resistance. Specifically, Oryza glaberrima, the cultivated African rice species, has provided several of the known resistance alleles/genes. In this study, 160 O. glaberrima landraces, 55 of their intra-specific progenies and two controls - Tog5681 (resistant) and IR64 (susceptible) - were screened against five RYMV isolates collected from Northern Benin. Disease severity was measured on plants at 21 and 42 days after inoculation. Two cultivars - IRGC104019 and IRGC96787 (Tog5644) - from Tanzania and Nigeria respectively - and 16 intra-specific lines were identified as highly resistant to all five isolates. The genotyping of IRGC104019 and IRGC96787 revealed that they share allele rymv1-3, identified in Tog5681 (the resistant control) and that confers resistance, bringing the number of O. glaberrima accessions known to date to harbor this allele to 11. The importance of this finding and the level of resistance displayed by these two accessions strengthen the hypothesis that the African rice collection is a potential RYMV resistance donor. It is, therefore, necessary to further screen it for valorizing its usefulness in breeding programs.

Response of 20 Rice Genotypes to the Rice yellow mottle virus (RYMV) under Natural Infection Conditions in the M'bé Valley of Côte d'Ivoire

One of the major constraints on rice production in Africa is the yellow mottle virus (RYMV) disease caused by Rice yellow mottle virus. In the context of the complex nature of this disease and the rapid development of its epidemics, only an integrated approach within a controlled ecological framework can lead to the development of an effective and sustainable control strategy. In order to search for varieties able to resist this virosis, a screening was carried out under natural infection conditions to assess the resistance capacity of 20 rice genotypes, including ten F1 hybrids and ten locally grown varieties. The study was carried out in Bouake using a split plot system with three replicates. NPK fertilizers (12 24 18) and urea (46% N) were applied at 150 and 100 kg/ha respectively. The incidence, AUSPC and progression rate of RYMV disease were evaluated in the different varieties tested. Serological analysis confirmed the presence of RYMV in the collected leaf samples. The results showed that Palawan (0.13), Wita 9 (0.11), AR051H (0.19) and AR034H (0.09) had the lowest disease progression rates compared to Kpate (2.3); Soungrouba (1.26); Marigbe (1.26); AR638H (1.56); Kouiklonle (0.88) and GT11 (0.89) in which the highest rates of disease progression were observed. Similarly, the incidence of RYMV recorded by stage of genotype development was lower in Palawan, Wita 9, AR051H and AR034H. The Palawan, Wita 9, AR051H and AR034H varieties can be deployed without great risk in central Cote d'Ivoire. However, an evaluation under semi-controlled conditions should be considered in order to confirm the behaviours of the different genotypes. These varieties could be exploited pending the large-scale deployment of improved, naturally resistant RYMV genotypes.

Role of QTL mapping to circumscribe various diseases in different crops with special emphasis on cotton.

Cotton not only provides the world’s best natural spinnable fibre but also its seed is a rich source oil and protein, which is best for food and livestock feed. A biotic and biotic stresses always a serious threat to cotton production world widely. There is a demand of such cultivars which could oppose these stresses with wide genetic variability. Molecular breeding along with marker technology opened new ways in crop improvement. Genome mapping which is the identification of genomic regions linked with different traits; using construction of linkage map and quantitative trait loci (QTL) analysis can be used to identify resistant sources with the use of marker assistant selection (MAS). Improvements in control of many biotic diseases like verticillium (V) and Fusarium Wilt (FW), Reniform and Root-knot Nematodes had been made using molecular breeding. Cotton leaf curl disease (CLCuD) is the most distressing diseases of cotton in Pakistan, north-western areas of India and some parts of Africa which could be improved using these biotechnological tools. In many agricultural crops viral diseases like tomato yellow leaf curl virus (TYLCV), tomato mosaic virus (ToMV), tomato spotted wilt virus (TSWV), rice black-streaked virus (RBSV), Maize Streak Virus (MSV), Maize dwarf mosaic virus (MDMV), SCMV (Sugarcane mosaic virus), WSMV (Wheat streak mosaic virus), MCDV (Maize chlorotic dwarf virus), MMV (Maize mosaic virus), MFSV (Maize fine streak virus), Rice Stripe Virus (RSV), Rice yellow mottle virus (RYMV), rice black-streaked dwarf virus (RBSDV) and Barley Yellow Dwarf Virus (BYDV) had been studied using molecular markers. This Review study provides explanation of molecular markers involved in crop improvement especially for disease resistance in cotton and other field crop which could carry out to find out CLCuD resistant sources in upland cotton.

English

Virus is the most constraint of rice production in West Africa. Genetic diversity of rice yellow mottle virus (RYMV) was assessed in two rice growing areas of Mali. Forty-three (43) infected rice leaf samples were collected from five locations within the Niger Office and Selingue Development Rural Office rice’s growing areas. The infected samples were confirmed by Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) using primers pair Prymv1 and Prymv2. A total of twenty-six RYMV isolates were obtained and classified into two genotypes A and B with Prymv1 and one genotype with Prymv2. Sequencing of the cDNA fragments with Prymv2 shared isolates into three distinct groups I, II and III. Most of the isolates were under Group I whereas isolates from the Selingue Development Rural Office area and Moussa-Were (Niger Office) area constituted respectively Groups II and III. This study provided baseline data for monitoring the genetic diversity of rice yellow mottle virus in the two rice-growing areas of Mali which could contribute to strategies development for the disease control.   Key words: Genetic diversity, reverse transcriptase polymerase chain reaction (RT-PCR), rice yellow mottle virus (RYMV), sequencing, Mali.

Croton golden mosaic virus: a new bipartite begomovirus isolated from Croton hirtus in Colombia.

A new begomovirus infecting Croton hirtus (Euphorbiaceae) from Colombia has been characterized. The complete DNA-A and DNA-B components were determined to be 2613 and 2551nt in length, respectively, showing the typical genome organization of bipartite New World begomoviruses. DNA-A showed the highest nucleotide sequence identity (81.2%) to sida yellow mottle virus (JN411687), a begomovirus isolated from Sida rhombifolia in Cuba. Based on the current ICTV species demarcation criterion for the genus Begomovirus, we report a new member of this genus infecting C. hirtus. We propose that it be named Croton golden mosaic virus (CroGMV), based on the symptoms observed in the weed. Phylogenetic analysis revealed that CroGMV segregates into a single clade and has some relationship with viruses from Central America and the Caribbean. CroGMV is the first Croton-infecting bipartite begomovirus reported in the world.

First report of canna yellow mottle virus in China

First report of canna yellow mottle virus in China

On the importance of negative controls in viral landscape phylogeography.

Phylogeographic reconstructions are becoming an established procedure to evaluate the factors that could impact virus spread. While a discrete phylogeographic approach can be used to test predictors of transition rates among discrete locations, alternative continuous phylogeographic reconstructions can also be exploited to investigate the impact of underlying environmental layers on the dispersal velocity of a virus. The two approaches are complementary tools for studying pathogens' spread, but in both cases, care must be taken to avoid misinterpretations. Here, we analyse rice yellow mottle virus (RYMV) sequence data from West and East Africa to illustrate how both approaches can be used to study the impact of environmental factors on the virus’ dispersal frequency and velocity. While it was previously reported that host connectivity was a major determinant of RYMV spread, we show that this was a false positive result due to the lack of appropriate negative controls. We also discuss and compare the phylodynamic tools currently available for investigating the impact of environmental factors on virus spread.

Evaluation of rice cultivars for resistance to rice yellow mottle virus

Rice yellow mottle virus (RYMV), which is only found in Africa, threatens rice farming on the continent. A local Oryza sativa cultivar collected from Burkina Faso (named BM24), was evaluated with that of well known highly resistant and tolerant cultivars. Firstly, three RYMV isolates were used to characterise the differential interaction within the cultivars. Secondly, disease kinetics of symptom expression and virus titer on leaves at 21 days after inoculation were assessed using the BF1 isolate. Thirdly, the allelic profile of O. sativa varieties using SSR marker RM101 located on chromosome 12 was also assessed. IR64 showed susceptibility to all isolates; while Tog5681 was resistant to all isolates. Ng122 overcame the resistance of Gigante, with mild leaf symptoms at 42 dpi. Azucena and BM24 had, therefore, different resistance level regarding the three isolates (Ng117b, Ng122 and Ng144). When infected with the isolate, BF1, BM24 and Azucena exhibited same resistance patterns in early growth stages with delayed of symptoms appearance, but BM24 outperformed Azucena at later stages. The virus content in the two accessions, at 14 days post inoculation, was statistically different with BM24, showing less virus compared to Azucena. However, the two accessions depicted an identical allelic profile at RM101 locus. Key words: Azucena, Burkina Faso, local variety, Oryza sativa

Full-Length Genome Sequences of Recombinant and Nonrecombinant Sympatric Strains of Rice yellow mottle virus from Western Kenya.

ABSTRACTFive isolates of Rice yellow mottle virus from western Kenya were fully sequenced. One isolate of strain S4lv had been collected in 1966. Two isolates belonged to the emerging strain S4ug recently described in Uganda. Two isolates collected in 2012 are putative recombinants between the S4lv and S4ug strains.

Pathogenicity of rice yellow mottle virus and screening of rice accessions from the Central African Republic

BackgroundRice yellow mottle virus (RYMV) of the genus Sobemovirus is the most important viral pathogen of rice causing more damage to rice crop in Sub Saharan Africa. The aim of this study was to conduct pathogenic characterization of RYMV isolates from the Central African Republic (CAR) and to screen commonly cultivated rice accessions in the country for resistance/tolerance to the virus.MethodsThe pathogenicity of RYMV isolates was studied by mechanical inoculation with comparison to differential rice lines highly resistant to RYMV available at the Institute of Environment and Agricultural Research (INERA) in Burkina Faso.To screen commonly cultivated rice accessions in CAR, characterized RYMV isolates from the country were used as inoculum sources. Resistant breaking (RB) isolates were used to prepare RB-inoculum, whereas non-resistant breaking isolates (nRB) were used for nRB-inoculum.ResultsOverall 102 isolates used in this study, 29.4% were able to overcome the high resistance genes in the rice cultivars Gigante and Tog7291. All isolates were distributed within three distinct pathogenic profiles. The first profile constituted of 6.9% of the isolates was able to break down the resistance in rice cultivar Gigante only. The second pathogenic profile made of 19.6% of isolates was able to infect Tog7291 only. The third profile, 2.9% of isolates overcame simultaneously resistance genes in both rice cultivars Gigante and Tog7291. Out of isolates able to break down the resistance gene in cultivar Gigante, a single isolate was found to be non-infectious to the susceptible control IR64.Data from screening showed that all accessions were susceptible to RYMV, although IRAT213 was found to be partially resistant to both nRB-inoculum and RB-inoculum.ConclusionThe present study can be considered as the first in the Central African Republic, it gives a caution on the high risk of RYMV damage to rice production in the country. Beside, skills of pathogenic profiles of RYMV isolates will contribute to better disease management.

Molecular Variability and Genetic Structure of IYMV in Burkina Faso

Imperata yellow mottle virus (IYMV, Sobemovirus) was first described in 2008 in the south-western region of Burkina Faso (West Africa). The genetic diversity of IYMV was not documented up to day. In this study, the variability of CP of IYMV was evaluated through the molecular characterization of 38 isolates collected in the western part of Burkina Faso. Comparison of sequences of these new isolates and one IYMV sequence available in GenBank revealed that the average nucleotide diversity was low. The ratio of non-synonymous over synonymous nucleotide substitutions per site was low, indicating a CP diversification under strong purifying selection. Despite of the low nucleotide diversity, phylogenetic analyses revealed segregation of IYMV isolates into six major clades. There was no correlation of phylogenetic grouping of isolates based on geographical location. This is the first study of the genetic diversity of IYMV.

Isolation and Characterization of Two Distinct Types of Unmodified Spherical Plant Sobemovirus-Like Particles for Diagnostic and Technical Uses.

Plant virus-like particles (VLPs) structurally resemble their progenitor viruses, but are noninfectious due to absence of viral nucleic acids. Since the 1980s, VLPs have been actively studied with the aim of constructing different nanomaterials, including immunologically active carriers for peptides and whole proteins and proteinaceous shells for the packaging of different ligands.The technological developments using VLPs require large amounts of purified particles. Here, we describe the laboratory process for isolation and purification of two unmodified plant VLPs, derived from two sobemoviruses, cocksfoot mottle virus (CfMV) and rice yellow mottle virus (RYMV), which is based on cultivation of recombinant Escherichia coli cells, VLP precipitation from bacterial extracts and ultracentrifugation. The suggested purification scheme allows the production of 4-45 mg of purified sobemoviral VLPs from a 1l bacterial culture, depending on the required purity level. Additionally, we provide short protocols for VLP characterization using SDS-PAGE, agarose gel electrophoresis, ultraviolet and mass spectrometry, dynamic light scattering, and electron microscopy.

Protocol for RYMV Inoculation and Resistance Evaluation in Rice Seedlings.

Rice yellow mottle virus (RYMV), a mechanically transmitted virus that causes serious damage to cultivated rice plants, is endemic to Africa. Varietal selection for resistance is considered to be the most effective and sustainable management strategy. Standardized resistance evaluation procedures are required for the identification and characterization of resistance sources. This paper describes a protocol for mechanical inoculation of rice seedlings with RYMV and two methods of resistance evaluation - one based on a symptom severity index and the other on virus detection through double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA).