Cereal and grass viruses
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Cereal and grass viruses
News about cereal and grass infecting viruses
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Genome Sequences of Poaceae-Associated Gemycircularviruses from the Pacific Ocean Island of Tonga

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Frontiers | Interplays between Soil-Borne Plant Viruses and RNA Silencing-Mediated Antiviral Defense in Roots | Virology

Frontiers | Interplays between Soil-Borne Plant Viruses and RNA Silencing-Mediated Antiviral Defense in Roots | Virology | Cereal and grass viruses | Scoop.it
Although the majority of plant viruses are transmitted by arthropod vectors and invade the host plants through the aerial parts, there is a considerable number of plant viruses that infect roots via soil-inhabiting vectors such as plasmodiophorids, chytrids, and nematodes. These soil-borne viruses belong to diverse families, and many of them cause serious diseases in major crop plants. Thus, roots are important organs for the life cycle of many viruses. Compared to shoots, roots have a distinct metabolism and particular physiological characteristics due to the differences in development, cell composition, gene expression patterns, and surrounding environmental conditions. RNA silencing is an important innate defense mechanism to combat virus infection in plants, but the specific information on the activities and molecular mechanism of RNA silencing-mediated viral defense in root tissue is still limited. In this review, we summarize and discuss the current knowledge regarding RNA silencing aspects of the interactions between soil-borne viruses and host plants. Overall, research evidence suggests that soil-borne viruses have evolved to adapt to the distinct mechanism of antiviral RNA silencing in roots.
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First Report of Barley virus G in Foxtail Millet (Setaria italica) in Korea

Abstract
Foxtail millet (Setaria italica) is an important cereal grain crop and has been used as a functional food for promoting human health in Korea. Until now, only Rice black-streaked dwarf virus (RBSDV) and Rice stripe virus (RSV) have been reported infecting S. italica in Korea (Choi et al. 1989; Yoon et al. 2014). To find unreported viral disease of S. italica, a nationwide virus survey in foxtail millet was conducted from 2015 to 2016. A total of 133 S. italica leaf samples showing necrotic spots, streaking, and yellowing stripe symptoms were collected and stored for future virus testing. To identify viruses associated with the symptoms, all collected symptomatic leaves were combined into one sample and total RNA was extracted from the pooled sample with an Easy-Spin total RNA extraction kit (iNtRON Biotechnology, Seoul, Korea). Next-generation sequencing (NGS) was performed using an Illumina HiSeq2500 sequencer as described previously (Lim et al. 2015) and the whole NGS procedure was performed by Theragen Etex Bio Institute (Suwon, Korea). Among the analyzed contigs, 129 viral contigs [123 contigs matching RSV and 6 contigs matching Barley virus G (BVG)] were obtained in the range of 110 bp to 9216 bp. The NGS result was confirmed by reverse transcription-polymerase chain reaction (RT-PCR) with primers encompassing the coat protein (CP) gene of BVG (Park et al. 2016). RT-PCR product (988 bp) from 10 BVG-positive samples was cloned and sequenced. Nucleotide blast search revealed that the BVG CP gene has 99% identity with BVG isolate Uiseong and Gimje (GenBank Accession Nos. LC159487 and KT962089). The sequence of the CP gene was deposited in GenBank under accession number LC159486 (BVG Jeju isolate). BVG is a proposed new species in the genus Polerovirus that was recently described in proso millet (Panicum miliaceum L.) and barley (Hordeum vulgare L.) from Korea (Park et al. 2016; Zhao et al. 2016). In the survey, 39 samples of the 133 collected samples were positive for BVG. Of the 39 BVG-positive samples, 10 samples were single infection with BVG and 29 samples were mixed infection with RSV and another unreported virus. The most common symptoms of BVG-positive samples were yellowing stripe and mosaic, but single infection with BVG or RSV and mixed infection with both BVG and RSV showed the similar symptoms, thus specific symptoms of BVG were unclear at the moment. Further research will be required to determine the natural host range, prevalence, and pathological properties of BVG. To our knowledge, this is the first report of BVG in S. italica in Korea and the world.
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Efficiency of phytovirological monitoring of cereal crop breeding in Primorsky krai

Efficiency of phytovirological monitoring of cereal crop breeding in Primorsky krai | Cereal and grass viruses | Scoop.it
Data on the extent and dynamics of the viral diseases affecting cereal crops in breeding nurseries have been obtained as a result of the phytovirological monitoring. The deterious pathogens affecting
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MAIZE CHLOROTIC MOTTLE VIRUS – EUROPE: FIRST REPORT (SPAIN)

MAIZE CHLOROTIC MOTTLE VIRUS – EUROPE: FIRST REPORT (SPAIN) | Cereal and grass viruses | Scoop.it
A ProMED-mail post ProMED-mail is a program of the International Society for Infectious Diseases Date: November 2016 Source: Plant Disease [edited] [ref: MA Achon, et al (2016). First report of _Maize chlorotic mottle virus_ on a perennial host, _Sorghum halepense_, and maize in Spain. Plant Disease 100, posted online; DOI: 10.1094/PDIS-09-16-1261-PDN] ---------------------------------------------------------------------…
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The speed of tubule formation of two fijiviruses corresponds with their dissemination efficiency in their insect vectors

The speed of tubule formation of two fijiviruses corresponds with their dissemination efficiency in their insect vectors | Cereal and grass viruses | Scoop.it
Rice black-streaked dwarf virus (RBSDV) and Southern rice black-streaked dwarf virus (SRBSDV) are two closely related fijiviruses transmitted by the small brown planthopper (SBPH) and white-backed planthopper (WBPH), respectively. SRBSDV has a latent period 4 days shorter than that of RBSDV, implying a more efficient spread in insect vector. Currently, the mechanisms underlying this higher efficiency are poorly understood. However, our recent studies have implicated a role of virus induced tubular structures in the dissemination of fijiiruses within their insect vectors. Immunofluorescence labeling was performed to visualize and compare the dynamics of P7-1 tubule formation of the RBSDV and SRBSDV in their own vector insects and nonhost Spodoptera frugiperda (Sf9) cells. Tubule formation of SRBSDV P7-1 was faster than that of RBSDV P7-1. For RBSDV, P7-1 formed tubules were observed at 3-days post-first access to diseased plants (padp) in SBPH. For SRBSDV, these structures were detected as early as 1 day padp in WBPH. Importantly, similar phenomena were observed when P7-1 proteins from the two viruses were expressed alone in Sf9 cells. Our research revealed a relationship between the speed of P7-1 tubule formation and virus dissemination efficiency and also supports a role of such tubular structures in the spread of reoviruses within insect vectors.
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FISA - Viruses in grasses as potential threat for cereal crops

FISA bündelt alle Informationen zur Forschung in den Agrarwissenschaften und Ernährungswissenschaften in Deutschland, insbesondere zur Forschungsförderung.


Description: Grasses can be infected by a wide range of different viruses but so far there is very limited knowledge on the importance of infected grasses as infection reservoirs for cereal crops. Besides the direct effect on the yield of grasslands (forage grasses, meadows and pastures) the corresponding viruses can potentially threaten the different cereal species grown in Germany, too. Aim of the project is to analyze the occurrence and the distribution of the spectrum of grasses infecting viruses. Moreover, biological, serological and genetic characterization of viruses that were recently isolated from tall oatgrass and brome within boundary ridges will be performed. If not already available, specific diagnostic methods have to be developed for the newly discovered virus species. Most of the viruses occurring in fodder or wild grasses (s. Table 1 in Rabenstein, 2014) are able to infect experimentally also cereals. Except for the insect transmitted viruses of the Barley yellow dwarf virus/Wheat dwarf complex, these other viruses seem so far hardly to play a role for cultivation of cereals in Germany. This includes, inter alia, the Brome mosaic virus (BMV), which is occasionally observed on various fodder and wild grasses. About the occurrence of BMV in wheat in Germany has been hitherto reported only once (Rabenstein & Proeseler 1982). All the more surprising has been that this virus appeared in 2013 not only in field plots of several breeding companies in Germany and Austria, but also in DH lines of wheat breeding material grown in the greenhouse of one company, so that all the material had to be destroyed. Unclear is the economic importance of a new satellite virus of BMV that was isolated from winter wheat samples from a German breeding station from Russia (Rabenstein et al. 2013). Further research seems to be required in this connection. A number of other isometric viruses that in part not yet been finally characterized, were isolated from forage grasses (Lolium species L. perenne, L. multiflorum, L. westerwoldicum and Datylis glomerata) and from wild grass grow on field edges. This is firstly the Ryegrass mottle virus (genus Sobemovirus), which could be isolated from both ryegrass and cocksfoot. The virus seems to be potentially especially harmful for winter barley since all varieties were highly susceptible and the inoculated plants died completely about 28 dpi. Further viruses with isometric particle morphology of the genus Sobemovirus (Cocksfoot mottle virus, Cynosurus mottle virus, CyMoV) or Panicovirus (Cocksfoot mild mosaic virus, Brome strem leaf mottle virus, and Phleum mottle virus) caused after inoculation on wheat and barley clearly visible symptoms, but were not lethal. All virus isolates with spherical particle structure found in tall oatgrass (Arrhenatherum elatius) reacted with two antisera to CyMoV, but differed in their host range from two CyMoV-isolates from crested dog’s tail (Cynosurus cristatus). While the both CyMoV-isolates CV-123 and CV-104 caused onto the oat variety 'Jumbo' only mild symptoms, caused all Arrhenatherum-isolates a dieback of the inoculated oat plants. All antisera against the mentioned viruses from the JKI collection were checked in DAS-ELISA. In addition, further antisera were produced against new spherical viruses from grasses and added to the serum bank of JKI. Viruses with flexible, filamentous morphology of the grasses genera Dactylis, Festuca and Arrhenatherum were less aggressive towards cereals. Significant symptoms were only visible on Avena-species (Avena barbata, A. fatua, A. sativa), while in winter wheat and winter barley no or latent infections occurred. From cocksfoot (D. glomerata, two samples from Germany, one sample from Austria) and from giant fescue (Festuca gigantea, originating from the Harz region), two new virus species could be isolated, which both belonging to different genera within the family Potyviridae. The complete RNA sequence was determined of the virus isolated from orchard grass in Germany. This virus, for which the designation 'cocksfoot streak mosaic virus' is proposed, can be assigned to the genus Tritimovirus. Likewise, the complete sequence of the virus from giant fescue was determined and assigned to the new genus Poacevirus. Tall oatgrass samples from field margins contained more different flexible viruses that could also be isolated, propagated and purified. Against all virus isolates antisera have been produced in rabbits and then added to the antisera collection of the JKI. Previous results suggest that the filamentous viruses isolated from Arrhenatherum represent two different (new) potyviruses and a further unknown virus that does not belong to this family, because it does not induce characteristic pinwheel inclusion bodies.

Executive Institute: Institute for Epidemiology and Pathogen Diagnostics (JKI-EP) Details of Institute for Epidemiology and Pathogen Diagnostics

Parent institution: Federal Research Centre for Cultivated Plants – Julius Kühn-Institut (JKI) Details of (JKI) (Saxony-Anhalt)


Contract period: 01. 01. 2014 - 31. 12. 2015


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Truncated yet functional viral protein produced via RNA polymerase slippage implies underestimated coding capacity of RNA viruses

Truncated yet functional viral protein produced via RNA polymerase slippage implies underestimated coding capacity of RNA viruses | Cereal and grass viruses | Scoop.it

Abstract


RNA viruses use various strategies to condense their genetic information into small genomes. Potyviruses not only use the polyprotein strategy, but also embed an open reading frame, pipo, in the P3 cistron in the –1 reading frame. PIPO is expressed as a fusion protein with the N-terminal half of P3 (P3N-PIPO) via transcriptional slippage of viral RNA-dependent RNA polymerase (RdRp). We herein show that clover yellow vein virus (ClYVV) produces a previously unidentified factor, P3N-ALT, in the +1 reading frame via transcriptional slippage at a conserved G1–2A6–7 motif, as is the case for P3N-PIPO. The translation of P3N-ALT terminates soon, and it is considered to be a C-terminal truncated form of P3. In planta experiments indicate that P3N-ALT functions in cell-to-cell movement along with P3N-PIPO. Hence, all three reading frames are used to produce functional proteins. Deep sequencing of ClYVV RNA from infected plants endorses the slippage by viral RdRp. Our findings unveil a virus strategy that optimizes the coding capacity.

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Identification and molecular characterization of a novel sugarcane streak mastrevirus and an isolate of the A-strain of maize streak virus from sugarcane in Nigeria

Identification and molecular characterization of a novel sugarcane streak mastrevirus and an isolate of the A-strain of maize streak virus from sugarcane in Nigeria | Cereal and grass viruses | Scoop.it

Abstract


Sugarcane and maize plants showing symptoms typical of those described for the so-called “African streak viruses” (AfSVs) were encountered during field surveys conducted from February to July 2015 to document viruses infecting both crops across the northern Guinea savannah region of Nigeria. As part of this study, two categories of complete mastrevirus-like genome sequences were obtained from nine samples (maize = 2; sugarcane = 7). In pairwise comparisons, the full-length genomes of the first sequence category (2,687 nt each; maize = 2; sugarcane = 2) shared 96 to 99% identity with global isolates of the A-strain of maize streak virus (MSV-A), indicating that sugarcane may also serve as a reservoir host to MSV-A. Analysis of the complete genomes belonging to the second sequence category (2,757 nt each; sugarcane = 5) showed that they shared 42 to 67% identity with their closest AfSV relatives, thus indicating that they represent sequences of a novel mastrevirus. Both sequence categories shared 61-62% sequence identity with each other. Further analysis revealed that the novel sugarcane-infecting virus, tentatively named as sugarcane chlorotic streak virus (SCSV), arose from a putative interspecific recombination event involving two grass-infecting mastreviruses, eragrostis streak virus and urochloa streak virus, as putative parental sequences. The results of this study add to the repertoire of diverse AfSVs present in cereal and sugarcane mixed cropping landscapes in the northern Guinea savannah region of Nigeria, with implications for disease epidemiology.

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Colorimetric detection of Maize chlorotic mottle virus by reverse transcription loop-mediated isothermal amplification (RT-LAMP) with hydroxynapthol blue dye - RSC Advances (RSC Publishing)

Colorimetric detection of Maize chlorotic mottle virus by reverse transcription loop-mediated isothermal amplification (RT-LAMP) with hydroxynapthol blue dye - RSC Advances (RSC Publishing) | Cereal and grass viruses | Scoop.it

Maize chlorotic mottle virus causes corn lethal necrosis disease, and can be transmitted via infected maize seeds. It remains a challenge to detect this virus to prevent its introduction, infection and wide transmission in fields. For this purpose, a colorimetric assay for the detection of Maize chlorotic mottle virus was developed, which utilises RT-LAMP and hydroxynapthol blue dye (HNB). The reaction was performed for amplification in one step in a single tube at the optimum conditions (64 °C for 60 min, 150 μM HNB and 2 mM MgSO4). Samples infected with MCMV developed a characteristic sky blue color after the reaction but those uninfected with MCMV or infected with other plant pathogenic viruses did not. The results of the HNB staining method were reconfirmed through gel electrophoresis of the RT-LAMP products. The sensitivity of this assay was 4.8 pg μl−1 of RNA of Maize chlorotic mottle virus per reaction, which was approximately 10-fold higher sensitivity over a conventional RT-PCR test. The results indicate that this assay is highly species-specific, simple, low-cost, and visual for easy detection of Maize chlorotic mottle virus in plant tissues. Therefore, colorimetric detection of Maize chlorotic mottle virus is a potentially useful tool for middle or small-scale corporations and entry-exit inspection and quarantine bureaus to detect maize seeds or plant tissues infected with Maize chlorotic mottle virus. Graphical abstract: Colorimetric detection of Maize chlorotic mottle virus by reverse transcription loop-mediated isothermal amplification (RT-LAMP) with hydroxynapthol blue dye



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Virus Disease Resistance In Wheat -

Virus Disease Resistance In Wheat - | Cereal and grass viruses | Scoop.it
K-State plant geneticist Harold Trick and USDA plant pathologist John Fellers report on a major advance in developing virus disease resistance in wheat, using genetic engineering to build a durable defense in wheat varieties against a host of costly diseases, including wheat streak mosaic, barley yellow dwarf and soil borne mosaic…and even though genetically-engineered wheat …
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Wheat Curl Mite Resistance in Hard Winter Wheat in the US Great Plains

Wheat Curl Mite Resistance in Hard Winter Wheat in the US Great Plains | Cereal and grass viruses | Scoop.it
Abstract

Viral diseases transmitted by wheat curl mite (WCM, Aceria tosichella Keifer) have been a persistent concern to farmers and researchers for at least six decades. Yield losses caused by mite–virus complexes up to 100% at the field level have been reported in several states of the Great Plains. This study was conducted to evaluate the level of resistance of hard winter wheat (Triticum aestivum L.) germplasm lines and cultivars to WCM. Four sets of wheat lines from 2014 trials were screened, including 40 lines from the Northern Regional Performance Nursery, 40 lines from the Southern Regional Performance Nursery, 40 Texas elite wheat lines, and 52 cultivars and elite breeding lines. Two different mite collections, Texas WCM collection 1 (TWCMC1) and Texas WCM collection 2 (TWCMC2), were used to screen wheat lines. All cultivars and lines were infested with WCM at the two-leaf stage and scored on the first and second week after the second infestation. A total of 43 wheat lines and cultivars showed resistance to TWCMC1, but only 18 of them consistently exhibited resistance to TWCMC2, which is virulent to wheat-rye translocation 1AL.1RS. All the lines having the ‘Amigo’ 1AL.1RS translocation (Cmc3) across the four tests showed resistance to TWCMC1 but not to TWCMC2. Among the 22 lines with ‘TAM 112’ in their pedigree, 19 lines were resistant to TWCMC1, but only a subset of 12 showed resistance to TWCMC2. TWCMC2 and mite collections from Kansas and Nebraska were differentiated based on the high-resolution melting curves and sequence analysis of mite DNA. Results from this study will help wheat breeders and geneticists to select WCM-resistant parental lines for their breeding programs.
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Survey of Barley yellow dwarf virus incidence in winter cereal crops, and assessment of wheat and barley resistance to the virus

Survey of Barley yellow dwarf virus incidence in winter cereal crops, and assessment of wheat and barley resistance to the virus | Cereal and grass viruses | Scoop.it
Abstract. A survey of Barley yellow dwarf virus (BYDV) incidence in cereal crops in the Czech Republic over 4 years showed, on average, 13.3% BYDV-positive, randomly tested wheat and barley samples. The cultivated wheat and barley cultivars had different levels of susceptibility to BYDV infection. Field trials were performed with different barley and wheat breeding lines and cultivars, and resistance traits were evaluated after arti fi cial inculcation by the viruliferous aphid vector Rhopalosiphum padi L. with BYDV-PAV. Our results showed high variability of visual symptom score (VSS) and reduction ingrain weightper spike (GWS-R) in trials withinthe testedlines andcultivars. The barley line(WBON 96-123)and cultivars (Wysor, Travira) that contained RYd2 differed signi fi cantly from other cultivars in VSS. Line WBON 96-123 and cvv. Wysor and Yatzi showed the lowest GWS-R. Wheat line PSR 3628 and cvv. Altigo, Elan, Sparta, Aladin and Hewit showed signi fi cant difference from other cultivars in VSS. PSR 3628, Sparta, and Elan showed the lowest GWS-R. Similar results were obtained from BYDV titre analysis by RT-qPCR corresponding to the VSS and GWS-R traits. A low virus titre corresponded to low VSS and GWS-R. Hence, our results suggest that laborious and time-consuming GWS-R analysis could be replaced in some cases by qPCR-based BYDV titre analysis and, together with VSS evaluation, could enhance the ef fi ciency of resistance assessment.
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Protect this house: cytosolic sensing of viruses

Protect this house: cytosolic sensing of viruses | Cereal and grass viruses | Scoop.it
The ability to recognize invading viral pathogens and to distinguish their components from those of the host cell is critical to initiate the innate immune response. The efficiency of this detection is an important factor in determining the susceptibility of the cell to viral infection. Innate sensing of viruses is, therefore, an indispensable step in the line of defense for cells and organisms. Recent discoveries have uncovered novel sensors of viral components and hallmarks of infection, as well as mechanisms by which cells discriminate between self and non-self. This review highlights the mechanisms used by cells to detect viral pathogens in the cytosol, and recent advances in the field of cytosolic sensing of viruses.


Via Ed Rybicki
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Genome-wide association mapping in winter barley for grain yield and culm cell wall polymer content using the high-throughput CoMPP technique

Genome-wide association mapping in winter barley for grain yield and culm cell wall polymer content using the high-throughput CoMPP technique | Cereal and grass viruses | Scoop.it
A collection of 112 winter barley varieties (Hordeum vulgare L.) was grown in the field for two years (2008/09 and 2009/10) in northern Italy and grain and straw yields recorded. In the first year of the trial, a severe attack of barley yellow mosaic virus (BaYMV) strongly influenced final performances with an average reduction of ~ 50% for grain and straw harvested in comparison to the second year. The genetic determination (GD) for grain yield was 0.49 and 0.70, for the two years respectively, and for straw yield GD was low in 2009 (0.09) and higher in 2010 (0.29). Cell wall polymers in culms were quantified by means of the monoclonal antibodies LM6, LM11, JIM13 and BS-400-3 and the carbohydrate-binding module CBM3a using the high-throughput CoMPP technique. Of these, LM6, which detects arabinan components, showed a relatively high GD in both years and a significantly negative correlation with grain yield (GYLD). Overall, heritability (H2) was calculated for GYLD, LM6 and JIM and resulted to be 0.42, 0.32 and 0.20, respectively. A total of 4,976 SNPs from the 9K iSelect array were used in the study for the analysis of population structure, linkage disequilibrium (LD) and genome-wide association study (GWAS). Marker-trait associations (MTA) were analyzed for grain yield and cell wall determination by LM6 and JIM13 as these were the traits showing significant correlations between the years. A single QTL for GYLD containing three MTAs was found on chromosome 3H located close to the Hv-eIF4E gene, which is known to regulate resistance to BaYMV. Subsequently the QTL was shown to be tightly linked to rym4, a locus for resistance to the virus. GWAs on arabinans quantified by LM6 resulted in the identification of major QTLs closely located on 3H and hypotheses regarding putative candidate genes were formulated through the study of gene expression levels based on bioinformatics tools.
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Geographical distribution and first molecular detection of an Emaravirus, High Plains wheat mosaic virus, in Argentina

Geographical distribution and first molecular detection of an Emaravirus, High Plains wheat mosaic virus, in Argentina | Cereal and grass viruses | Scoop.it

Abstract

High Plains wheat mosaic virus (HPWMoV) has recently been assigned to genus Emaravirus and is the causal agent of High Plains disease. In this work the geographical distribution and first molecular detection of HPWMoV in Argentina are reported. The virus was detected in six provinces and nine hosts, including wheat, corn, oat and barley, as well as weeds, which play an important role in the epidemiology of this disease. Molecular and phylogenetic analyses of a portion of RNA3 nucleoprotein gene sequence showed that five HPWMoV isolates from different wheat growing regions of Argentina were identical, and suggest a single introduction of HPWMoV to this country, possibly through corn seeds. To the best of our knowledge, this is the first molecular detection of HPWMoV in South America. These results highlight the importance of certification of viruses-free cereal seeds and strict controls for material transfer between different countries to prevent the entry not only of new pathogens but also of new variants or strain at sites where the pest has already been detected.


Keywords High Plains virus (HPV)Molecular and phylogenetic analysesCereals

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Characterization of ORF0 and ORF1 and their Roles in Recombination and Replication of Sugarcane yellow leaf virus

Characterization of ORF0 and ORF1 and their Roles in Recombination and Replication of Sugarcane yellow leaf virus | Cereal and grass viruses | Scoop.it

Abstract

Background: Two open reading frames (ORF0 and ORF1) of Sugarcane yellow leaf virus (SCYLV) genome which play an important role in virus replication and accumulation in plants have been characterized.

Materials and Methods: The RT-PCR and qRT-PCR have been used to evaluate the degree of infection with SCYLV using different genome locations (ORF0 and ORF1). Possible recombination events in two ORFs were identified using TOPALi (v2.5), RECCO and RDP software’s.

Results: Transcript levels of two genes varied among infected plants but overall expression of ORF1 was higher than ORF0. Cultivar H73-6110 (susceptible) yielded the highest transcript levels of ORF1 whereas cultivar H78-4153 (resistant) exhibited the lowest levels. No significant differences were found between the sugarcane cultivars for the ORF0 transcripts in mature leaves and seedling tissues. Amino acid sequence similarity of ORF0 and ORF1 varied among SCYLV isolates and ranged from 69-99 and 73-99%, respectively. Possible recombination events located in the two ORFs were identified using TOPALi (v2.5), RECCO and RDP software’s.

Conclusion: The results showed strong presence of recombination in aligned sequences of ORF0 and ORF1 when TOPALi and RECCO programs were used.

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The Triticum Mosaic Virus 5’ Leader Binds to Both eIF4G and eIFiso4G for Translation

The Triticum Mosaic Virus 5’ Leader Binds to Both eIF4G and eIFiso4G for Translation | Cereal and grass viruses | Scoop.it
We recently identified a remarkably strong (739 nt-long) IRES-like element in the 5’ untranslated region (UTR) of Triticum mosaic virus (TriMV, Potyviridae). Here, we define the components of the cap-binding translation initiation complex that are required for TriMV translation. Using bio-layer interferometry and affinity capture of the native translation apparatus, we reveal that the viral translation element has a ten-fold greater affinity for the large subunit eIF4G/eIFiso4G than to the cap binding protein eIF4E/eIFiso4E. This data supports a translation mechanism that is largely dependent on eIF4G and its isoform. The binding of both scaffold isoforms requires an eight base-pair-long hairpin structure located 270 nucleotides upstream of the translation initiation site, which we have previously shown to be crucial for IRES activity. Despite a weak binding affinity to the mRNA, eIFiso4G alone or in combination with eIFiso4E supports TriMV translation in a cap-binding factor-depleted wheat germ extract. Notably, TriMV 5’ UTR-mediated translation is dependent upon eIF4A helicase activity, as the addition of the eIF4A inhibitor hippuristanol inhibits 5’ UTR-mediated translation. This inhibition is reversible with the addition of recombinant wheat eIF4A. These results and previous observations demonstrate a key role of eIF4G and eIF4A in this unique mechanism of cap-independent-translation. This work provides new insights into the lesser studied translation mechanisms of plant virus-mediated internal translation initiation.
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Chapter Three - Future Scenarios for Plant Virus Pathogens as Climate Change Progresses

Abstract

Knowledge of how climate change is likely to influence future virus disease epidemics in cultivated plants and natural vegetation is of great importance to both global food security and natural ecosystems. However, obtaining such knowledge is hampered by the complex effects of climate alterations on the behavior of diverse types of vectors and the ease by which previously unknown viruses can emerge. A review written in 2011 provided a comprehensive analysis of available data on the effects of climate change on virus disease epidemics worldwide. This review summarizes its findings and those of two earlier climate change reviews and focuses on describing research published on the subject since 2011. It describes the likely effects of the full range of direct and indirect climate change parameters on hosts, viruses and vectors, virus control prospects, and the many information gaps and deficiencies. Recently, there has been encouraging progress in understanding the likely effects of some climate change parameters, especially over the effects of elevated CO2, temperature, and rainfall-related parameters, upon a small number of important plant viruses and several key insect vectors, especially aphids. However, much more research needs to be done to prepare for an era of (i) increasingly severe virus epidemics and (ii) increasing difficulties in controlling them, so as to mitigate their detrimental effects on future global food security and plant biodiversity.
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NON-UNIFORM PATTERN OF SEQUENCE DIVERGENCE BETWEEN OAT NECROTIC MOTTLE VIRUS AND WHEAT STREAK MOSAIC VIRUS)

NON-UNIFORM PATTERN OF SEQUENCE DIVERGENCE BETWEEN OAT NECROTIC MOTTLE VIRUS AND WHEAT STREAK MOSAIC VIRUS) | Cereal and grass viruses | Scoop.it
Technical Abstract:
The sequence of the 3'-terminal 1729 nucleotides (nts) of two ONMV isolates were determined and compared with sequences of WSMV isolates Czech Republic, Hungary, Iran, Mexico, Russia, Turkey and the U.S.A. The WSMV sequences shared 73-74% (nt) and 79¿81% (amino acid [aa]) identity with ONMV. In contrast, ONMV is only 37% (nt) and 24% (aa) identical to RGMV. Thus, ONMV should be removed from the genus Rymovirus (where it appears in the 7th report of the ICTV) and placed in the genus Tritimovirus. The coat protein (CP) cistron of ONMV was 12 codons shorter than the WSMV consensus sequence. However, sequence identities were sufficiently high such that the 11 sequences could be aligned with little ambiguity. The missing codons in ONMV were all near the CP amino-terminus, a region that is also variable among WSMV isolates. Given the codon based alignment, several non-uniform patterns of divergence between and within the two virus species became apparent. Within species transitions (ts) are about 4-fold more frequent than transversions (tv) while between WSMV and ONMV the ts/tv ratio is 1.1. This indicates that one or both branches leading to their common ancester may be longer than lengths based on the number of nt differences alone. The two species differ by an average of 106 aa replacements out of a total of 527 codons. The vast majority (86%) of replacement codons have nt substitutions in multiple codon positions, and even 14 of 217 silent codons involved multiple nt substitutions. Further, only 54 aa replacements between ONMV and WSMV were at sites monomorphic in the WSMV data set. Thus, it seems that the rate of evolution varies widely among sites for these two viruses and that not all substitution events are independent of each other.
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Characterisation of siRNAs derived from new isolates of bamboo mosaic virus and their associated satellites in infected ma bamboo (Dendrocalamus latiflorus)

Characterisation of siRNAs derived from new isolates of bamboo mosaic virus and their associated satellites in infected ma bamboo (Dendrocalamus latiflorus) | Cereal and grass viruses | Scoop.it

Abstract

We characterised the virus-derived small interfering RNAs (vsiRNA) of bamboo mosaic virus (Ba-vsiRNAs) and its associated satellite RNA (satRNA)-derived siRNAs (satsiRNAs) in a bamboo plant (Dendrocalamus latiflorus) by deep sequencing. Ba-vsiRNAs and satsiRNAs of 21–22 nt in length, with both (+) and (-) polarity, predominated. The 5′-terminal base of Ba-vsiRNA was biased towards A, whereas a bias towards C/U was observed in sense satsiRNAs, and towards A in antisense satsiRNAs. A large set of bamboo genes were identified as potential targets of Ba-vsiRNAs and satsiRNAs, revealing RNA silencing-based virus-host interactions in plants. Moreover, we isolated and characterised new isolates of bamboo mosaic virus (BaMV; 6,350 nt) and BaMV-associated satRNA (satBaMV; 834 nt), designated BaMV-MAZSL1 and satBaMV-MAZSL1, respectively.

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One-step reverse transcription loop-mediated isothermal amplification for the detection of Maize chlorotic mottle virus in maize

Highlights
 • A one-step RT-LAMP was developed for the diagnosis of MCMV in field-grown maize.
 • The RT-LAMP procedure could be completed within 60 min using the primers designed in the CP gene.
• The RT-LAMP assay was about 10-fold more sensitive than RT-PCR in this study. • The RT-LAMP for detecting MCMV is specific and feasible.

Abstract
Maize chlorotic mottle virus (MCMV) is spreading in many regions worldwide, causing maize lethal necrosis when co-infected with a potyvirid. In this study, one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to detect MCMV in maize. A set of four specific primers was designed based on the conserved coat protein gene sequences of MCMV. The RT-LAMP could be completed within 60 min under isothermal condition at 63 °C. The sensitivity test showed that the RT-LAMP was about 10-fold more sensitive than RT-PCR and no cross-reactivity was detected with other viral pathogens infecting maize in China. Moreover, the results of RT-LAMP could be visually inspected by SYBR Green I staining in a closed-tube, facilitating high-throughput application of MCMV detection. This method was further verified by testing field-collected samples. These results suggested that the developed MCMV RT-LAMP technique is a rapid, efficient and sensitive method which could be used as a routine screen for MCMV infection.
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Heredity - Abstract of article: Introgression of chromosome segments from multiple alien species in wheat breeding lines with wheat streak mosaic virus resistance

Abstract


 Pyramiding of alien-derived Wheat streak mosaic virus (WSMV) resistance and resistance enhancing genes in wheat is a cost-effective and environmentally safe strategy for disease control. PCR-based markers and cytogenetic analysis with genomic in situ hybridisation were applied to identify alien chromatin in four genetically diverse populations of wheat (Triticum aestivum) lines incorporating chromosome segments from Thinopyrum intermedium and Secale cereale (rye). Out of 20 experimental lines, 10 carried Th. intermedium chromatin as T4DL*4Ai#2S translocations, while, unexpectedly, 7 lines were positive for alien chromatin (Th. intermedium or rye) on chromosome 1B. The newly described rye 1RS chromatin, transmitted from early in the pedigree, was associated with enhanced WSMV resistance. Under field conditions, the 1RS chromatin alone showed some resistance, while together with the Th. intermedium 4Ai#2S offered superior resistance to that demonstrated by the known resistant cultivar Mace. Most alien wheat lines carry whole chromosome arms, and it is notable that these lines showed intra-arm recombination within the 1BS arm. The translocation breakpoints between 1BS and alien chromatin fell in three categories: (i) at or near to the centromere, (ii) intercalary between markers UL-Thin5 and Xgwm1130 and (iii) towards the telomere between Xgwm0911 and Xbarc194. Labelled genomic Th. intermedium DNA hybridised to the rye 1RS chromatin under high stringency conditions, indicating the presence of shared tandem repeats among the cereals. The novel small alien fragments may explain the difficulty in developing well-adapted lines carrying Wsm1 despite improved tolerance to the virus. The results will facilitate directed chromosome engineering producing agronomically desirable WSMV-resistant germplasm.


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The complete genome sequence for a Turkish isolate of Wheat dwarf virus (WDV) from barley confirms the presence of two distinct WDV strains

The complete genome sequence for a Turkish isolate of Wheat dwarf virus (WDV) from barley confirms the presence of two distinct WDV strains | Cereal and grass viruses | Scoop.it

Abstract


The complete genome for a barley isolate of Wheat dwarf virus (WDV) from Tekirdağ, Turkey, WDV-Bar[TR], was isolated and sequenced. The genome was found to be 2739 nucleotides long, which is shorter than wheat-infecting WDV isolates, and with a genome organization typical for mastreviruses. The complete genome of WDV-Bar[TR] showed 83–84% nucleotide identity to wheat isolates of WDV, with the non-coding regions SIR and LIR least conserved (72–74% identity). The deduced amino acid sequences for Rep and RepA were most conserved (92–93%), while CP and MP were less conserved (87% and 79–80%, respectively). The identity to other mastrevirus species was significantly lower. In phylogenetic analyses, the WDV isolates formed a distinct clade, well separated from the other mastreviruses with the wheat isolates grouping closely together. Phylogenetic analyses of WDV-Bar[TR], the partial sequence for another Turkish barley isolate (WDV-Bar[TR2]) and published WDV sequences further supported the division of WDV into two distinct strains. The barley strain could also be divided into three subtypes based on relationships and geographic origin. This study shows the first complete published sequence for a barley isolate of WDV.

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Wheat Streak Mosaic Arrives Early

Wheat Streak Mosaic Arrives Early | Cereal and grass viruses | Scoop.it

Deep down in your heart you knew it was going to happen. With all the volunteer wheat we had this past summer and fall, what are the odds that the new wheat crop would not get infected with wheat streak mosaic virus? Correct. The answer is zero.

As we all know, wheat streak mosaic is a very serious viral disease. It is transmitted to the new wheat crop by microscopic wheat curl mites which have been living on volunteer wheat which serves as the intermediate host. At some point in their lives, these tiny little mites make their way to the edge of the volunteer wheat leaves. And then they just jump off. The wind carries them very long distances until they land on another wheat plant. Then they go to work. A plant pathologist explained to me once that they have snouts just like hogs and they root around on the wheat leaves rupturing plant cells. They feed on that plant material. But at the same time, they are infecting the plant with the wheat streak mosaic virus which they carry in their little bodies. This virus can be extremely dangerous. I have personally seen wheat yield reductions of near 100 percent in areas of fields adjacent to heavily infected volunteer. Usually, though, you won’t see the actual damage until later next spring. If you are seeing symptoms in the fall, you have a real problem. Well, we have a real problem. I was talking recently with Chris Long, Lane County Extension agent, who told me a farmer east of Dighton had him out to look at a wheat field, which he suspected was infected. The farmer said it wasn’t planted all that early, but there were fields of big volunteer on two sides of the field at planting time. Chris took some plant samples and sent them to K-State. And, yes, it is wheat streak mosaic. Chris says this is the first time in his career that he’s been asked to look at fields and to get samples in the fall to see if the problem is wheat streak mosaic. “I’ve been asked on a number of occasions to get samples in the spring, but never in the fall.” This is really bad news for several reasons. Chris looked at the field earlier this week and said, “The field on Monday looked pretty much entirely destroyed by the disease. But in addition, the wheat variety was Oakley Cl—which is supposed to have extremely good resistance to the disease. On a scale of 1 to 10, Oakley had been rated a 2—and the next best resistance to it are several varieties with ratings of 5.” In addition, a Scott County farmer said that several wheat fields that had been planted quite early for wheat grazing had also been killed. However, I am not sure what those varieties were. KSU wheat breeder Allan Fritz says there are two potential issues with Oakley. “One is that the resistance is temperature sensitive and even if the field weren’t planted early, the warm conditions could have caused the resistance to not be effective. There is also the possibility the virus has changed and now overcomes that resistance gene.” Fritz goes on to say that they have screened some new wild relatives for wheat streak resistance. “There are some promising candidates but it’s too early to tell what we will be able to get out of it.” Fellow wheat breeder Guorong Zhang confirms that they have found a new race of wheat streak mosaic virus at Hays which can break the resistance gene in Oakley. Making our situation even more precarious is the fact we’ve had a very long and mild fall. Here in Lane County, we didn’t have a hard-killing frost until the first week in November—almost three weeks late. That has given the wheat curl mites even more time to do more damage. And if you think seed treatments are going to help minimize the problem, think again. I asked K-State plant pathologist Erick DeWolf and K-State entomologist Sarah Zukoff about whether seed treatments with insecticides would help with control of wheat streak mosaic through control of wheat curl mites. Erick said, “I am not aware of any seed treatments that would influence wheat curl mite populations and, thus, reduce risk of WSM”. Sarah added, “I haven’t seen any data that says seed treatments will work on fall armyworms, army cutworms or wheat curl mites.” Pulling things together, there is still a fair amount of volunteer wheat out there that has not been controlled. I know it is late in the day, but you can do yourself and the entire neighborhood a favor if you get that stuff killed. And finally, if you are going to plant early for grazing, forget wheat and go with rye or triticale. Both will produce a lot more forage than wheat will and you won’t have to worry about wheat streak mosaic. Vance and Louise Ehmke grow certified seed wheat in Lane County, Kansas. This article originally ran on kansasagland.com.

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