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MicroRNAs (miRNAs) play an essential regulatory role in plant-virus interaction. However, few studies have focused on the roles of miRNAs and their targets after sugarcane mosaic virus (SCMV) infection in sugarcane. To address this issue, we conducted small RNA (sRNA) and degradome sequencing on two contrasting sugarcanes (SCMV-resistant 'Fuoguo1' [FG1] and susceptible 'Badila') infected by SCMV at five time points. A total of 1,578 miRNAs were profiled from 30 sRNA libraries, comprising 660 known miRNAs and 380 novel miRNAs. Differential expression analysis of miRNAs revealed that most were highly expressed during the SCMV exponential phase in Badila at 18 h postinfection, with expression profiles positively correlated with virus replication dynamics as observed through clustering. Analysis of degradome data indicated a higher number of differential miRNA targets in Badila compared to FG1 at 18 h postinfection. Gene ontology (GO) enrichment analysis significantly enriched the stimulus-response pathway, suggesting negative regulatory roles to SCMV resistance. Specifically, miR160 upregulated expression patterns and validated in Badila through quantitative real-time PCR (qRT-PCR) in the early stages of SCMV multiplication. Our research provides new insights into the dynamic response of plant miRNA and virus replication and contributes valuable information on the intricate interplay between miRNAs and SCMV infection dynamics. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license., Competing Interests: The author(s) declare no conflict of interest.

Sugarcane streak mosaic virus (SCSMV), now assigned to the genus Poacevirus of the family Potyviridae , was reported for the first time in 1932 in Louisiana and was believed to be strain F of sugarcane mosaic virus (SCMV) for more than six decades. SCMV-F was renamed SCSMV in 1998 after partial sequencing of its genome and phylogenetic investigations. Following the development of specific molecular diagnostic methods in the 2000s, SCSMV was recurrently found in sugarcane exhibiting streak mosaic symptoms in numerous Asian countries but not in the Western hemisphere or in Africa. In this review, we give an overview of the current knowledge on this disease and the progression in research on SCSMV. This includes symptoms, geographical distribution and incidence, diagnosis and genetic diversity of the virus, epidemiology, and control. Finally, we highlight future challenges, as sugarcane streak mosaic has recently been found in Africa, where this disease represents a new threat to sugarcane production., Competing Interests: The author(s) declare no conflict of interest.

Sugarcane mosaic virus (SCMV), which belongs to the Potyvirus genus of the family Potyviridae, causes mosaic diseases in canna, sugarcane and maize worldwide. Previously, the genetic variations, timescale, codon usage patterns and host adaptions of SCMV were determined. However, the dinucleotide composition and the dinucleotide bias from hosts or the protein coding regions of the virus have yet to be investigated. In this study, comprehensive analyses of the dinucleotide composition and dinucleotide bias from hosts, lineages and protein coding regions of SCMV were performed using 131 complete genomic sequences. We found that UpG and CpA were largely overrepresented while UpA, CpC, and CpG were largely underrepresented in the polyprotein and 11 protein coding region data sets. SCMV dinucleotide composition bias is more strongly dependent on the protein coding regions than on hosts. A weak association between the dinucleotide composition and SCMV lineages was also observed. Our analysis provides a novel perspective on the molecular evolutionary mechanisms of SCMV and may provide a better understanding of future research on the origin and evolutionary patterns of SCMV., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)

Sugarcane mosaic virus (SCMV) is one of the major pathogens of sugarcane. SCMV infection causes dynamic changes in plant cells, including decreased photosynthetic rate, respiration, and sugar metabolism. To understand the basics of pathogenicity mechanism, we performed transcriptome and proteomics analysis in two sugarcane genotypes (Badila: susceptible to SCMV and B-48: SCMV resistant). Using Saccharum spontaneum L. genome as a reference, we identified the differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) that participate in sugar metabolism, transport of their metabolites, and Carbohydrate Activating enZYmes (CAZymes). Sequencing data revealed 287 DEGs directly or indirectly involved in sugar metabolism, transport, and storage, while 323 DEGs are associated with CAZymes. Significant upregulation of glucose, sucrose, fructose, starch, and SWEET-related transcripts was observed in the Badila after infection of SCMV. B-48 showed resistance against SCMV with a limited number of sugar transcripts up-regulation at the post-infection stage. For CAZymes, only glycosyltransferase (GT)1 and glycosyl hydrolase (GH)17 were upregulated in B-48. Regulation of DEGs was analyzed at the proteomics level as well. Starch, fructose, glucose, GT1, and GH17 transcripts were expressed at the post-translational level. We verified our transcriptomic results with proteomics and qPCR data. Comprehensively, this study proved that Badila upregulated sugar metabolizing and transporting transcripts and proteins, which enhance virus multiplication and infectionl.

Sugarcane mosaic virus (SCMV) is a serious disease of monocotyledonous plants, including sugarcane, causing deterioration in both growth and productivity. RNA interference (RNAi) inhibits gene expression through RNA-mediated sequence-specific interactions and is considered an effective approach to control viral infection in plants. In this study, the SCMVCp gene encoding the coat protein (CP) was inserted into the pGreen-0179 plasmid in both sense and antisense orientations. Cauliflower mosaic virus (CaMV) and Zea mays ubiquitin (Ubi) promoters were selected to drive the transcription of the intron-hairpin constructs, called HpSCMVCp-CaMV and HpSCMVCp-Ubi, respectively. Transgenic sugarcane expressing these constructs was generated through Agrobacterium-mediated transformation. This transformation method produced a high percentage of transgenic plants for both HpSCMVCp-CaMV and HpSCMVCp-Ubi, as confirmed by PCR analysis. Southern blotting revealed a single stable insertion of the DNA target in the genome of transgenic sugarcane lines. After artificial virus infection, lines that developed mosaic symptoms were classified as susceptible, whereas those that remained green without symptoms were classified as resistant at 42 days post-inoculation. Immunoblotting revealed CP expression at 37 kDa in susceptible and non-transgenic sugarcane, but not in resistant lines. RT-PCR analysis confirmed viral Cp and Nib gene expression in susceptible lines and their absence in resistant lines. Interestingly, upon comparison of effectivity, CaMV and Ubi promoter-driven gene expression resulted in 57.69% and 82.35% resistant sugarcane lines, respectively. Thus, we concluded that RNAi is effective for inducing resistance against SCMV and that the Ubi promoter is an effective promoter for producing transgenic sugarcane.

Background: Viruses are infectious pathogens, and plant virus epidemics can have devastating consequences to crop yield and quality. Sugarcane mosaic virus (SCMV, belonging to family Potyviridae) is one of the leading pathogens that affect the sugarcane crop every year. To combat the pathogens' attack, plants generate reactive oxygen species (ROS) as the first line of defense whose sophisticated balance is achieved through well-organized antioxidant scavenging pathways., Results: In this study, we investigated the changes occurring at the transcriptomic level of ROS associated and ROS detoxification pathways of SCMV resistant (B-48) and susceptible (Badila) sugarcane genotypes, using Saccharum spontaneum L. genome assembly as a reference genome. Transcriptomic data highlighted the significant upregulation of ROS producing genes such as NADH oxidase, malate dehydrogenase and flavin-binding monooxygenase, in Badila genotype after SCMV pathogenicity. To scavenge the ROS, the Badila genotype illustrated a substantial enhancement of antioxidants i.e. glutathione s-transferase (GST), as compared to its resistant counterpart. GST is supposed to be a key indicator of pathogen attacks on the plant. A remarkably lower GST expression in B-48, as compared to Badila, indicated the development of resistance in this genotype. Additionally, we characterized the critical transcription factors (TFs) involved in endowing resistance to B-48. Among these, WRKY, AP2, NAC, bZIP, and bHLH showed enhanced expression in the B-48 genotype. Our results also confirmed the linkage of transcriptomic data with the enzymatic and qPCR data. The estimation of enzymatic activities for superoxide dismutase, catalase, ascorbate peroxidase, and phenylalanine ammonia-lyase supported the transcriptomic data and evinced higher resistance in B-48 genotype., Conclusion: The current study supported the efficiency of the B-48 genotype under SCMV infection. Moreover, comparative transcriptomic data has been presented to highlight the role of significant transcription factors conferring resistance to this genotype. This study provides an in-depth knowledge of the expression profiling of defense mechanisms in sugarcane.

Sugarcane mosaic virus (SCMV) is the causal agent of sugarcane mosaic disease (SMD) in Brazil; it is mainly controlled by using resistant cultivars. Studies on the changes in sugarcane transcriptome provided the first insights about the molecular basis underlying the genetic resistance to SMD; nonetheless, epigenetic modifications such as cytosine methylation is also informative, considering its roles in gene expression regulation. In our previous study, differentially transcribed fragments (DTFs) were obtained using cDNA-amplified fragment length polymorphism by comparing mock- and SCMV-inoculated plants from two sugarcane cultivars with contrasting responses to SMD. In this study, the identification of unexplored DTFs was continued while the same leaf samples were used to evaluate SCMV-mediated changes in the cytosine methylation pattern by using methylation-sensitive amplification polymorphism. This analysis revealed minor changes in cytosine methylation in response to SCMV infection, but distinct changes between the cultivars with contrasting responses to SMD, with higher hypomethylation events 24 and 72 h post-inoculation in the resistant cultivar. The differentially methylated fragments (DMFs) aligned with transcripts, putative promoters, and genomic regions, with a preponderant distribution within CpG islands. The transcripts found were associated with plant immunity and other stress responses, epigenetic changes, and transposable elements. The DTFs aligned with transcripts assigned to stress responses, epigenetic changes, photosynthesis, lipid transport, and oxidoreductases, in which the transcriptional start site is located in proximity with CpG islands and tandem repeats. Real-time quantitative polymerase chain reaction results revealed significant upregulation in the resistant cultivar of aspartyl protease and VQ protein, respectively, selected from DMF and DTF alignments, suggesting their roles in genetic resistance to SMD and supporting the influence of cytosine methylation in gene expression. Thus, we identified new candidate genes for further validation and showed that the changes in cytosine methylation may regulate important mechanisms underlying the genetic resistance to SMD., Competing Interests: The authors have declared that no competing interests exist.

Background: Virus-free sugarcane is difficult to achieve due to the multiple vegetative propagation cycles employed commercially. In vitro culture using small (1 mm) meristematic shoot tips has eliminated viruses but survival is low with small explants., Objective: Droplet-Vitrification (D-V) and V-Cryoplate protocols were investigated for the elimination of Sugarcane mosaic virus (SCMV) from large (c. 3 mm) in vitro-derived shoot tips., Materials and Methods: Shoot tips excised from NCo376 and N19 cultivars were exposed to both cryogenic procedures. Virus indexing by RT-qPCR was performed 16 weeks after recovery., Results: Explants exposed to cryo-treatments that recovered and multiplied was 30-92%, while at least 90% of control explants regenerated. No virus was detected in multiplied shoots from either cultivar after D-V and liquid nitrogen immersion. In NCo376, virus was eliminated after D-V without cooling., Conclusion: The preliminary findings suggest that cryotherapy and/or osmotherapy are viable options for SCMV removal from infected plants.

Sugarcane mosaic virus (SCMV) is distributed worldwide and infects three major crops: sugarcane, maize, and sorghum. The impact of SCMV is increased by its interaction with Maize chlorotic mottle virus which causes the synergistic maize disease maize lethal necrosis. Here, we characterised maize lethal necrosis-infected maize from multiple sites in East Africa, and found that SCMV was present in all thirty samples. This distribution pattern indicates that SCMV is a major partner virus in the East African maize lethal necrosis outbreak. Consistent with previous studies, our SCMV isolates were highly variable with several statistically supported recombination hot- and cold-spots across the SCMV genome. The recombination events generate conflicting phylogenetic signals from different fragments of the SCMV genome, so it is not appropriate to group SCMV genomes by simple similarity.

The 6K2 protein of potyviruses plays a key role in the viral infection in plants. In the present study, the coding sequence of 6K2 was cloned from Sugarcane mosaic virus (SCMV) strain FZ1 into pBT3-STE to generate the plasmid pBT3-STE-6K2, which was used as bait to screen a cDNA library prepared from sugarcane plants infected with SCMV based on the DUALmembrane system. One hundred and fifty-seven positive colonies were screened and sequenced, and the corresponding full-length genes were cloned from sugarcane cultivar ROC22. Then, 24 genes with annotations were obtained, and the deduced proteins were classified into three groups, in which eight proteins were involved in the stress response, 12 proteins were involved in transport, and four proteins were involved in photosynthesis based on their biological functions. Of the 24 proteins, 20 proteins were verified to interact with SCMV-6K2 by yeast two-hybrid assays. The possible roles of these proteins in SCMV infection on sugarcane are analyzed and discussed. This is the first report on the interaction of SCMV-6K2 with host factors from sugarcane, and will improve knowledge on the mechanism of SCMV infection in sugarcane.

Sugarcane mosaic is a historically important disease in Louisiana currently caused by sorghum mosaic virus (SrMV). Successful breeding for resistance reduced the disease to low incidence in commercial cultivars. However, mosaic was detected in experimental clone evaluations at multiple locations, leading to uncertainty concerning the current distribution and incidence in the state. Field surveys were conducted from 2016 to 2018 in breeding program yield trials and experimental clone seed cane increase fields. Mosaic symptomatic plants were observed in a newly released cultivar, HoCP 09-804, in three of five production areas, with incidences ranging from 0 to 10%. Mosaic also was observed in nine additional experimental clones. Single leaf samples were tested for SrMV using reverse transcription PCR. All symptomatic samples and a low percentage (0.3%) of asymptomatic samples tested positive for SrMV, confirming that it continues to be the causal species. Runs analysis detected aggregation of infected plants within at least 70% of rows in 94% of surveyed fields. The spatial pattern and geographical distribution of disease incidence suggested that infected seed cane was the source of the disease. Surveys conducted in the same fields of HoCP 09-804 through two subsequent crops detected disease incidence increases in some fields and decreases in the others in first ratoon, but observed incidence was lower compared with plant cane in all fields in second ratoon. The results indicated that disease increase owing to aphid transmission did not occur under the prevailing conditions.

Maize and sugarcane are two economically important crops often grown in adjacent fields or co-cultivated in the northern guinea savannah agroecological zone, a major cereal production region of Nigeria. This study was conducted to determine the prevalence of mosaic disease in sugarcane and maize fields in the northern guinea savannah agroecological zone and to molecularly characterize the associated sugarcane mosaic virus (SCMV, genus Potyvirus ) isolates. Surveys were conducted from June to July 2015, and sugarcane mosaic disease (SCMD) incidence was assessed across 21 farmer's fields. Mean SCMD incidence varied across states with ∼82% (308/376), ∼66% (143/218), and ∼67% (36/54) recorded in Kaduna, Kano, and Katsina states, respectively. RT-PCR analysis of 415 field-collected samples using genus-specific primers confirmed potyvirus infection in 63.7% (156/245) of sugarcane, 29.7% (42/141) of maize crops, and 45% (13/29) of itch grass samples. Cloning and sequencing of gene-specific DNA amplicons from a subset of 45 samples (sugarcane = 33, maize = 9, itch grass = 3) confirmed their specificities to SCMV. Phylogenetic analysis of the partial gene sequences showed that they all belong to a single monophyletic clade of SCMV. These results were supported by analysis of complete polyprotein sequences of representative maize and sugarcane isolates from Nigeria. Both isolates shared 94.9%/97.3% complete polyprotein nucleotide (nt)/amino acid (aa) identities with each other and 75.2%/97.6% nt/aa identities with corresponding sequences of global SCMV isolates. The detection of identical populations of SCMV isolates in both crop species and a weed host suggests possible vector mediated interspecies spread within cereal landscapes in the study area with implications for the integrated and sustainable management of SCMD in cereal cropping systems in Nigeria.

Objective: The selection of reference genes in sugarcane under Sugarcane mosaic virus (SCMV) infection has not been reported and is indispensable to get reliable reverse transcription quantitative PCR (RT-qPCR) results for validation of transcriptome analysis. In this regard, seven potential reference genes were tested by RT-qPCR and ranked according to their stability using BestKeeper, NormFinder and GeNorm algorithms, and RefFinder WEB-based software in an experiment performed with samples from two sugarcane cultivars contrasting for SCMV resistance, when mechanically inoculated with a severe SCMV strain and using mock inoculated plant controls., Results: The genes Uridylate kinase (UK) and Ubiquitin-conjugating enzyme 18 (UBC18) were the most stable according to GeNorm algorithm and the Pearson correlation coefficients with the BestKeeper index. On the other hand, ribosomal protein L35-4 (RPL1), Actin (ACT) and Ubiquitin1 (UBQ1) were the least stable genes for all algorithms tested.

Sugarcane mosaic virus (SCMV) is a plant pathogenic virus of the family Potyviridae that causes chlorosis, stunting and significantly reduced sugar productivity in sugarcane. Pathogen-derived resistance is a method used to develop SCMV-resistant sugarcane by overexpression of viral DNA. In this study, the gene encoding the coat protein (CP) of SCMV was amplified by reverse transcriptase PCR from symptomatic sugarcane leaves and used to generate transgenic sugarcane. Nucleotide sequence analysis of amplified cDNA indicated that the 998-bp-long cDNA, termed ScMVCp cDNA, codes for the CP of SCMV from the PS881 isolate. The ScMVCp cDNA was inserted into the binary vector pRI101-ON with two constructs, a full nucleotide sequence (p927) and a sequence coding for N-terminally truncated protein (p702). The constructs were then introduced into sugarcane using Agrobacterium-mediated transformation. Southern blot analysis showed a single hybridized DNA copy inserted into the genome of transgenic sugarcane lines. The inserted genes were expressed at both the RNA transcript and protein levels in the transgenic sugarcane. The highest expression was found in transgenic lines 10, 11 and 13 from the p927 construct. Artificial infection by the virus showed that p927 generated a higher resistance to virus compared with p702. This resistance was passed on to the second generation of transgenic sugarcane with 100 and 20-40% levels of resistance in the p927 and p702 transgenic lines, respectively. This report shows that the full sequence of the CP gene is required to disrupt viral assembly and packaging, thereby generating resistance to SCMV infection.

The coding sequence of P3N-PIPO was cloned by fusion PCR from Sugarcane mosaic virus (SCMV), a main causal agent of sugarcane (Saccharum spp. hybrid) mosaic disease. SCMV P3N-PIPO preferentially localized to the plasma membrane (PM) compared with the plasmodesmata (PD), as demonstrated by transient expression and plasmolysis assays in the leaf epidermal cells of Nicotiana benthamiana. The subcellular localization of the P3N-PIPO mutants P3N-PIPOT1 and P3N-PIPOT2 with 29 and 63 amino acids deleted from the C-terminus of PIPO, respectively, revealed that the 19 amino acids at the N-terminus of PIPO contributed to the PD localization. Interaction assays showed that the 63 amino acids at the C-terminus of PIPO determined the P3N-PIPO interaction with PM-associated Ca 2+ -binding protein 1, ScPCaP1, which was isolated from the SCMV-susceptible sugarcane cultivar Badila. Like wild-type P3N-PIPO, P3N-PIPOT1 and P3N-PIPOT2 could translocate to neighbouring cells and recruit the SCMV cylindrical inclusion protein to the PM. Thus, interactions with ScPCaP1 may contribute to, but not determine, SCMV Pm3N-PIPO's localization to the PM or PD. These results also imply the existence of truncated P3N-PIPO in nature.

Sugarcane mosaic virus (SCMV) is the most prevalent virus causing sugarcane mosaic and maize dwarf mosaic diseases. Here, we presented the first two complete genomic sequences of Iranian SCMV isolates, NRA and ZRA from sugarcane and maize. The complete genome sequences of NRA and ZRA were, respectively, 9571 and 9572 nucleotides (nt) in length, excluding the 3'-terminal poly(A) tail. Both isolates contained a 5'-untranslated region (UTR) of 149 nt, an open reading frame of 9192 nt encoding a polyprotein of 3063 amino acids (aa), and 3'-UTR of 230 nt for NRA and 231 nt for ZRA. SCMV-NRA and -ZRA genome nucleotide sequences were 97.3 % identical and shared nt identities of 79.1-92 % with those of other 21 SCMV isolates available in the GenBank, highest with the isolate Bris-A (AJ278405) (92 and 91.7 %) from Australia. When compared for separate genes, most of their genes shared the highest identities with Australian and Argentinean isolates. Phylogenetic analysis of the complete genomic sequences reveals that SCMV can be clustered to three groups. Both NRA and ZRA were clustered with sugarcane isolates from Australia and Argentina in group III but formed a separate sublineage. Recombination analysis showed that both isolates were intraspecific recombinants, and represented two novel recombination patterns of SCMV (in the P1 coding region). NRA had six recombination sites within the P1, HC-Pro, CI, NIa-Vpg, and NIa-pro coding regions, while ZRA had four within the P1, HC-Pro, NIa-Pro, and NIb coding regions.

A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detecting Sugarcane mosaic virus (SCMV) and Sorghum mosaic virus (SrMV) in sugarcane. Six sets of four primers corresponding to the conserved coat protein gene were designed and tested for each virus. Three primer sets designed for detecting SCMV and four for detecting SrMV were successful in the RT-LAMP assay. The effective primer sets were not only specific for their target virus, but also able to detect multiple virus strains. The magnesium sulfate concentration of the reaction solution was optimized, with both viruses requiring a minimum of 5mM for detection. The sensitivity of this RT-LAMP assay was less than that of conventional and real-time RT-PCR., (Published by Elsevier B.V.)

Sugarcane mosaic virus (SCMV) is an important viral pathogen and has caused serious losses in grain and forage yield. To identify candidate SCMV resistance proteins and to explore the molecular mechanisms involved in the plant-SCMV interaction, we conducted proteomic analyses of leaf samples from resistant and susceptible ecotypes of maize infected with SCMV. Proteins were analyzed by quantitative two-dimensional differential gel electrophoresis (2D-DIGE), and 93 protein spots showed statistically significant differences after virus inoculation. Functional categorization showed that SCMV-responsive proteins were mainly involved in energy and metabolism, stress and defense responses, photosynthesis, and carbon fixation. The majority of the identified proteins were located in chloroplast and cytoplasm based on bioinformatic analysis. Among these identified proteins, 17 have not been identified previously as virus-responsive proteins, and 7 were new and did not have assigned functions. Western blotting analyses confirmed the expression patterns of proteins of specific interest, and the genes encoding these proteins were further analyzed by real-time PCR. The results of this study showed overlapping and specific proteomic responses to SCMV infection between resistant and susceptible maize ecotypes. This study provides further insight into the molecular events during compatible and incompatible interactions between viruses and host plants., Biological Significance: Sugarcane mosaic virus (SCMV) is an important viral pathogen and has caused serious losses in grain and forage yield. However, little is known about host-SCMV interactions from the proteome perspective. This study analyzed proteomic changes in resistant and susceptible plants that are infected with SCMV using DIGE based proteomics. We identified 17 proteins that have not been identified previously as virus-responsive proteins, and 7 new proteins without assigned functions. These proteins are interesting candidates for future research, as they may be associated with new biological functions and play important roles in plant-virus interactions. Real-time RT-PCR analysis of genes encoding several proteins of interest provided indication on whether the changes in protein abundance were regulated at the mRNA level. The results of this study showed overlapping and specific proteomic responses to SCMV infection between resistant and susceptible ecotypes. After inoculation, the proteins involved in energy and metabolism, stress and defense responses, photosynthesis and other four functional groups showed significant changes in both ecotypes, which suggested that SCMV infection influenced these physiological processes in both the resistant Siyi and the susceptible Mo17. However, the oxidative burst was more pronounced during incompatible plant-SCMV interactions, as compared to those defined as compatible. We also observed an increase of enzymes involved in glycolysis and gluconeogenesis pathways in the resistant maize ecotype Siyi, while decrease in the susceptible maize ecotype Mo17. In addition, there is a marked increase of guanine nucleotide-binding protein beta submit in the resistant Siyi, which suggests a possible involvement of G-protein associated pathways in the resistant responses of maize to SCMV. These observations may possibly reveal protein targets/markers that are useful in the design of future diagnosis or plant protection strategies and provide new insights into the molecular mechanism of plant-virus interactions., (Copyright © 2013 Elsevier B.V. All rights reserved.)

Sugarcane mosaic virus (SCMV) is one of the causal pathogens of mosaic diseases on sugarcane, maize, sorghum and some other graminaceous species with worldwide distribution. The global genetic diversity and molecular evolution of SCMV capsid protein (CP) gene were investigated with the nucleotide sequences available in the GenBank database. Phylogenetic analyses revealed that SCMV isolates clustered in relation to their original hosts, and geographically distinct isolates from maize or sugarcane clustered differently. The populations between maize and sugarcane showed frequent gene flows; but within maize or sugarcane geography distinct isolates had infrequent gene flow. Recombination existed in the region of CP cistron and 3'-untranslated region (UTR). Most of the codons in the CP gene were under negative selection or neutral evolution except for codons 27 and 48, which were under positive selection. This study provided systematic analyses of the evolutionary processes contributing to the observed diversification of SCMV populations., (Copyright © 2012 Elsevier B.V. All rights reserved.)

Triticum mosaic virus (TriMV) is the type species of the newly established Poacevirus genus in the family Potyviridae. In this study, we demonstrate that in contrast to the helper component-proteinase (HC-Pro) of Potyvirus species, the P1 proteins of TriMV and Sugarcane streak mosaic poacevirus function in suppression of RNA silencing (SRS). TriMV P1 effectively suppressed silencing induced by single- or double-stranded RNAs (ss/ds RNAs), and disrupted the systemic spread of silencing signals at a step after silencing signal production. Interestingly, contrary to enhanced SRS activity of potyviral HC-Pro by co-expression with P1, the presence of TriMV HC-Pro reduced SRS activity of TriMV P1. Furthermore, TriMV P1 suppressed systemic silencing triggered by dsRNA more efficiently than the HC-Pro of Turnip mosaic potyvirus. Furthermore, TriMV P1 enhanced the pathogenicity of a heterologous virus. Our results established poaceviral P1 as a potent RNA silencing suppressor that probably employs a novel mechanism to suppress RNA silencing-based antiviral defense., (Published by Elsevier Inc.)

Sugarcane mosaic virus (SCMV) is the most prevalent virus causing maize dwarf mosaic disease in northern China. A SCMV isolate, BD8, was obtained from the maize showing dwarf and mosaic symptoms in Baoding, China. The complete genomic sequence of BD8 is 9,576 nucleotides (nt) excluding the poly(A) tail. It contains one single open reading frame of 9,192 nt and encodes a large polyprotein of 3,063 amino acids (aa), flanked by a 5'-untranslated region (UTR) of 148 nt and a 3'-UTR of 236 nt. The entire genomic sequence of BD8 shares identities of 79.1-80.8% with those of other 13 SCMV isolates available in the GenBank at nt level, while their CP genes share identities of 76.9-82.6 and 82.8-86.9% at nt and aa levels, respectively. Phylogenetic analysis of the complete genomic sequences reveals that SCMV can be clustered to four groups: group I includes isolates from maize, group II consists of isolates from sugarcane or maize, groups III and IV contain single isolate of AU-A (AJ278405) and BD8, respectively. Thus, BD8 represents a new strain of SCMV. Furthermore analysis of the CP gene sequences of more isolates shows that BD8 is clustered to a group with the isolates from Thailand and Vietnam, which implies that isolates of this strain have been distributed in South Asia. In the greenhouse, BD8 can cause severe symptoms in all the 12 maize varieties tested with high incidence, indicating that BD8 is highly virulent.

Background: In order to obtain an initial and preliminary understanding of host and nonhost resistance in the initial step of potyvirus replication, both positive and negative Sugarcane mosaic virus (SCMV) strands where traced in inoculated and systemic leaves in host and nonhost resistant maize and sugarcane for one Mexican potyviral isolate (SCMV-VER1). Intermediary replication forms, such as the negative viral strand, seem to only move a short distance as surveyed by RT-PCR analysis and ELISA in different leaves. Virus purification was also done in leaves and stems., Results: Susceptible maize plants allowed for viral SCMV replication, cell-to-cell, and long distance movement, as indicated by the presence of the coat protein along the plant. In the host resistant maize plants for the SCMV-VER1 isolate, the virus was able to establish the disease though the initial steps of virus replication, as detected by the presence of negative strands, in the basal area of the inoculated leaves at six and twelve days post inoculation. The nonhost sugarcane for SCMV-VER1 and the host sugarcane for SCMV-CAM6 also allowed the initial steps of viral replication for the VER1 isolate in the local inoculated leaf. SCMV-VER1 virions could be extracted from stems of susceptible maize with higher titers than leaves., Conclusion: Nonhost and host resistance allow the initial steps of potyvirus SCMV replication, as shown by the negative strands' presence. Furthermore, both hosts allow the negative viral strands' local movement, but not their systemic spread through the stem. The presence of larger amounts of extractable virions from the stem (as compared to the leaves) in susceptible maize lines suggests their long distance movement as assembled particles. This will be the first report suggesting the long distance movement of a monocot potyvirus as a virion.

A sensitive duplex-immunocapture-RT-PCR (D-IC-RT-PCR) technique was developed for detection and discrimination of taxonomically distinct Sugarcane streak mosaic virus (SCSMV) and Sugarcane mosaic virus (SCMV) that naturally infect sugarcane. D-IC-RT-PCR was performed using polyclonal antisera for capture of virions. Oligo 5'-d(T)18(AGC)-3' as a common reverse primer for both viruses and virus specific forward primers, 5'-AAGTGGTTAAACGCCTGTGG-3' and 5'-ATGTC(GA)AAGAA(GA)ATGCGCTTGC-3' were used for amplifying approximately 1400 and approximately 900 bp fragments of SCSMV and SCMV genomes, respectively from their 3' termini. To assess the applicability of the developed technique, 67 mosaic affected sugarcane samples were initially screened by direct antigen coating-enzyme-linked immunosorbent assay (DAC-ELISA) followed by D-IC-RT-PCR. In DAC-ELISA, approximately 69% of tested samples were shown to be positive for presence of SCSMV, approximately 28% for SCMV and approximately 10% for both viruses. In D-IC-RT-PCR both viruses were detected up to the dilution of 10(-4). In D-IC-RT-PCR, approximately 76% of tested samples were found to be positive for SCSMV, approximately 37% for SCMV and approximately 16% for both viruses. The sequence analyses of D-IC-RT-PCR amplicons of 3 isolates of each virus revealed that the designed primers were virus-specific. The developed technique had potential application for sensitive parallel detection of two viruses in sugarcane.

Sugarcane mosaic disease (SMD) caused by the Sugarcane mosaic virus (SCMV), Sorghum mosaic virus (SrMV) and Sugarcane streak mosaic virus (SCSMV) and sugarcane yellow leaf disease (SYLD) caused by the Sugarcane yellow leaf virus (SCYLV) are the two most prevalent and economically important viral diseases of sugarcane. In this study, a one-step quadruplex reverse transcription (RT)-PCR method that employed virus-specific primers was developed for the simultaneous detection and differentiation of SCMV, SrMV, SCSMV and SCYLV. Several sets of primers for each target virus were evaluated for their sensitivity and specificity by simplex and quadruplex RT-PCR. The optimum primer combinations and concentrations, RT temperature and time, and PCR annealing temperature and extension time were determined for the quadruplex RT-PCR. The assay was then validated using sugarcane samples affected with SMD and/or SYLD collected from sugarcane breeding fields and farmers' fields in southern China.

Sugarcane mosaic virus (SCMV) is one of the two causative viruses of mosaic in sugarcane, a sugar crop widely grown under tropical and subtropical conditions worldwide. Although molecular characterization of SCMV strains was reported from many countries, strains occurring in India, a major sugarcane producer have not been reported so far. Twenty-six sugarcane samples represented by seven major sugarcane growing states in India and USA were subjected to reverse-transcription polymerase chain reaction (RT-PCR) using a pair of newly designed coat protein specific primers. Among them 17 were found positive to the SCMV infection. The lengths of the sequences derived in this study using the new set of primers varied between 812 and 866 nt. The amino acid sequence comparison of 30 Indian SCMV isolates showed wide range of sequence similarities in core region (88.80-100%) and hyper variable region (51.3-100%). In the N-terminal region of the five Indian isolates, a deletion of 12 aa residues between aa 11 and 30 was observed, whereas the deletion was between aa 45 and 50 in SCMV-B and -D and between aa 61 and 70 in SCMV-A. The phylogenetic analyses performed with 46 SCMV CP sequences for both hyper variable region and core region separated the isolates mostly according to their geographical origin. The 30 Indian SCMV isolates were included exclusively in four groups besides SCMV-IND, which was grouped with SCMV-SC, a type of strain from Australia. Nearly 97.0% of the Indian isolates have no signs for close relationships with previously characterized SCMV type strains (SCMV-A, -B, -D, -E, and -SC) reported from other countries. Our studies revealed that the sugarcane mosaic in India are caused by at least nine new SCMV variants (IND-CC1, -CC2, -CC3, -CC4, -CO1, -CO2, -CP, -CS, and -J) and a type strain SCMV-SC represented by SCMV-IND. This is the first report on the variability and occurrence of new SCMV population in India.

Sugarcane mosaic virus (SCMV) and sorghum mosaic virus (SrMV) diversity studies are important to characterize virus populations in sugarcane producing areas, enabling (i) identification of shifts in predominant strains, (ii) detecting associations of strains with specific varieties, and (iii) possibly exposing the appearance of new strains which may affect the performance of varieties in a region. Recent studies have shown significant sequence variability within SCMV populations around the world, indicating that isolate identification would be best achieved by direct analysis of sequence data. Because virus sequence-based studies that require the characterization of large numbers of isolates may be impractical using standard sample preparation and processing methodology, a simple protocol that yields quality sequence information, requiring neither viral RNA purification nor cloning of RT-PCR products was developed. Rapid virus release extracts are obtained by submerging a portion of leaf tissue into an extraction buffer, followed by a brief incubation at 95 degrees C. An aliquot of the extract is pipetted into an RT-PCR amplification mix for the detection of SCMV and the SrMV coat protein gene fragments. RT-PCR fragments are sequenced directly using oligonucleotide primers similar to the RT-PCR primers, yielding sequence information of an adequate quality. This rapid, cost effective protocol is practical for large scale virus diversity and evolutionary studies.

Symptom development of a plant viral disease is a result of molecular interactions between the virus and its host plant; thus, the elucidation of specific interactions is a prerequisite to reveal the mechanism of viral pathogenesis. Here, we show that the chloroplast precursor of ferredoxin-5 (Fd V) from maize (Zea mays) interacts with the multifunctional HC-Pro protein of sugar cane mosaic virus (SCMV) in yeast, Nicotiana benthamiana cells and maize protoplasts. Our results demonstrate that the transit peptide rather than the mature protein of Fd V precursor could interact with both N-terminal (residues 1-100) and C-terminal (residues 301-460) fragments, but not the middle part (residues 101-300), of HC-Pro. In addition, SCMV HC-Pro interacted only with Fd V, and not with the other two photosynthetic ferredoxin isoproteins (Fd I and Fd II) from maize plants. SCMV infection significantly downregulated the level of Fd V mRNA in maize plants; however, no obvious changes were observed in levels of Fd I and Fd II mRNA. These results suggest that SCMV HC-Pro interacts specifically with maize Fd V and that this interaction may disturb the post-translational import of Fd V into maize bundle-sheath cell chloroplasts, which could lead to the perturbation of chloroplast structure and function.

RNA silencing and suppression of silencing are host and virus interactions for defense and counter-defense. Here, we explored the function effect of HC-Pro encoded by Sugarcane mosaic virus (SCMV) on the suppression of RNA silencing. siRNA northern blotting assay indicated that the replication of SCMV was regulated by host RNA silencing machinery. Co-expression assay demonstrated that the HC-Pro encoded by SCMV suppressed the RNA silencing induced by sense RNA and dsRNA. Transitive RNA silencing assay showed that HC-Pro down-regulated the accumulation of 3' secondary siRNA, but not 5' secondary and primary siRNA. Meanwhile, the 2b gene of Tomato aspermy cucumovirus (Tav) evidently down-regulated the accumulation of 5' secondary siRNA. Importantly, we found that HC-Pro and Tav2b down-regulated the accumulation of RDR6 mRNA. Thus, HC-Pro, an RNA silencing suppressor encoded by SCMV, regulates the accumulation of different siRNAs and has more than one target in the RNA silencing pathway.

The genomes of Spanish isolates of Maize dwarf mosaic virus (MDMV-Sp) and Sugarcane mosaic virus (SCMV-Sp) were completely sequenced. Nucleotide sequence identities of SCMV-Sp to those of other SCMV isolates ranged from 79 to 90%. MDMV-Sp shared 85% nucleotide identity with the only other fully sequenced isolate of MDMV. MDMV-Sp and SCMV-Sp differed from each other by 31% in their nucleotide sequences. Phylogenetic analyses showed that SCMV isolates group by host rather than by geographical location. Two significant recombination signals were identified in the NIa and NIb regions of the SCMV-Sp genome.

The gene action of 2 sugarcane mosaic virus (SCMV) resistance loci in maize, Scmv1 and Scmv2, was evaluated for potyvirus resistance in an isogenic background. All 4 homozygous and 5 heterozygous isogenic genotypes were produced for introgressions of the resistant donor (FAP1360A) alleles at both loci into the susceptible parent (F7) genetic background using simple sequence repeat markers. For SCMV and maize dwarf mosaic virus (MDMV), virus symptoms appeared rapidly in the 3 homozygous genotypes, with susceptibility alleles fixed at 1 or both loci. Although the 9 isogenic genotypes revealed a high level of resistance to Zea mosaic virus (ZeMV), the same 3 homozygous genotypes were only partially resistant. This indicates that 1 resistance gene alone is not sufficient for complete resistance against SCMV, MDMV, and ZeMV. Scmv1 showed strong early and complete dominant gene action to SCMV, but it gradually became partially dominant. Scmv2 was not detected at the beginning, showing dominant gene action initially and additive gene action at later stages. Both genes interacted epistatically (for a high level of resistance, at least 1 resistance allele at each of both loci is required). This implies that double heterozygotes at the 2 loci are promising for producing SCMVresistant hybrids. Results are discussed with respect to prospects for isolation of SCMV and MDMV resistance genes.