Rationale for developing new virus vectors to analyze gene function in grasses through virus-induced gene silencing

Virus-Induced Gene Silencing in Wheat and Related Monocot Species

Advances made in genome sequencing projects and structural genomics are generating large repertoire of candidate genes in plants associated with specific agronomic traits. Rapid and high-throughput functional genomics approaches are therefore needed to validate the biological function of these genes especially for agronomically important crops beyond the few model plant species. This can be achieved by utilizing available gene knockout or transgenic methodologies, but these can take considerable time and effort particularly in crops with large and complex genomes such as wheat. Therefore, any tool that expedites the validation of gene function is of particular benefit especially in cereal crop plants that are genetically difficult to transform. One such reverse genetics tool is virus-induced gene silencing (VIGS) which relies on the plants' natural antiviral RNA silencing defence mechanism. VIGS is used to downregulate target gene expression in a transient manner which persists long enough to determine its effect on a specific trait. VIGS based on Barley stripe mosaic virus (BSMV) is rapid, powerful, efficient, and relatively inexpensive tool for the analysis of gene function in cereal species. Here we present detailed protocols for BSMV-mediated VIGS for robust gene silencing in bread wheat and related species.

An Efficient Brome mosaic virus-Based Gene Silencing Protocol for Hexaploid Wheat (Triticum aestivum L.)

Virus-induced gene silencing (VIGS) is a rapid and powerful method to evaluate gene function, especially for species like hexaploid wheat that have large, redundant genomes and are difficult and time-consuming to transform. The Brome mosaic virus (BMV)-based VIGS vector is widely used in monocotyledonous species but not wheat. Here we report the establishment of a simple and effective VIGS procedure in bread wheat using BMVCP5, the most recently improved BMV silencing vector, and wheat genes PHYTOENE DESATURASE (TaPDS) and PHOSPHATE2 (TaPHO2) as targets. Time-course experiments revealed that smaller inserts (~100 nucleotides, nt) were more stable in BMVCP5 and conferred higher silencing efficiency and longer silencing duration, compared with larger inserts. When using a 100-nt insert and a novel coleoptile inoculation method, BMVCP5 induced extensive silencing of TaPDS transcript and a visible bleaching phenotype in the 2nd to 5th systemically-infected leaves from nine to at least 28 days post inoculation (dpi). For TaPHO2, the ability of BMVCP5 to simultaneously silence all three homoeologs was demonstrated. To investigate the feasibility of BMV VIGS in wheat roots, ectopically expressed enhanced GREEN FLUORESCENT PROTEIN (eGFP) in a transgenic wheat line was targeted for silencing. Silencing of eGFP fluorescence was observed in both the maturation and elongation zones of roots. BMVCP5 mediated significant silencing of eGFP and TaPHO2 mRNA expression in roots at 14 and 21 dpi, and TaPHO2 silencing led to the doubling of inorganic phosphate concentration in the 2nd through 4th systemic leaves. All 54 wheat cultivars screened were susceptible to BMV infection. BMVCP5-mediated TaPDS silencing resulted in the expected bleaching phenotype in all eight cultivars examined, and decreased TaPDS transcript was detected in all three cultivars examined. This BMVCP5 VIGS technology may serve as a rapid and effective functional genomics tool for high-throughput gene function studies in aerial and root tissues and in many wheat cultivars.

Plant Virology Delivers Diverse Toolsets for Biotechnology

Over a hundred years of research on plant viruses has led to a detailed understanding of viral replication, movement, and host-virus interactions. The functions of vast viral genes have also been annotated. With an increased understanding of plant viruses and plant-virus interactions, various viruses have been developed as vectors to modulate gene expressions for functional studies as well as for fulfilling the needs in biotechnology. These approaches are invaluable not only for molecular breeding and functional genomics studies related to pivotal agronomic traits, but also for the production of vaccines and health-promoting carotenoids. This review summarizes the latest progress in these forefronts as well as the available viral vectors for economically important crops and beyond.

Gene silencing approaches through virus-based vectors: speeding up functional genomics in monocots

The design and use of existing VIGS vectors for revealing monocot gene functions are described and potential new vectors are discussed, which may expand their repertoire. Virus induced gene silencing (VIGS) is a method of transient gene silencing in plants, triggered by the use of modified viral vectors. VIGS has found widespread use in deciphering the functions of plant genes, mainly for dicots. In the last decade, however, its use in monocots has increased noticeably, involving not only previously described viruses for monocots, but also those described for dicots. Additional viruses have been modified for VIGS to bring a larger collection of monocots under the ambit of this method. For monocots, new methods of inoculation have been tried to obtain increased silencing efficiency. The issue of insert stability and duration of silencing have also been addressed by various research groups. VIGS has been used to unravel the functions of a fairly large collection of monocot genes. This review summarizes the above developments, bringing out some of the gaps in our understanding and identifies directions to develop this technology further in the coming years.

An efficient and improved method for virus-induced gene silencing in sorghum

BACKGROUND

Although the draft genome of sorghum is available, the understanding of gene function is limited due to the lack of extensive mutant resources. Virus-induced gene silencing (VIGS) is an alternative to mutant resources to study gene function. This study reports an improved and efficient method for Brome mosaic virus (BMV)-based VIGS in sorghum.

METHODS

Sorghum plants were rub-inoculated with sap prepared by grinding 2 g of infected Nicotiana benthamiana leaf in 1 ml 10 mM potassium phosphate buffer (pH 6.8) and 100 mg of carborundum abrasive. The sap was rubbed on two to three top leaves of sorghum. Inoculated plants were covered with a dome to maintain high humidity and kept in the dark for two days at 18 °C. Inoculated plants were then transferred to 18 °C growth chamber with 12 h/12 h light/dark cycle.

RESULTS

This study shows that BMV infection rate can be significantly increased in sorghum by incubating plants at 18 °C. A substantial variation in BMV infection rate in sorghum genotypes/varieties was observed and BTx623 was the most susceptible. Ubiquitin (Ubiq) silencing is a better visual marker for VIGS in sorghum compared to other markers such as Magnesium Chelatase subunit H (ChlH) and Phytoene desaturase (PDS). The use of antisense strand of a gene in BMV was found to significantly increase the efficiency and extent of VIGS in sorghum. In situ hybridization experiments showed that the non-uniform silencing in sorghum is due to the uneven spread of the virus. This study further demonstrates that genes could also be silenced in the inflorescence of sorghum.

CONCLUSION

In general, sorghum plants are difficult to infect with BMV and therefore recalcitrant to VIGS studies. However, by using BMV as a vector, a BMV susceptible sorghum variety, 18 °C for incubating plants, and antisense strand of the target gene fragment, efficient VIGS can still be achieved in sorghum.

Barley stripe mosaic virus (BSMV) as a virus-induced gene silencing vector in maize seedlings

Barley stripe mosaic virus (BSMV) was the first reported and still widely used virus-induced gene silencing (VIGS) vector for monocotyledons including wheat and barley. Despite BSMV's reported infectivity on maize (Zea mays), the use of the virus as a vector in maize has not been optimized. Here, we assayed infectivity of BSMV in different maize cultivars by vascular puncture inoculation. Through knockdown of the endogenous host phytoene desaturase gene, we demonstrate for the first time that BSMV can be used as a VIGS vector in maize. This adds BSMV to the repertoire of tools available for functional studies in maize.

Use of a Virus Gene Silencing Vector for Maize Functional Genomics Research

Virus-induced gene silencing (VIGS) is a genetic technology that exploits the RNA-mediated defense against virus. The method has great potential for plant reverse genetics as it could knock down gene expression in a rapid way, which is triggered by a replicating viral genome engineered to carry a fragment of host gene to be silenced. A number of efficient VIGS vectors are available for dicots, such as for model plant Nicotiana benthamiana; however, only a few of VIGS vectors for monocotyledonous cereal crops. Here, we describe the method for the use of a newly developed VIGS vector based on a maize-infecting Cucumber mosaic virus (CMV) strain ZMBJ-CMV for maize. The RNA2 of ZMBJ-CMV was modified as a vector pCMV201-2b_N81 having multiple cloning sites for the insert of 100-300 bp fragment of target gene. Using a method of vascular puncture inoculation of maize seeds with crude sap prepared from Agrobacterium-infiltrated N. benthamiana leaves, silencing of target genes could be obtained in 4 weeks.

Virus-Induced Gene Silencing (VIGS) in Aegilops tauschii and Its Use in Functional Analysis of AetDREB2

Among the available reverse genetic approaches for studying gene function, virus-induced gene silencing (VIGS) has several advantages. It allows rapid characterization of gene function independent of stable transformation, which is basically difficult to achieve in monocots, and offers the potential to silence individual or multiple genes of a gene family. In order to establish a VIGS system in Aegilops tauschii, modified vectors derived from Barley stripe mosaic virus (BSMV) were used for silencing a phytoene desaturase gene that provides a convenient visual reporter for silencing. The results demonstrated a high efficiency of BSMV-VIGS in A. tauschii. Moreover, the BSMV-VIGS system was used to target a 354 bp specific region of the Dehydration-responsive element-binding (AetDreb2) gene, resulting in successful silencing of the gene in A. tauschii plants, as verified by real-time qRT-PCR. Indeed, in comparison with plants that were inoculated with an empty vector (BSMV:00), a faster rate of wilting and a lower relative water content were observed in plants inoculated with BSMV:AetDreb2 when they were exposed to drought stress. Therefore, BSMV-VIGS can be efficiently employed as a novel tool for reverse genetics in A. tauschii. It can also be used to study the effects of polyploidization on the gene function by a comparative analysis between bread wheat and its diploid progenitor.

Analysis of the Role of the Drought-Induced Gene DRI15 and Salinity-Induced Gene SI1 in Alternanthera philoxeroides Plasticity Using a Virus-Based Gene Silencing Tool

Alternanthera philoxeroides is a notoriously invasive weed that can readily adapt to different environmental conditions. Control of this weed is difficult, and it spreads easily and causes damage to native habitats and agriculture. In this study, our goal was to investigate the molecular mechanisms that lead to the ability of A. philoxeroides to invade new habitats, to adapt to environmental stresses, and to cause damage. We developed a simple and highly effective potato virus X-based virus-induced gene silencing (VIGS) approach. The VIGS approach was first used to silence the phytoene desaturase gene, which resulted in the expected photo-bleaching phenotype. Next, the VIGS approach was used to silence two additional genes, drought-induced protein gene 15 (ApDRI15) and salinity-induced protein gene 1 (ApSI1). When ApDRI15 was knocked down, the plants were more sensitive to drought stress than the control plants, with smaller leaves, shorter internodes, and lower biomass. The ApDRI15-silenced plants had lower relative water content, lower free proline levels, and higher water loss rates than the control. Silencing of ApSI1 significantly decreased tolerance to salinity, and the ApSI1-silenced plants were withered and smaller. These results indicate that the pgR107 VIGS approach is a simple and highly effective tool for dissecting gene function in A. philoxeroides. Further experiments with the VIGS approach will enhance our understanding of the molecular mechanisms of the adaptability and plasticity of A. philoxeroides and improve our ability to combat the damage caused by this weed.

An efficient virus-induced gene silencing vector for maize functional genomics research

Maize is a major crop whose rich genetic diversity provides an advanced resource for genetic research. However, a tool for rapid transient gene function analysis in maize that may be utilized in most maize cultivars has been lacking, resulting in reliance on time-consuming stable transformation and mutation studies to obtain answers. We developed an efficient virus-induced gene silencing (VIGS) vector for maize based on a naturally maize-infecting cucumber mosaic virus (CMV) strain, ZMBJ-CMV. An infectious clone of ZMBJ-CMV was constructed, and a vascular puncture inoculation method utilizing Agrobacterium was optimized to improve its utility for CMV infection of maize. ZMBJ-CMV was then modified to function as a VIGS vector. The ZMBJ-CMV vector induced mild to moderate symptoms in many maize lines, making it useful for gene function studies in critically important maize cultivars, such as the sequenced reference inbred line B73. Using this CMV VIGS system, expression of two endogenous genes, ZmPDS and ZmIspH, was found to be decreased by 75% and 78%, respectively, compared with non-silenced tissue. Inserts with lengths of 100-300 bp produced the most complete transcriptional and visual silencing phenotypes. Moreover, genes related to autophagy, ZmATG3 and ZmATG8a, were also silenced, and it was found that they function in leaf starch degradation. These results indicate that our ZMBJ-CMV VIGS vector provides a tool for rapid and efficient gene function studies in maize.

Identification of an attenuated barley stripe mosaic virus for the virus-induced gene silencing of pathogenesis-related wheat genes

BACKGROUND

Virus-induced gene silencing (VIGS) has become an emerging technology for the rapid, efficient functional genomic screening of monocot and dicot species. The barley stripe mosaic virus (BSMV) has been described as an effective VIGS vehicle for the evaluation of genes involved in wheat and barley phytopathogenesis; however, these studies have been obscured by BSMV-induced phenotypes and defense responses. The utility of BSMV VIGS may be improved using a BSMV genetic background which is more tolerable to the host plant especially upon secondary infection of highly aggressive, necrotrophic pathogens such as Fusarium graminearum.

RESULTS

BSMV-induced VIGS in Triticum aestivum (bread wheat) cv. 'Fielder' was assessed for the study of wheat genes putatively related to Fusarium Head Blight (FHB), the necrotrophism of wheat and other cereals by F. graminearum. Due to the lack of 'Fielder' spike viability and increased accumulation of Fusarium-derived deoxynivalenol contamination upon co-infection of BSMV and FHB, an attenuated BSMV construct was generated by the addition of a glycine-rich, C-terminal peptide to the BSMV γ b protein. This attenuated BSMV effectively silenced target wheat genes while limiting disease severity, deoxynivalenol contamination, and yield loss upon Fusarium co-infection compared to the original BSMV construct. The attenuated BSMV-infected tissue exhibited reduced abscisic, jasmonic, and salicylic acid defense phytohormone accumulation upon secondary Fusarium infection. Finally, the attenuated BSMV was used to investigate the role of the salicylic acid-responsive pathogenesis-related 1 in response to FHB.

CONCLUSIONS

The use of an attenuated BSMV may be advantageous in characterizing wheat genes involved in phytopathogenesis, including Fusarium necrotrophism, where minimal viral background effects on defense are required. Additionally, the attenuated BSMV elicits reduced defense hormone accumulation, suggesting that this genotype may have applications for the investigation of phytohormone-related signaling, developmental responses, and pathogen defense.

Strategies for altering plant traits using virus-induced gene silencing technologies

The rapid progress in genome sequencing and transcriptome analysis in model and crop plants has made possible the identification of a vast number of genes potentially associated with economically important complex traits. The ultimate goal is to assign functions to these genes by using forward and reverse genetic screens. Plant viruses have been developed for virus-induced gene silencing (VIGS) to generate rapid gene knockdown phenotypes in numerous plant species. To fulfill its potential for high-throughput phenomics, it is of prime importance to ensure that parameters conditioning the VIGS response, i.e., plant-virus interactions and associated loss-of-function screens, are "fit for purpose" and optimized to unequivocally conclude the role of a gene of interest in relation to a given trait. This chapter will review and discuss the different strategies used for the development of VIGS-based phenomics in model and crop species.

Virus-induced gene silencing (VIGS) for functional genomics in rice using Rice tungro bacilliform virus (RTBV) as a vector

The large-scale functional analysis of genes in plants depends heavily on robust techniques for gene silencing. Virus-induced gene silencing (VIGS) is a transient gene silencing method for plants, triggered by the inoculation of a modified viral vector carrying a fragment of the gene targeted for silencing. Here we describe a VIGS protocol for rice, based on the Rice tungro bacilliform virus (RTBV, a DNA virus). We present an updated and detailed protocol for silencing of the gene encoding Phytoene desaturase in rice, using the RTBV-VIGS system.

Maize Elongin C interacts with the viral genome-linked protein, VPg, of Sugarcane mosaic virus and facilitates virus infection

The viral genome-linked protein, VPg, of potyviruses is involved in viral genome replication and translation. To determine host proteins that interact with Sugarcane mosaic virus (SCMV) VPg, a yeast two-hybrid screen was used and a maize (Zea mays) Elongin C (ZmElc) protein was identified. ZmELC transcript was observed in all maize organs, but most highly in leaves and pistil extracts, and ZmElc was present in the cytoplasm and nucleus of maize cells in the presence or absence of SCMV. ZmELC expression was increased in maize tissue at 4 and 6 d post SCMV inoculation. When ZmELC was transiently overexpressed in maize protoplasts the accumulation of SCMV RNA was approximately doubled compared with the amount of virus in control protoplasts. Silencing ZmELC expression using a Brome mosaic virus-based gene silencing vector (virus-induced gene silencing) did not influence maize plant growth and development, but did decrease RNA accumulation of two isolates of SCMV and host transcript encoding ZmeIF4E during SCMV infection. Interestingly, Maize chlorotic mottle virus, from outside the Potyviridae, was increased in accumulation after silencing ZmELC expression. Our results describe both the location of ZmElc expression in maize and a new activity associated with an Elc: support of potyvirus accumulation.

Virus-induced gene silencing is a versatile tool for unraveling the functional relevance of multiple abiotic-stress-responsive genes in crop plants

Virus-induced gene silencing (VIGS) is an effective tool for gene function analysis in plants. Over the last decade, VIGS has been successfully used as both a forward and reverse genetics technique for gene function analysis in various model plants, as well as crop plants. With the increased identification of differentially expressed genes under various abiotic stresses through high-throughput transcript profiling, the application of VIGS is expected to be important in the future for functional characterization of a large number of genes. In the recent past, VIGS was proven to be an elegant tool for functional characterization of genes associated with abiotic stress responses. In this review, we provide an overview of how VIGS is used in different crop species to characterize genes associated with drought-, salt-, oxidative- and nutrient-deficiency-stresses. We describe the examples from studies where abiotic stress related genes are characterized using VIGS. In addition, we describe the major advantages of VIGS over other currently available functional genomics tools. We also summarize the recent improvements, limitations and future prospects of using VIGS as a tool for studying plant responses to abiotic stresses.