Wheat streak mosaic virus: a century old virus with rising importance worldwide

Viral Challenges in Wheat: Comprehensive Diagnosis and Innovative Management Approaches

Wheat (Triticum aestivum L.) is a staple crop cultivated globally, providing essential nutrition to billions. However, viral diseases pose a major challenge, causing yield losses of up to 80% and significant economic damage. More than 50 distinct viruses infect wheat, with key threats including wheat streak mosaic virus (WSMV), barley yellow dwarf viruses (BYDVs), high plains wheat mosaic virus (HPWMoV), soilborne wheat mosaic virus (SBWMV), and wheat yellow mosaic virus (WYMV). These viruses are primarily transmitted by vectors such as wheat curl mites (Aceria tosichella), aphids, and soilborne fungi like Polymyxa graminis. Diagnosing wheat viral infections is challenging due to overlapping symptoms with other plant stresses and the microscopic nature of viruses. Recent advancements in molecular and serological diagnostics, including Enzyme-Linked Immunosorbent Assay (ELISA), RT-Polymerase Chain Reaction (RT-PCR), CRISPR-based detection, and biosensors, have improved virus identification and monitoring. Since chemical treatments are ineffective, integrated management strategies such as breeding virus-resistant varieties, controlling vector populations, adjusting cultural practices, and utilizing RNA interference (RNAi) are essential for mitigating disease spread. This review provides a comprehensive analysis of wheat viral diseases, focusing on cutting-edge diagnostic tools and sustainable management approaches. By addressing knowledge gaps and highlighting future research directions, it aims to support the development of virus-resistant wheat, ensuring global food security.

Plant Viral Synergism: Co-expression of P1 and NIaPro Cistrons of Wheat Streak Mosaic Virus and Triticum Mosaic Virus Is Required for Synergistic Interaction in Wheat

Synergistic interactions among unrelated viruses in mixed infections can cause significant yield losses, and viral determinants of these interactions are poorly understood. Wheat (Triticum aestivum L.) co-infection with wheat curl mite-transmitted wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) results in disease synergism with a drastically increased symptom phenotype of stunted growth, leaf bleaching, and enhanced titers of both viruses compared with individual virus infections. In this study, we examined the viral determinants responsible for WSMV-TriMV disease synergism through transient expression of select cistrons of WSMV in wheat through TriMV and vice-versa. We found that expression of WSMV P1, NIa, or NIaPro in wheat through TriMV or vice-versa elicited moderate to severe symptoms with a moderate or no increase in virus titer. However, co-expression of P1 and NIaPro of WSMV in wheat through TriMV or vice-versa exhibited a WSMV-TriMV disease synergism-like phenotype with enhanced accumulation of genomic RNA copies and coat protein. Additionally, we found that the P3 of both viruses is dispensable for synergism. HCPro and NIaVPg of WSMV and TriMV are not the primary determinants but might have a minor role in efficient synergism. In co-infected wheat, the accumulation of virus-specific small interfering RNAs (vsiRNAs) was increased, similar to viral genomic RNA copies, despite the presence of two viral RNA-silencing suppressors (VRSS), which function through sequestration of vsiRNAs. Our findings revealed that WSMV-TriMV disease synergism is not caused by the suppression of host posttranscriptional gene silencing by two VRSS proteins in co-infected wheat, and the P1 and NIaPro of both viruses collectively drive synergistic interactions between WSMV and TriMV in wheat. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2025.

Triticum mosaic virus: An overview of biology, functional genomics, gene expression vector, and management strategies

Triticum mosaic virus (TriMV; Poacevirus tritici) is the founding member of the genus Poacevirus within the family Potyviridae. TriMV is one of the components of the wheat streak mosaic disease (WSMD) complex, an economically significant wheat disease in the Great Plains region of the USA. TriMV contains a single-stranded positive-sense RNA genome of 10,266 nts with an unusually long 5'-nontranslated region of 739 nts. TriMV is transmitted only by the Type-2 genotype of wheat curl mites (Aceria tosichella Keifer) and is mostly found as a co-infection with another wheat curl mite-transmitted wheat streak mosaic virus (WSMV). TriMV and WSMV synergistically interact in co-infected wheat with exacerbated disease symptoms. The development of an infectious cDNA clone and GFP or RFP-tagged stable expression vectors has advanced the functional genomics of TriMV, including virus-virus and virus-host interactions. NIa-Pro and CP, and P1 and NIa-Pro cistrons of TriMV are identified as elicitors of superinfection exclusion and determinants of synergistic interaction with WSMV, respectively. TriMV stably maintained P1 (1083 nts) plus NIa (1305 nts) cistrons of WSMV for more than 28 days postinoculation, suggesting that TriMV can be used as a stable gene expression vector in wheat. Because of the synchrony of the mites and viruses in this disease complex, primary management efforts should focus on the timing and presence of vector hosts. Importantly, an enhanced understanding of TriMV biology and its interactions with plants, mites, and WSMV will facilitate the development of effective tools to improve the sustainable management of the wheat-mite-virus complex.

Sensing Technologies for Outdoor/Indoor Farming

To face the increasing requirement for grains as the global population continues to grow, improving both crop yield and quality has become essential. Plant health directly impacts crop quality and yield, making the development of plant health-monitoring technologies essential. Variable sensing technologies for outdoor/indoor farming based on different working principles have emerged as important tools for monitoring plants and their microclimates. These technologies can detect factors such as plant water content, volatile organic compounds (VOCs), and hormones released by plants, as well as environmental conditions like humidity, temperature, wind speed, and light intensity. To achieve comprehensive plant health monitoring for multidimensional assessment, multimodal sensors have been developed. Non-invasive monitoring approaches are also gaining attention, leveraging biocompatible and flexible sensors for plant monitoring without interference with its natural growth. Furthermore, wireless data transmission is crucial for real-time monitoring and efficient farm management. Reliable power supplies for these systems are vital to ensure continuous operation. By combining wearable sensors with intelligent data analysis and remote monitoring, modern agriculture can achieve refined management, resource optimization, and sustainable production, offering innovative solutions to global food security and environmental challenges.

Viromes of Monocotyledonous Weeds Growing in Crop Fields Reveal Infection by Several Viruses Suggesting Their Virus Reservoir Role

In 2019, random samples of Panicum miliaceum growing as a weed were surveyed to uncover their virus infections at two locations in Hungary. This pilot study revealed infection with three viruses, two appearing for the first time in the country. As follow-up research, in the summer of 2021, we collected symptomatic leaves of several monocotyledonous plants in the same locations and determined their viromes using small RNA high-throughput sequencing (HTS). As a result, we have identified the presence of wheat streak mosaic virus (WSMV), barley yellow striate mosaic virus (BYSMV), barley virus G (BVG), and two additional viruses, namely Aphis glycines virus 1 (ApGlV1) and Ljubljana dicistrovirus 1 (LDV1), which are described for the first time in Hungary. New hosts of the viruses were identified: Cynodon dactylon is a new host of BYSMV and LDV1, Echinocloa crus-galli is a new host of BVG, ApGlV1 and LDV1, Sorghum halepense is a new host of ApGlV1, and Panicum miliaceum is a new host of LDV1. At the same time, Zea mays is a new host of ApGlV1 and LDV1. Small RNA HTS diagnosed acute infections but failed to detect persistent ones, which could be revealed using RT-PCR. The infection rates at the different locations and plant species were different. The phylogenetic analyses of the sequenced virus variants suggest that the tested monocotyledonous weeds can host different viruses and play a virus reservoir role. Viral spread from the reservoir species relies on the activity of insect vectors, which is why their management requires an active role in plant protection strategies, which need careful planning in the changing environment.

Viral Threats to Fruit and Vegetable Crops in the Caribbean

Viruses pose major global challenges to crop production as infections reduce the yield and quality of harvested products, hinder germplasm exchange, increase financial inputs, and threaten food security. Small island or archipelago habitat conditions such as those in the Caribbean are particularly susceptible as the region is characterized by high rainfall and uniform, warm temperatures throughout the year. Moreover, Caribbean islands are continuously exposed to disease risks because of their location at the intersection of transcontinental trade between North and South America and their role as central hubs for regional and global agricultural commodity trade. This review provides a summary of virus disease epidemics that originated in the Caribbean and those that were introduced and spread throughout the islands. Epidemic-associated factors that impact disease development are also discussed. Understanding virus disease epidemiology, adoption of new diagnostic technologies, implementation of biosafety protocols, and widespread acceptance of biotechnology solutions to counter the effects of cultivar susceptibility remain important challenges to the region. Effective integrated disease management requires a comprehensive approach that should include upgraded phytosanitary measures and continuous surveillance with rapid and appropriate responses.

Distribution of Wheat-Infecting Viruses and Genetic Variability of Wheat Streak Mosaic Virus and Barley Stripe Mosaic Virus in Kazakhstan

Wheat is an essential cereal crop for the economy and food safety of Kazakhstan. In the present work, a screening of wheat and barley from different regions of Kazakhstan was conducted using newly developed specific primers for reverse transcription PCR and loop-mediated isothermal amplification (LAMP) assays. In total, 82 and 19 of 256 samples of wheat and barley tested positive for wheat streak mosaic virus (WSMV) and barley stripe mosaic virus (BSMV), respectively. A phylogenetic analysis using two independent methods revealed that most of the analyzed isolates had a European origin. Molecular data on the distribution and diversity of cereal viruses in Kazakhstan were obtained for the first time and will help lay a foundation for the implementation of genetics and genomics in wheat phyto-epidemiology in the country.

Evaluation of Seed Transmission Rates of Wheat Streak Mosaic Virus in Mechanically Inoculated Winter and Spring Wheat Cultivars in Montana

Wheat streak mosaic disease is caused by wheat streak mosaic virus (WSMV) and two other viruses and persistently limits wheat yields in the Great Plains region of the United States. Seed transmission of viruses is an important consideration in international movement and is important epidemiologically. Seed transmission of WSMV in wheat was first reported from Australia in 2005, but there is little data from United States cultivars on the rate of seed transmission. In 2018, mechanically inoculated winter and spring wheat cultivars were evaluated in Montana. We found differences in WSMV seed transmission rates between winter and spring wheat, with average transmission rates in spring wheat (3.1%) being five times higher compared to winter wheat (0.6%). Seed transmission rates in spring wheat were twice as high as the highest previously reported transmission rate for individual genotypes, 1.5%. The results from this study provide a strong argument for increasing the current testing of seed for breeding purposes prior to international movement when WSMV has been observed and caution against using grain from WSMV-infected fields as seed source because it can heighten the risk of wheat streak mosaic outbreaks.

Analysis of Wheat Virome in Korea Using Illumina and Oxford Nanopore Sequencing Platforms

Wheat (Triticum aestivum L.) is one of the most important staple crops in the world, along with maize and rice. More than 50 plant viruses are known to infect wheat worldwide. To date, there are no studies on the identification of viruses infecting wheat in Korea. Therefore, we investigated virome in wheat from three different geographical regions where wheat is mainly cultivated in Korea using Oxford Nanopore Technology (ONT) sequencing and Illumina sequencing. Five viral species, including those known to infect wheat, were identified using high-throughput sequencing strategies. Of these, barley virus G (BVG) and Hordeum vulgare endornavirus (HvEV) were consistently present in all libraries. Sugarcane yellow leaf virus (SCYLV) and wheat leaf yellowing-associated virus (WLYaV) were first identified in Korean wheat samples. The viruses identified by ONT and Illumina sequencing were compared using a heatmap. Though the ONT sequencing approach is less sensitive, the analysis results were similar to those of Illumina sequencing in our study. Both platforms served as reliable and powerful tools for detecting and identifying wheat viruses, achieving a balance between practicality and performance. The findings of this study will provide deeper insights into the wheat virosphere and further help improve disease management strategies.

6K1, NIa-VPg, NIa-Pro, and CP of Wheat Streak Mosaic Virus Are Collective Determinants of Wheat Streak Mosaic Disease in Wheat

Wheat streak mosaic virus (WSMV; genus Tritimovirus, family Potyviridae) is the causal agent of the most economically important wheat streak mosaic disease of wheat (Triticum aestivum) in the Great Plains region of the United States. WSMV determinants responsible for wheat streak mosaic disease in wheat are unknown. Triticum mosaic virus (TriMV), a wheat-infecting virus, was used as an expression vector for the transient expression of each of the WSMV-encoded cistrons in wheat. WSMV-encoded 6K1, NIa-VPg, NIa-Pro, and CP cistrons in TriMV elicited symptoms specific to different stages of wheat streak mosaic disease without significantly affecting the genomic RNA accumulation. WSMV 6K1 produced early wheat streak mosaic disease-like symptoms of severe chlorotic streaks and patches. NIa-VPg and CP caused severe chlorotic streaks, followed by moderate stunting (only with NIa-VPg) of wheat, mimicking early- and mid-stage symptoms of wheat streak mosaic disease. WSMV NIa-Pro caused mild chlorotic streaks, followed by dark green leaves with severe stunting, representing the late symptoms of wheat streak mosaic disease. Collectively, these data suggest that cumulative effects of WSMV-encoded 6K1, NIa-VPg, NIa-Pro, and CP are responsible for different stages of wheat streak mosaic disease symptoms in wheat. Furthermore, deletion analysis of wheat streak mosaic disease determinants revealed that complete 6K1 and NIa-Pro, amino acids 3 to 60 and 121 to 197 of NIa-VPg, and amino acids 101 to 294 of CP are responsible for wheat streak mosaic disease-like symptoms in wheat. This study suggests that management strategies for wheat streak mosaic disease in wheat should target WSMV determinants of the disease phenotype.

Plant Viruses of Agricultural Importance: Current and Future Perspectives of Virus Disease Management Strategies

Plant viruses cause significant losses in agricultural crops worldwide, affecting the yield and quality of agricultural products. The emergence of novel viruses or variants through genetic evolution and spillover from reservoir host species, changes in agricultural practices, mixed infections with disease synergism, and impacts from global warming pose continuous challenges for the management of epidemics resulting from emerging plant virus diseases. This review describes some of the most devastating virus diseases plus select virus diseases with regional importance in agriculturally important crops that have caused significant yield losses. The lack of curative measures for plant virus infections prompts the use of risk-reducing measures for managing plant virus diseases. These measures include exclusion, avoidance, and eradication techniques, along with vector management practices. The use of sensitive, high throughput, and user-friendly diagnostic methods is crucial for defining preventive and management strategies against plant viruses. The advent of next-generation sequencing technologies has great potential for detecting unknown viruses in quarantine samples. The deployment of genetic resistance in crop plants is an effective and desirable method of managing virus diseases. Several dominant and recessive resistance genes have been used to manage virus diseases in crops. Recently, RNA-based technologies such as dsRNA- and siRNA-based RNA interference, microRNA, and CRISPR/Cas9 provide transgenic and nontransgenic approaches for developing virus-resistant crop plants. Importantly, the topical application of dsRNA, hairpin RNA, and artificial microRNA and trans-active siRNA molecules on plants has the potential to develop GMO-free virus disease management methods. However, the long-term efficacy and acceptance of these new technologies, especially transgenic methods, remain to be established.

Comparative profiling of volatile organic compounds associated to temperature sensitive resistance to wheat streak mosaic virus (WSMV) in resistant and susceptible wheat cultivars at normal and elevated temperatures

To investigate changes in wheat resistance to wheat streak mosaic virus (WSMV) at normal and elevated temperatures and their effects on the emission of volatile organic compounds (VOCs), the profile of these compounds in WSMV-resistant (R) and susceptible (S) wheat cultivars were analyzed. VOCs were discovered in leaves of R and S cultivars inoculated to WSMV at 20 °C and 32 °C at 24, 48 and 72 h post inoculation (hpi) by GC. MS-HS-SPME. Many VOCs and related metabolic pathways of WSMV inoculated and control plants responded differently at low/high temperatures in R/S cultivars. Compounds such as 6-methyl-5-hepten-2-one and heptanal, represented the maximum abundance in R plants compared to S plants at earlier times especially, 48 hpi/20 °C. Also, at 32 °C, VOCs including heptanal and 2-pentenal had the highest increase in abundance at a later time. In addition, in R plants, several pathways were up-regulated commonly at 20 °C and 32 °C. Although, at 20 °C, they were activated at an earlier time. At 32 °C, most of these pathways were up-regulated at 72 hpi. The most important pathways correlated to combined stresses included lipoxygenase, cuticular wax biosynthesis, fatty acid and lipid biosynthesis. The pathway of phenyl ethanol biosynthesis was up-regulated only at 32 °C, which probably is specifically related to resistance to heat stress. Up-regulation of the lipoxygenase pathway appears to increase vector attractiveness and tolerance to biotic and abiotic stresses. Based on these results, is suggested that there is a particular synchronized regulation of defense-related multi-dimensional VOCs emitting network that is necessary for the occurrence of wheat defense responses against WSMV and/or heat. This research highlights the challenge of global warming and the breakdown of plant resistance to viruses which requires metabolic engineering of VOCs for sustainable agriculture.

Genomic High Plains Wheat Mosaic Virus Sequences from Australia: Their Phylogenetics and Evidence for Emaravirus Recombination and Reassortment

High Plains wheat mosaic virus (HPWMoV) causes a serious disease in major wheat-growing regions worldwide. We report here the complete or partial genomic sequences of five HPWMoV isolates from Australian wheat samples. Phylogenetic analysis of the nucleotide sequences of the eight genomic segments of these five isolates together with others from Genbank found all eight genes formed two lineages, L1 and L2. L1 contained a single isolate from Colorado in the North American Great Plains Region (GPR), and L2 had two unresolved clusters, A and B, of isolates from Australia and the GPR. A quarter of the L2B isolate sequences of the nucleocapsid gene (RNA3) were recombinant, which is unexpected as little evidence of recombination exists in viruses with negative single-stranded RNA genomes. Phylogenies calculated from the amino acid sequences of HPWMoV's RNA-dependent RNA-polymerase (RNA1), glycoprotein (RNA2), and nucleocapsid protein (RNA3) showed they were closest to those of Palo Verde broom virus. However, its movement protein (RNA4) was closer to those of Ti ringspot-associated and common oak ringspot-associated viruses, indicating the RNA4 segments of their ancestors reassorted to produce the current emaraviruses. To avoid increased yield losses from co-infection, biosecurity measures are advised to avoid HPWMoV introduction to countries where wheat streak mosaic virus already occurs.

Important wheat diseases in the US and their management in the 21st century

Wheat is a crop of historical significance, as it marks the turning point of human civilization 10,000 years ago with its domestication. Due to the rapid increase in population, wheat production needs to be increased by 50% by 2050 and this growth will be mainly based on yield increases, as there is strong competition for scarce productive arable land from other sectors. This increasing demand can be further achieved using sustainable approaches including integrated disease pest management, adaption to warmer climates, less use of water resources and increased frequency of abiotic stress tolerances. Out of 200 diseases of wheat, 50 cause economic losses and are widely distributed. Each year, about 20% of wheat is lost due to diseases. Some major wheat diseases are rusts, smut, tan spot, spot blotch, fusarium head blight, common root rot, septoria blotch, powdery mildew, blast, and several viral, nematode, and bacterial diseases. These diseases badly impact the yield and cause mortality of the plants. This review focuses on important diseases of the wheat present in the United States, with comprehensive information of causal organism, economic damage, symptoms and host range, favorable conditions, and disease management strategies. Furthermore, major genetic and breeding efforts to control and manage these diseases are discussed. A detailed description of all the QTLs, genes reported and cloned for these diseases are provided in this review. This study will be of utmost importance to wheat breeding programs throughout the world to breed for resistance under changing environmental conditions.

CRISPR/Cas technology: Opportunities for phytopathogenic viruses detection

Detection and monitoring of viruses are essential for healthy plants and prosperity. Recent development in CRISPR/Cas system in diagnosis has open an avenue well suited for pathogen detection. Variety of CRISPR associated proteins are being discovered, suggesting array of application and detection strategies in diagnosis. Phytopathogenic viruses are diverse with respect to their nucleic acid compositions, which presents a challenge in developing a single device applicable for almost all viruses. The review describes about the efficient use of CRISPR/Cas Technology in diagnosis, such as SHERLOCK, DETECTR and SATORI. These methods are different in their characteristic to identify specific nucleic acids and processing the detectable signals. These technologies are in their infancy and lot of scope is there to develop commercial kits. Plant tissue culture-based industries, climate control green houses, indoor cultivation facilities etc. has been considered as few examples. This review will be beneficial for researchers seeking to develop detection mechanism based on CRISPR/Cas technology. The outcome in the form of cost-effective detection of viruses will be boon for agro-based industries, which are facing challenges through virus contamination.

Resistance genes on the verge of plant-virus interaction

Viruses are acellular pathogens that cause severe infections in plants, resulting in worldwide crop losses every year. The lack of chemical agents to control viral diseases exacerbates the situation. Thus, to devise proper management strategies, it is important that the defense mechanisms of plants against viruses are understood. Resistance (R) genes regulate plant defense against invading pathogens by eliciting a hypersensitive response (HR). Compatible interaction between plant R gene and viral avirulence (Avr) protein activates the necrotic cell death response at the site of infection, resulting in the cessation of disease. Here, we review different aspects of R gene-mediated dominant resistance against plant viruses in dicotyledonous plants and possible ways for developing crops with better disease resistance.

Effective specialist or jack of all trades? Experimental evolution of a crop pest in fluctuating and stable environments

Understanding pest evolution in agricultural systems is crucial for developing effective and innovative pest control strategies. Types of cultivation, such as crop monocultures versus polycultures or crop rotation, may act as a selective pressure on pests' capability to exploit the host's resources. In this study, we examined the herbivorous mite Aceria tosichella (commonly known as wheat curl mite), a widespread wheat pest, to understand how fluctuating versus stable environments influence its niche breadth and ability to utilize different host plant species. We subjected a wheat-bred mite population to replicated experimental evolution in a single-host environment (either wheat or barley), or in an alternation between these two plant species every three mite generations. Next, we tested the fitness of these evolving populations on wheat, barley, and on two other plant species not encountered during experimental evolution, namely rye and smooth brome. Our results revealed that the niche breadth of A. tosichella evolved in response to the level of environmental variability. The fluctuating environment expanded the niche breadth by increasing the mite's ability to utilize different plant species, including novel ones. Such an environment may thus promote flexible host-use generalist phenotypes. However, the niche expansion resulted in some costs expressed as reduced performances on both wheat and barley as compared to specialists. Stable host environments led to specialized phenotypes. The population that evolved in a constant environment consisting of barley increased its fitness on barley without the cost of utilizing wheat. However, the population evolving on wheat did not significantly increase its fitness on wheat, but decreased its performance on barley. Altogether, our results indicated that, depending on the degree of environmental heterogeneity, agricultural systems create different conditions that influence pests' niche breadth evolution, which may in turn affect the ability of pests to persist in such systems.

Occurrence of Wheat Curl Mite and Mite-Vectored Viruses of Wheat in Colorado and Insights into the Wheat Virome

The wheat curl mite (WCM) is a vector of three important wheat viruses in the U.S. Great Plains: wheat streak mosaic virus (WSMV), triticum mosaic virus (TriMV), and High Plains wheat mosaic virus (HPWMoV). This study was conducted to determine the current profile of WCM and WCM-transmitted viruses of wheat and their occurrence in Colorado, including novel wheat viruses via virome analysis. There was a high rate of virus incidence in symptomatic wheat samples collected in 2019 (95%) and 2020 (77%). Single infection of WSMV was most common in both years, followed by coinfection with WSMV + TriMV and WSMV + HPWMoV. Both type 1 and type 2 mite genotypes were found in Colorado. There was high genetic diversity of WSMV and HPWMoV isolates, whereas TriMV isolates showed minimal sequence variation. Analysis of WSMV isolates revealed novel virus variants, including one isolate from a variety trial, where severe disease symptoms were observed on wheat varieties carrying Wsm2, a known virus resistance locus. Virome analysis identified two to four sequence variants of all eight RNA segments of HPWMoV, which suggests co-occurrence of multiple genotypes within host populations and presence of a variant of HPWMoV. A possible novel virus in the family Tombusviridae and several mycoviruses were identified. Overall, the data presented here highlight the need to define the effect of novel WCM-transmitted virus variants on disease severity and the role of novel viruses.

Challenges and opportunities for plant viruses under a climate change scenario

There is an increasing societal awareness on the enormous threat that climate change may pose for human, animal and plant welfare. Although direct effects due to exposure to heat, drought or elevated greenhouse gasses seem to be progressively more obvious, indirect effects remain debatable. A relevant aspect to be clarified relates to the relationship between altered environmental conditions and pathogen-induced diseases. In the particular case of plant viruses, it is still unclear whether climate change will primarily represent an opportunity for the emergence of new infections in previously uncolonized areas and hosts, or if it will mostly be a strong constrain reducing the impact of plant virus diseases and challenging the pathogen's adaptive capacity. This review focuses on current knowledge on the relationship between climate change and the outcome plant-virus interactions. We summarize work done on how this relationship modulates plant virus pathogenicity, between-host transmission (which include the triple interaction plant-virus-vector), ecology, evolution and management of the epidemics they cause. Considering these studies, we propose avenues for future research on this subject.

Genomic and Molecular Characterization of Wheat Streak Mosaic Virus Resistance Locus 2 (Wsm2) in Common Wheat (Triticum aestivum L.)

Wheat streak mosaic virus (WSMV) is an economically important viral pathogen that threatens global wheat production, particularly in the Great Plains of the United States. The Wsm2 locus confers resistance to WSMV and has been widely deployed in common wheat varieties adapted to this region. Characterizing the underlying causative genetic variant would contribute to our understanding of viral resistance mechanisms in wheat and aid the development of perfect markers for breeding. In this study, linkage mapping in a doubled-haploid (DH) mapping population confirmed Wsm2 as a major locus conferring WSMV resistance in wheat. The Wsm2 flanking markers were mapped to a 4.0 Mbp region at the distal end of chromosome 3BS containing 142 candidate genes. Eight haplotypes were identified from seventeen wheat genotypes collected from different agroecological zones, indicating that Wsm2 lies in a dynamic region of the genome with extensive structural variation and that it is likely a rare allele in most available genome assemblies of common wheat varieties. Exome sequencing of the variety "Snowmass", which carries Wsm2, revealed several loss-of-function mutations and copy number variants in the 142 candidate genes within the Wsm2 interval. Six of these genes are differentially expressed in "Snowmass" compared to "Antero," a variety lacking Wsm2, including a gene that encodes a nucleotide-binding site leucine-rich repeat (NBS-LRR) type protein with homology to RPM1. A de novo assembly of unmapped RNA-seq reads identified nine transcripts expressed only in "Snowmass," three of which are also induced in response to WSMV inoculation. This study sheds light on the variation underlying Wsm2 and provides a list of candidate genes for subsequent validation.

Occurrence and Characterization of Wheat Streak Mosaic Virus Found in Mono- and Mixed Infection with High Plains Wheat Mosaic Virus in Winter Wheat in Ukraine

Although wheat streak mosaic virus (WSMV) is a well-known pathogen inducing significant crop losses and endangering wheat production worldwide, the recent discovery of High Plains wheat mosaic virus (HPWMoV) in Ukraine raises questions on the co-existence of these two viruses having a similar host range and the same mite vector. Here we report on the screening of winter wheat industrial plantings in several important regions of Ukraine for WSMV and HPWMoV. WSMV was identified in an extremely high number of symptomatic plants (>85%) as compared to HPWMoV detected in 40% of wheat samples. Importantly, the preferred mode of HPWMoV circulation in Ukraine was mixed infection with WSMV (>30%) as opposed to WSMV, which was typically found in monoinfection (60%). Screening wheat varieties for possible virus resistance indicated that all but one were susceptible to WSMV, whereas over 50% of the same varieties were not naturally infected with HPWMoV. Overall, phylogenetic analysis of the collected WSMV and HPWMoV isolates indicated their high identity and similarity to other known isolates of the respective viruses. Here we first characterize WSMV isolates found in winter wheat plants in mono- or mixed infection with HPWMoV, which was recently reported as a typical wheat pathogen in Ukraine.

Virus Diseases of Cereal and Oilseed Crops in Australia: Current Position and Future Challenges

This review summarizes research on virus diseases of cereals and oilseeds in Australia since the 1950s. All viruses known to infect the diverse range of cereal and oilseed crops grown in the continent's temperate, Mediterranean, subtropical and tropical cropping regions are included. Viruses that occur commonly and have potential to cause the greatest seed yield and quality losses are described in detail, focusing on their biology, epidemiology and management. These are: barley yellow dwarf virus, cereal yellow dwarf virus and wheat streak mosaic virus in wheat, barley, oats, triticale and rye; Johnsongrass mosaic virus in sorghum, maize, sweet corn and pearl millet; turnip yellows virus and turnip mosaic virus in canola and Indian mustard; tobacco streak virus in sunflower; and cotton bunchy top virus in cotton. The currently less important viruses covered number nine infecting nine cereal crops and 14 infecting eight oilseed crops (none recorded for rice or linseed). Brief background information on the scope of the Australian cereal and oilseed industries, virus epidemiology and management and yield loss quantification is provided. Major future threats to managing virus diseases effectively include damaging viruses and virus vector species spreading from elsewhere, the increasing spectrum of insecticide resistance in insect and mite vectors, resistance-breaking virus strains, changes in epidemiology, virus and vectors impacts arising from climate instability and extreme weather events, and insufficient industry awareness of virus diseases. The pressing need for more resources to focus on addressing these threats is emphasized and recommendations over future research priorities provided.

Impact of Wheat Streak Mosaic Virus on Peroxisome Proliferation, Redox Reactions, and Resistance Responses in Wheat

Although peroxisomes play an essential role in viral pathogenesis, and viruses are known to change peroxisome morphology, the role of genotype in the peroxisomal response to viruses remains poorly understood. Here, we analyzed the impact of wheat streak mosaic virus (WSMV) on the peroxisome proliferation in the context of pathogen response, redox homeostasis, and yield in two wheat cultivars, Patras and Pamir, in the field trials. We observed greater virus content and yield losses in Pamir than in Patras. Leaf chlorophyll and protein content measured at the beginning of flowering were also more sensitive to WSMV infection in Pamir. Patras responded to the WSMV infection by transcriptional up-regulation of the peroxisome fission genes PEROXIN 11C (PEX11C), DYNAMIN RELATED PROTEIN 5B (DRP5B), and FISSION1A (FIS1A), greater peroxisome abundance, and activation of pathogenesis-related proteins chitinase, and β-1,3-glucanase. Oppositely, in Pamir, WMSV infection suppressed transcription of peroxisome biogenesis genes and activity of chitinase and β-1,3-glucanase, and did not affect peroxisome abundance. Activity of ROS scavenging enzymes was higher in Patras than in Pamir. Thus, the impact of WMSV on peroxisome proliferation is genotype-specific and peroxisome abundance can be used as a proxy for the magnitude of plant immune response.

Full Genome Evolutionary Studies of Wheat Streak Mosaic-Associated Viruses Using High-Throughput Sequencing

Wheat streak mosaic (WSM), a viral disease affecting cereals and grasses, causes substantial losses in crop yields. Wheat streak mosaic virus (WSMV) is the main causal agent of the complex, but mixed infections with Triticum mosaic virus (TriMV) and High plains wheat mosaic emaravirus (HPWMoV) were reported as well. Although resistant varieties are effective for the disease control, a WSMV resistance-breaking isolate and several potential resistance-breaking isolates have been reported, suggesting that viral populations are genetically diverse. Previous phylogenetic studies of WSMV were conducted by focusing only on the virus coat protein (CP) sequence, while there is no such study for either TriMV or HPWMoV. Here, we studied the genetic variation and evolutionary mechanisms of natural populations of WSM-associated viruses mainly in Kansas fields and fields in some other parts of the Great Plains using high-throughput RNA sequencing. In total, 28 historic and field samples were used for total RNA sequencing to obtain full genome sequences of WSM-associated viruses. Field survey results showed WSMV as the predominant virus followed by mixed infections of WSMV + TriMV. Phylogenetic analyses of the full genome sequences demonstrated that WSMV Kansas isolates are widely distributed in sub-clades. In contrast, phylogenetic analyses for TriMV isolates showed no significant diversity. Recombination was identified as the major evolutionary force of WSMV and TriMV variation in KS fields, and positive selection was detected in some encoding genomic regions in the genome of both viruses. Furthermore, the full genome sequence of a second Kansas HPWMoV isolate was reported. Here, we also identified previously unknown WSMV isolates in the Great Plains sharing clades and high nucleotide sequence similarities with Central Europe isolates. The findings of this study will provide more insights into the genetic structure of WSM-associated viruses and, in turn, help in improving strategies for disease management.

Resistance to the wheat curl mite and mite-transmitted viruses: challenges and future directions

Wheat curl mite (WCM) is the only known arthropod vector of four wheat viruses, the most important of which is Wheat streak mosaic virus (WSMV). Host resistance to WCM and WSMV is limited to a small number of loci, most of which are introgressed from wild relatives and are often associated with linkage drag and temperature sensitivity. Reports of virulent WCM populations and potential resistance-breaking WSMV isolates highlight the need for more diverse sources of resistance. Genome sequencing will be critical to fully characterize the genetic diversity in WCM and WSMV populations to better understand the incidence of WCM-transmitted viruses and to evaluate the potential stability of resistance genes. Characterizing host resistance genes will help build a mechanistic understanding of wheat-WCM-WSMV interactions and inform strategies to identify and engineer more durable resistance sources.

Temperature-dependent development and survival of an invasive genotype of wheat curl mite, Aceria tosichella

Quantifying basic biological data, such as the effects of variable temperatures on development and survival, is crucial to predicting and monitoring population growth rates of pest species, many of which are highly invasive. One of the most globally important pests of cereals is the eriophyoid wheat curl mite (WCM), Aceria tosichella, which is the primary vector of several plant viruses. The aim of this study was to evaluate temperature-dependent development and survival of WCM at a wide range of constant temperatures in the laboratory (17-33 °C). The development time of each stage depended significantly on temperature and it was negatively correlated with temperature increase. At high temperatures (27-33 °C), individuals had shorter developmental times, with the shortest (6 days) at 33 °C, whereas at the lowest tested temperatures (17-19 °C), developmental time was almost 3× longer. Moreover, temperature had a clear effect on survival: the higher the temperature, the lower the survival rate. These data provide information promoting more efficient and effective manipulation of WCM laboratory colonies, and further our understanding of the ramifications of temperature change on WCM physiology and implications for the growth and spread of this globally invasive pest.

Development of an RT-PCR assay to detect genetically divergent wheat streak mosaic virus isolates for plant quarantine inspections in South Korea

Wheat streak mosaic virus (WSMV), a member of the genus Tritimovirus in the family Potyviridae, has been designated as a plant quarantine pathogen in South Korea. Several diagnostic methods can be applied to diagnose viral infections in plants, but polymerase chain reaction and enzyme-linked immunosorbent assay, which can identify viral species with speed and accuracy, are mainly used in Korean plant quarantine. Many variants of different viral species with highly divergent genomic sequences are constantly being discovered by high-throughput sequencing technology. This means that previously established primers may no longer be suitable for diagnostic use. In this study, we developed a reverse transcription polymerase chain reaction assay for detecting WSMV isolates/strains using all of the WSMV sequences available in NCBI GenBank. All 13 primer sets were able to produce amplicons of the expected sizes from WSMV-infected samples. To check whether nonspecific reactions occur, some closely related viruses (one tritimovirus and five potyviruses) and target imported plants (wheat, maize, oat, and proso millet) were tested. Consequently, four primer sets, which did not produce nonspecific bands, were finally selected among the 13 primer sets. Concentration-dependent amplification tests showed that the four primer sets are adequate for use in the diagnosis of WSMV in Korean plant quarantine.

Global Plant Virus Disease Pandemics and Epidemics

The world's staple food crops, and other food crops that optimize human nutrition, suffer from global virus disease pandemics and epidemics that greatly diminish their yields and/or produce quality. This situation is becoming increasingly serious because of the human population's growing food requirements and increasing difficulties in managing virus diseases effectively arising from global warming. This review provides historical and recent information about virus disease pandemics and major epidemics that originated within different world regions, spread to other continents, and now have very wide distributions. Because they threaten food security, all are cause for considerable concern for humanity. The pandemic disease examples described are six (maize lethal necrosis, rice tungro, sweet potato virus, banana bunchy top, citrus tristeza, plum pox). The major epidemic disease examples described are seven (wheat yellow dwarf, wheat streak mosaic, potato tuber necrotic ringspot, faba bean necrotic yellows, pepino mosaic, tomato brown rugose fruit, and cucumber green mottle mosaic). Most examples involve long-distance virus dispersal, albeit inadvertent, by international trade in seed or planting material. With every example, the factors responsible for its development, geographical distribution and global importance are explained. Finally, an overall explanation is given of how to manage global virus disease pandemics and epidemics effectively.

A Newly Identified Virus in the Family Potyviridae Encodes Two Leader Cysteine Proteases in Tandem That Evolved Contrasting RNA Silencing Suppression Functions

Potyviridae is the largest family of plant-infecting RNA viruses and includes many agriculturally and economically important viral pathogens. The viruses in the family, known as potyvirids, possess single-stranded, positive-sense RNA genomes with polyprotein processing as a gene expression strategy. The N-terminal regions of potyvirid polyproteins vary greatly in sequence. Previously, we identified a novel virus species within the family, Areca palm necrotic spindle-spot virus (ANSSV), which was predicted to encode two cysteine proteases, HCPro1 and HCPro2, in tandem at the N-terminal region. Here, we present evidence showing self-cleavage activity of these two proteins and define their cis-cleavage sites. We demonstrate that HCPro2 is a viral suppressor of RNA silencing (VSR), and both the variable N-terminal and conserved C-terminal (protease domain) moieties have antisilencing activity. Intriguingly, the N-terminal region of HCPro1 also has RNA silencing suppression activity, which is, however, suppressed by its C-terminal protease domain, leading to the functional divergence of HCPro1 and HCPro2 in RNA silencing suppression. Moreover, the deletion of HCPro1 or HCPro2 in a newly created infectious clone abolishes viral infection, and the deletion mutants cannot be rescued by addition of corresponding counterparts of a potyvirus. Altogether, these data suggest that the two closely related leader proteases of ANSSV have evolved differential and essential functions to concertedly maintain viral viability.IMPORTANCE The Potyviridae represent the largest group of known plant RNA viruses and account for more than half of the viral crop damage worldwide. The leader proteases of viruses within the family vary greatly in size and arrangement and play key roles during the infection. Here, we experimentally demonstrate the presence of a distinct pattern of leader proteases, HCPro1 and HCPro2 in tandem, in a newly identified member within the family. Moreover, HCPro1 and HCPro2, which are closely related and typically characterized with a short size, have evolved contrasting RNA silencing suppression activity and seem to function in a coordinated manner to maintain viral infectivity. Altogether, the new knowledge fills a missing piece in the evolutionary relationship history of potyvirids and improves our understanding of the diversification of potyvirid genomes.

Millet Could Be both a Weed and Serve as a Virus Reservoir in Crop Fields

Millet is a dangerous weed in crop fields. A lack of seed dormancy helps it to spread easily and be present in maize, wheat, and other crop fields. Our previous report revealed the possibility that millet can also play a role as a virus reservoir. In that study, we focused on visual symptoms and detected the presence of several viruses in millet using serological methods, which can only detect the presence of the investigated pathogen. In this current work, we used small RNA high-throughput sequencing as an unbiased virus diagnostic method to uncover presenting viruses in randomly sampled millet grown as a volunteer weed in two maize fields, showing stunting, chlorosis, and striped leaves. Our results confirmed the widespread presence of wheat streak mosaic virus at both locations. Moreover, barley yellow striate mosaic virus and barley virus G, neither of which had been previously described in Hungary, were also identified. As these viruses can cause severe diseases in wheat and other cereals, their presence in a weed implies a potential infection risk. Our study indicates that the presence of millet in fields requires special control to prevent the emergence of new viral diseases in crop fields.

A novel cysteine-rich receptor-like kinase gene, TaCRK2, contributes to leaf rust resistance in wheat

Leaf rust, caused by Puccinia triticina, is one of the most destructive fungal diseases in wheat production worldwide. The hypersensitive reaction (HR) is an important defence response against P. triticina infection. In this study, the physiological races 165 and 260 of P. triticina were combined with a line derived from the bread wheat cultivar Thatcher with the leaf rust resistance locus Lr26 to form compatible and incompatible combinations, respectively. Based on an RNA-Seq database of the interaction systems, a new wheat cysteine-rich receptor-like kinase gene, TaCRK2, is specifically induced and up-regulated in the incompatible combination. We identified that TaCRK2 was regulated in a Ca²⁺ -dependent manner. Knockdown of TaCRK2 by virus-induced gene silencing and RNAi leads to a dramatic increase in HR area and the number of haustorial mother cells at the single infection site. In addition, urediniospores, a P. triticina-specific pathogenic marker in compatible combinations, were observed on leaf surfaces of silenced plants at approximately 15 days after inoculation in the incompatible combination. Moreover, transcription levels of TaPR1, TaPR2, and TaPR5 were obviously reduced in TaCRK2-silenced plants. TaCRK2 overexpression in Nicotiana benthamiana induced strong HR-like cell death. Finally, transient expression of green fluorescent protein fused with TaCRK2 in N. benthamiana indicated that TaCRK2 localizes in the endoplasmic reticulum. Thus, TaCRK2 plays an important role in the resistance to P. triticina infection and has a positive regulation effect on the HR cell death process induced by P. triticina.

The Biological Impact of the Hypervariable N-Terminal Region of Potyviral Genomes

Potyviridae is the largest family of plant-infecting RNA viruses, encompassing over 30% of known plant viruses. The family is closely related to animal picornaviruses such as enteroviruses and belongs to the picorna-like supergroup. Like all other picorna-like viruses, potyvirids employ polyprotein processing as a gene expression strategy and have single-stranded, positive-sense RNA genomes, most of which are monopartite with a long open reading frame. The potyvirid polyproteins are highly conserved in the central and carboxy-terminal regions. In contrast, the N-terminal region is hypervariable and contains position-specific mutations resulting from transcriptional slippage during viral replication, leading to translational frameshift to produce additional viral proteins essential for viral infection. Some potyvirids even lack one of the N-terminal proteins P1 or helper component-protease and have a genus-specific or species-specific protein instead. This review summarizes current knowledge about the conserved and divergent features of potyvirid genomes and biological relevance and discusses future research directions.

RNAi-Mediated Resistance Against Viruses in Perennial Fruit Plants

Small RNAs (sRNAs) are 20–30-nucleotide-long, regulatory, noncoding RNAs that induce silencing of target genes at the transcriptional and posttranscriptional levels. They are key components for cellular functions during plant development, hormone signaling, and stress responses. Generated from the cleavage of double-stranded RNAs (dsRNAs) or RNAs with hairpin structures by Dicer-like proteins (DCLs), they are loaded onto Argonaute (AGO) protein complexes to induce gene silencing of their complementary targets by promoting messenger RNA (mRNA) cleavage or degradation, translation inhibition, DNA methylation, and/or histone modifications. This mechanism of regulating RNA activity, collectively referred to as RNA interference (RNAi), which is an evolutionarily conserved process in eukaryotes. Plant RNAi pathways play a fundamental role in plant immunity against viruses and have been exploited via genetic engineering to control disease. Plant viruses of RNA origin that contain double-stranded RNA are targeted by the RNA-silencing machinery to produce virus-derived small RNAs (vsRNAs). Some vsRNAs serve as an effector to repress host immunity by capturing host RNAi pathways. High-throughput sequencing (HTS) strategies have been used to identify endogenous sRNA profiles, the “sRNAome”, and analyze expression in various perennial plants. Therefore, the review examines the current knowledge of sRNAs in perennial plants and fruits, describes the development and implementation of RNA interference (RNAi) in providing resistance against economically important viruses, and explores sRNA targets that are important in regulating a variety of biological processes.

Convergent Evolution of Effector Protease Recognition by Arabidopsis and Barley

The Pseudomonas syringae cysteine protease AvrPphB activates the Arabidopsis resistance protein RPS5 by cleaving a second host protein, PBS1. AvrPphB induces defense responses in other plant species, but the genes and mechanisms mediating AvrPphB recognition in those species have not been defined. Here, we show that AvrPphB induces defense responses in diverse barley cultivars. We also show that barley contains two PBS1 orthologs, that their products are cleaved by AvrPphB, and that the barley AvrPphB response maps to a single locus containing a nucleotide-binding leucine-rich repeat (NLR) gene, which we termed AvrPphB Response 1 (Pbr1). Transient coexpression of PBR1 with wild-type AvrPphB but not with a protease inactive mutant triggered defense responses, indicating that PBR1 detects AvrPphB protease activity. Additionally, PBR1 coimmunoprecipitated with barley and Nicotiana benthamiana PBS1 proteins, suggesting mechanistic similarity to detection by RPS5. Lastly, we determined that wheat cultivars also recognize AvrPphB protease activity and contain two putative Pbr1 orthologs. Phylogenetic analyses showed, however, that Pbr1 is not orthologous to RPS5. Our results indicate that the ability to recognize AvrPphB evolved convergently and imply that selection to guard PBS1-like proteins occurs across species. Also, these results suggest that PBS1-based decoys may be used to engineer protease effector recognition-based resistance in barley and wheat.