Search Results (317)

Saffron (Crocus sativus L.) is a vegetatively propagated crop of high economic and cultural value, potentially affected by viral infections that may impact its productivity. Despite Iran’s dominance in global saffron production, knowledge of its virome remains limited. In this study, we conducted the first nationwide virome survey of saffron in Iran employing a high-throughput sequencing (HTS) approach on pooled samples obtained from eleven provinces in Iran and one location in Afghanistan. Members of three virus families were detected—Potyviridae (Potyvirus), Solemoviridae (Polerovirus), and Geminiviridae (Mastrevirus)—as well as one satellite from the family Alphasatellitidae (Clecrusatellite). A novel Potyvirus, tentatively named saffron Iran virus (SaIRV) and detected in three provinces, shares less than 68% nucleotide identity with known Potyvirus species, thus meeting the ICTV criteria for designation as a new species. Genetic diversity analyses revealed substantial intrapopulation SNP variation but no clear geographical clustering. Among the two wild Crocus species sampled, only Crocus speciosus harbored turnip mosaic virus. Virome network and phylogenetic analyses confirmed widespread viral circulation likely driven by corm-mediated propagation. Our findings highlight the need for targeted certification programs and biological characterization of key viruses to mitigate potential impacts on saffron yield and quality. Full article

Cowpea (Vigna unguiculata) is a crop of significant socioeconomic importance, particularly in the semi-arid regions of Africa and America. However, its productivity has been adversely affected by viral diseases, including the cowpea aphid-borne mosaic virus (CABMV), a single-stranded RNA virus. It is known that the VPg protein interacts with the host’s translation initiation factor (eIF4E), promoting viral replication. This study aimed to investigate the relationship between mutations in the cowpea eIF4E gene and resistance to CABMV. Twenty-seven cultivars were screened by PCR and bioassays for presence/absence of mutations associated with resistance or susceptibility to Potyviruses. Of the cultivars with mutations previously associated with susceptibility, 88.24% exhibited viral symptoms, while 62.5% associated with resistance remained asymptomatic. The in silico analyses revealed that non-synonymous mutations (Pro68Arg, Gly109Arg) alter the structure of the eIF4E protein, reducing its affinity to VPg. Molecular dynamics simulations also pointed to an enhanced structural stability of eIF4E in resistant cultivars and reinforced, for the first time, key mutations and the functional role of the eIF4E gene in resistance to CABMV in cowpea. Our results offer valuable insights for virus disease management and for genetic improvement programs for this important crop. Full article

The wheat curl mite (WCM, Aceria tosichella Keifer), a complex of eriophyid mite species, transmits wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV), which in single or mixed infections cause wheat streak mosaic (WSM) disease—a major threat to wheat production across the U.S. Great Plains. Resistant wheat cultivars bearing Cmc3 and Cmc4 (targeting WCM), Wsm1 and Wsm2 (targeting WSMV), and Wsm1 (targeting TriMV) are widely used to manage this pest–pathogen complex. However, comprehensive studies investigating how these resistance mechanisms influence both vector biology and virus transmission remain scarce. To address this gap, we evaluated disease development and WCM fitness across nine wheat cultivars with differential resistance profiles under single and mixed infections of WSMV and TriMV. We found strong viral synergy in co-infected plants, with TriMV accumulation markedly enhanced during mixed infections, irrespective of host genotype. Symptom severity and virus titers (both WSMV and TriMV) were highest in the cultivars carrying Wsm2, suggesting a potential trade-off in resistance effectiveness under mixed infection pressure. While mite development time (egg to adult) was unaffected by host genotype or infection status, mite fecundity was significantly reduced on infected plants carrying Wsm1 or Wsm2, but not on those with Cmc3 and Cmc4. Notably, virus accumulation in mites was reduced on the cultivars with Cmc3 and Cmc4, correlating with virus titers in the host tissues. Our findings highlight the complex interplay between host resistance, virus dynamics, and vector performance. Cultivars harboring Cmc3 and Cmc4 may offer robust field-level protection by simultaneously suppressing mite reproduction and limiting virus accumulation in both plant and vector. Full article

Soybean mosaic virus (SMV) causes systemic infections in soybean plants, leading to chlorotic mosaic and significant yield losses. In Argentina, during the 1990s, three isolates were collected in Marcos Juárez (MJ), Manfredi (M), and Northwestern Argentina (NOA), along with the “Planta Vinosa” (PV) isolate, which causes severe necrosis in some cultivars. These isolates were freeze-dried and stored at −70 °C for several years. They were recovered by mechanical inoculation and biologically, molecularly, and physiologically characterized for the first time. Three of the four isolates showed low genetic divergence in the P1, CI, and CP genes. Although SMV-NOA and SMV-PV had high nucleotide sequence identity, they differed in pathogenicity, seed mottling, and transmission efficiency by seeds or aphids. SMV-NOA caused early changes in photosystem II quantum efficiency (ɸPSII) and malondialdehyde (MDA) content before symptom expression (BS). After symptom development (LS), SMV-M significantly increased MDA, total soluble sugars, and starch compared to the other isolates. Thus, early changes in ɸPSII and sugars may influence late viral symptoms. Likewise, SMV-MJ induced more severe symptoms in the susceptible Davis cultivar than in Don Mario 4800. Therefore, our results demonstrate genomic, biological, and physiological differences among SMV isolates and variable interactions of SMV-MJ with two soybean cultivars. Full article

Beans (Phaseolus vulgaris and P. lunatus) are the major hosts of bean golden mosaic begomovirus (BGMV). Robust taxonomic criteria were established for Begomovirus species demarcation. However, DNA–A identities among BGMV isolates display a continuous variation (89–100%), which conflicts with the current concept of a single viral species. The diversity of 146 Brazilian isolates designated in the GenBank as BGMV was assessed by comparing their complete DNA–A sequences. The isolates were clustered into four groups, being discriminated mainly by their original Fabaceae hosts. Additional Sequence Demarcation Tool analyses indicated that BGMV-related viruses comprise two clear-cut groups: isolates reported infecting mainly P. vulgaris (identities of 96–97% to the reference NC_004042 isolate) and a group associated with P. lunatus (identities of 89–91%). Moreover, we recognized a distinct set of genomic features in the iterons and Rep-associated protein motifs across these two diversity groups. The host prevalence and genomic differences suggest that most P. lunatus isolates are currently misclassified as BGMV strains, being more likely samples of a closely related (but distinct) Begomovirus species. Hence, the implications of this BGMV diversity should be taken into consideration by classical and biotech breeding programs aiming for large-spectrum viral resistance in Phaseolus species. Full article

A dearth of knowledge exists on identifying the begomoviruses and distributing cassava mosaic viruses across key cassava-growing regions of Sierra Leone. The study aimed to identify and map the distribution of cassava mosaic disease (CMD)-associated viruses in farmers’ fields in Sierra Leone. Cassava (Manihot esculenta Crantz) leaf samples were collected in 109 smallholder farms during a geo-referenced survey conducted from 10th May to 5th June 2024. Molecular diagnostics were carried out to identify the viral strains associated with CMD. Findings revealed that infection by stem cutting was more predominant in the south, east, north, and northwest regions than in the west region. In contrast, infection by whitefly was predominant in the west, north, and northwest regions. PCR screening of 426 samples coupled with sequence analysis revealed the presence of African cassava mosaic-like (ACMV-like) viruses, and East African cassava mosaic-like (EACMV-like) viruses as single infections at 78.1% and 1.3%, respectively. Co-infections of ACMV-like and EACMV-like viruses were detected in 20.6% of the tested samples. In addition, 70.6% of the samples positive for EACMV-like virus (single and mixed infections) were found to be positive for East African cassava mosaic Cameroon virus (EACMCMV). The ACMV and co-infection of ACMV and EACMV viruses were present in all regions, while EACMCV was detected in all regions except the western area. The results indicate more prevalence of the EACMCMV variant in Sierra Leone. This study suggests utilization of participatory surveillance and good agronomic practices to manage CMD in Sierra Leone. Full article

Kazakhstan is recognized as one of the primary centers of origin of the wild apple Malus sieversii, concentrated mainly in the mountains like Trans-Ile and Zhongar Alatau, as well as parts of the Tarbagatay, Talas Alatau, and Karatau ranges. As the wild progenitor of Malus domestica, M. sieversii harbors a critical genetic diversity essential for apple breeding and conservation efforts. However, its natural populations are increasingly threatened by latent viral infection, which weakens trees, reduces reproduction, and hinders regeneration. In this study, the spread of apple chlorotic leaf spot virus (ACLSV) and apple stem pitting virus (ASPV) was documented in four wild apple populations, with detection rates of 50.2% and 42.2%, respectively. Mixed infections were observed in 28.8% of sampled trees. Apple stem grooving virus (ASGV) was detected exclusively in cultivated orchards, whereas apple mosaic virus (ApMV) and apple necrotic mosaic virus (ApNMV) were not found in either wild forests or cultivated orchards. Using Geographic Information System (GIS) technology, we developed the first spatial distribution maps of these viruses in wild apple forests in the Tian Shan region, revealing site-specific variation and infection rates. These results underscore the importance of monitoring viral infections in wild M. sieversii populations to preserve genetically valuable, virus-free germplasm critical for apple breeding, crop improvement, and sustainable orchard management. Full article

Apple mosaic disease (AMD) is a widespread viral disease affecting apple-growing regions around the world. Recent studies have identified a novel ilarvirus, apple necrotic mosaic virus (ApNMV), as the major causal agent of AMD in China. However, the molecular mechanisms underlying AMD pathogenesis and the global gene expression changes during mosaic symptom development remain largely unknown. In this study, we performed transcriptome analysis to investigate apple gene responses to AMD. A total of 815 differentially expressed genes (DEGs) were identified in mosaic leaves compared to healthy controls, while 1050 DEGs were found between symptomless leaves (infected with ApNMV) and mosaic leaves. Functional enrichment analysis revealed that these DEGs were predominantly involved in carbohydrate metabolism, oxidation-reduction processes, secondary metabolite biosynthesis, and plant hormone signal transduction. Further biological assays demonstrated that the manifestation of mosaic symptoms in apple leaves was associated with reactive oxygen species (ROS) accumulation and downregulation of ROS-scavenging genes. Collectively, our findings provide new insights into the molecular basis of ApNMV-induced mosaic symptom development in apple and offer potential targets for the management of AMD. Full article

Viral infections in stone fruit crops cause substantial economic losses across all sectors of production. Despite their significance, viruses affecting stone fruits remain under-investigated in Kazakhstan. Among these, plum pox virus (PPV, genus Potyvirus, family Potyviridae), commonly known as Sharka, is the most critical viral pathogen worldwide, severely threatening the sustainable cultivation of stone fruits and posing risks to food security. This study aimed to evaluate virus management strategies in stone fruit crops to facilitate the production of healthy planting material from valuable genotypes. Field surveys were conducted in plum and apricot orchards located in the Almaty region (Southeast Kazakhstan) and the Saryagash region (Southern Kazakhstan). Plant samples were tested for the presence of the following viruses: apple chlorotic leaf spot virus (ACLSV), apple mosaic virus (ApMV), PPV, prune dwarf virus (PDV), prunus necrotic ringspot virus (PNRSV), cherry green ring mottle virus (CGRMV), and myrobalan latent ringspot virus (MLRSV). Real-time RT-PCR diagnostics confirmed the presence of PPV in the ‘Stanley’ and ‘Ansar’ cultivars and Prunus armeniaca genotypes, while both PPV and ACLSV were detected in the ‘Ayana’ variety. Chemotherapy (Ribavirin), thermotherapy, cryotherapy, and shoot apical meristem (SAM) culture, both individually and in combination, were used to eliminate viruses and regenerate virus-free plants. Successful virus eradication was achieved for PPV and ACLSV. However, the ‘Stanley’ and ‘Ansar’ cultivars did not survive the treatment process, likely due to high thermo- or cryo-sensitivity. As a result of this research, an in vitro collection of virus-free plants was established, comprising eight rootstocks, six plum cultivars, and three apricot genotypes. Full article

Tomato brown rugose fruit virus (ToBRFV) is a recently emerged viral pathogen in the Tobamovirus genus first observed in 2014 in the Middle East that has since spread worldwide, causing significant losses in greenhouse tomato production. ToBRFV is easily mechanically transmitted and can escape the durable Tm-2² resistance gene, facilitating its global spread. Seed companies have identified novel sources of resistance and introduced these resistance traits into commercial cultivars. The identity, number, and mechanisms of these putative novel resistance genes are largely unknown but could be exerting selective pressures on ToBRFV. Here, we report 15 new ToBRFV genomic sequences from Canadian greenhouse production systems in susceptible and novel resistant or tolerant cultivars collected since 2023. We combined these sequences with five other Canadian ToBRFV genomes previously deposited in Genbank and a further five consensus sequences derived from metagenomic-based wastewater monitoring sequence data and conducted phylogenetic analysis. Most Canadian sequences grouped together when compared with 332 publicly available international sequences, but several isolates appeared distantly related, suggesting multiple introductions to Canadian production systems. High sequence identity between samples suggest movement of ToBRFV between independent greenhouses, highlighting areas where biosecurity can be improved. Several novel non-synonymous polymorphisms identified in the p126 and movement protein (MP) open reading frames (ORFs) were unique to Canadian sequences and associated with infection of novel resistant tomato cultivars. Many polymorphisms in the p126 ORF are located in a region of the protein associated with Tm-1 resistance-breaking isolates of tomato mosaic virus and ToBRFV, but have not been previously reported. Four novel polymorphisms in MP were also identified and do not appear to be associated with sites previously identified as interacting with Tm-2² and could be related to other unknown resistance genes. Together, these results confirm the difficulties in preventing the transmission of ToBRFV, identify putative adaptations to novel and existing resistance genes, and emphasize the urgent need for the cloning and characterization of these new sources of resistance to ToBRFV. Full article

Peonies (Paeonia spp.) are renowned for their beautiful ornamental flowers and significant cultural, medicinal, and economic values. Based on growth habit, peonies are categorized into herbaceous and tree peonies. Viral infections in peonies, historically referred to as “peony ringspot” or “peony mosaic” diseases, have been reported worldwide over decades. Infections symptoms typically include leaf discoloration and diminished flowering, substantially reducing both ornamental and commercial quality. In severe cases, viral diseases can cause stunted plant growth and impaired flowering, directly affecting peony cultivation and the floriculture profitability. This review systematically summarizes the current research on key viral diseases in peonies, addressing disease classification, symptomatology, causative viruses, pathogenesis, molecular virus–host interactions, and contemporary approaches for prevention and management. The insights provided in this review offer a theoretical foundation and practical guidelines to facilitate effective control of peony viral diseases, potentially promoting sustainable development within the peony industry. Full article

Peaches (Prunus persica L. Batsch) and nectarines (Prunus persica L. Batsch var. nectarina [Ait.] Maxim) are economically important stone fruits consumed worldwide, both fresh and processed. Viruses and viroids significantly constrain the cultivation and productivity of peach orchards. Climate change may alter vector populations and lead to shifts in agricultural practices, influencing the spread of these viruses and viroids. Additionally, market globalization further intensifies the pressure on peach crops by facilitating the movement of pathogens, increasing the incidence of virus-induced diseases. In this study, we identified the viral and viroid communities in five peach cultivars from Bulgaria and assessed their impact on symptom development. RNA sequencing of symptomatic leaf samples revealed the presence of common peach viruses, such as plum pox virus and prunus necrotic ringspot virus. Notably, we identified peach latent mosaic viroid and cherry green ring mottle virus in Bulgarian peach orchards for the first time. Furthermore, bioassays of indicator plants, ELISA, and Sanger sequencing were performed for each peach tree to complement the RNA sequencing data. These findings provide valuable insights into the composition of viral and viroid pathogens affecting peaches in Bulgaria and will support the development of targeted strategies for monitoring and managing these pathogens, contributing to the sustainable production of peaches in the region. Full article

High-throughput sequencing (HTS) was employed for the first time to investigate plant viruses infecting solanaceous crops, including potato (Solanum tuberosum), tomato (Solanum lycopersicum), and pepper (Capsicum annuum), in Kosovo. Leaf samples showing virus-like symptoms were collected from various regions during the summer of 2023. Based on ribodepleted RNA sequencing and bioinformatics analysis, six viruses were identified: cucumber mosaic virus, broad bean wilt virus 2 (BBWV2), potato virus Y, pepper cryptic virus 2 (PCV2), bell pepper endornavirus (BPEV), and ranunculus white mottle virus. BBWV2, PCV2, and BPEV are reported for the first time in the Balkan region. Virus presence was validated using RT-PCR. Phylogenetic analyses revealed that the identified viral strains did not cluster according to their hosts and geographical origins. CMV and BBWV2 variants exhibited reassortment events, indicating possible local evolution or novel virus introductions. This research highlights the widespread occurrence of mixed infections in pepper plants and highlights the need for additional research into the virus transmission dynamics and potential reservoir hosts. These findings emphasize the need for continuous surveillance and integrated plant protection strategies to mitigate the impacts of viral infections on pepper and other economically important crops in Kosovo. Full article

Background: Cassava mosaic disease (CMD), caused by the Sri Lankan cassava mosaic virus (SLCMV), significantly increases cassava yield losses in Thailand, with losses ranging from 30% to 80%, and is exacerbated by limited access to healthy planting materials. Methods: This study explored salicylic acid (SA) as a potential treatment for enhancing disease resistance in CMD infected cassava plants. SA was applied at 100 and 200 mg/mL, and its effects were evaluated using quantitative real-time polymerase chain reaction (qPCR) and reverse transcription qPCR (RT-qPCR) to measure viral loads and the expression levels of resistance genes. Results: Although SA treatment did not considerably affect disease severity, foliar CMD symptoms visibly decreased, particularly with 200 mg/mL SA, which also reduced SLCMV particle counts at 1- and 2-weeks post-treatment. SA upregulated the expression of pathogenesis-related proteins (PRs), including HSP90.9, WRKY59, SRS1, and PR9e. Additionally, SA enhanced the regulation of secondary metabolite pathways involving L-serine within the glycine, serine, and threonine metabolism, as well as the phenylpropanoid biosynthesis pathways. Conclusions: These findings collectively indicate that SA enhances resistance through the systemic acquired resistance (SAR) pathway and can serve as a potential strategy for the management of CMD, particularly in regions where healthy cassava planting materials are scarce. The study highlights the efficacy of SA in reducing viral particles, inducing the immune response, and providing a promising approach for controlling CMD. Full article

Cassava mosaic disease (CMD) is caused by viruses such as Sri Lankan cassava mosaic virus (SLCMV). It poses a significant threat to the cassava (Manihot esculenta) yield in Southeast Asia. Here, we investigated the expression of WRKY transcription factors (TFs) in SLCMV-infected cassava cultivars KU 50 (tolerant) and R 11 (susceptible) at 21, 32, and 67 days post-inoculation (dpi), representing the early, middle/recovery, and late infection stages, respectively. The 34 identified WRKYs were classified into the following six groups based on the functions of their homologs in the model plant Arabidopsis thaliana (AtWRKYs): plant defense; plant development; hormone signaling (abscisic, salicylic, and jasmonic acid); reactive oxygen species production; basal immune mechanisms; and other related hormones, metabolites, and abiotic stress responses. Regarding the protein interactions of the identified WRKYs, based on the interactions of their homologs (AtWRKYs), WRKYs increased reactive oxygen species production, leading to salicylic acid accumulation and systemic acquired resistance (SAR) against SLCMV. Additionally, some WRKYs were involved in defense-related mitogen-activated protein kinase signaling and abiotic stress responses. Furthermore, crosstalk among WRKYs reflected the robustly restricted viral multiplication in the tolerant cultivar, contributing to CMD recovery. This study highlights the crucial roles of WRKYs in transcriptional reprogramming, innate immunity, and responses to geminivirus infections in cassava, providing valuable insights to enhance disease resistance in cassava and, potentially, other crops. Full article