Large year-to-year variation in the composition of YDV strains in Nebraska cereal crops is demonstrated and the utility of multiplex RT-PCR for field diagnosis is confirmed, supporting the role of aphid vectors in shaping strain distribution and composition.
Abstract
Yellow dwarf viruses (YDV), comprising strains of barley yellow dwarf virus (BYDV) and cereal yellow dwarf virus (CYDV), cause economically important diseases in cereal crops in the United States. Although YDV are widespread in Nebraska, information on species distribution and their temporal variability is limited. A statewide survey was conducted during the 2023 and 2024 growing seasons to characterize YDV strain diversity and associated aphid vectors in cereal crops. Total RNA was extracted from symptomatic leaf samples collected from commercial and experimental fields, and viral detection was performed using a multiplex one-step reverse transcription polymerase chain reaction (RT-PCR). Aphid abundance was assessed separately using Berlese funnel from the field-collected plant materials, and species were determined morphologically. In 2023, 68.1% (644/946) of the tested samples were positive for at least one YDV strain, whereas in 2024, only 25.5% (144/564) of the samples tested positive. BYDV-SGV was the predominant strain in 2023, particularly in oats and wheat, whereas SGV+MAV and RPV+SGV strains were the most common coinfections. In contrast, CYDV-RPV and BYDV-MAV predominated in wheat and barley in 2024, whereas PAV was most frequently detected in oats. The bird cherry-oat aphid (Rhopalosiphum padi) was the most abundant aphid species across all crops and locations. These results demonstrate substantial year-to-year variation in the composition of YDV strains in Nebraska cereal crops and confirm the utility of multiplex RT-PCR for field diagnosis. Furthermore, the observed patterns of virus prevalence and aphid abundance emphasize the epidemiological relevance of these findings and support the role of aphid vectors in shaping strain distribution and composition.
Yellow dwarf viruses (YDV), comprising strains of barley yellow dwarf virus (BYDV) and cereal yellow dwarf virus (CYDV), constrain cereal production in the United States by causing yellow dwarf disease (YDD). Five principal B/CYDV strains occur in cereals: BYDV-PAV, -MAV, -RMV, -SGV, and CYDV-RPV. Although YDV has been reported in Nebraska, cultivar-specific responses and field-level strain composition remain poorly characterized. We conducted a two-year (2024-2025), multi-location field study at Mead, Fairbury, and Concord, Nebraska to evaluate 10 widely grown wheat and barley cultivars for YDD incidence, virus strain diversity, and aphid infestation. Across years and locations, YDV infection was higher in wheat (29.73%) than in barley (12.53%). In wheat, cv. SY Monument exhibited the highest YDV incidence (36-92%) and the greatest aphid abundance, whereas cv. Ruth consistently showed the lowest incidence (4-20%) and minimal aphid infestation. In barley, cv. Fortress had the highest infection levels (8-48%) and aphid abundance, while cvs. NB19420 and NB21427 were generally the least infected (0-20% and 4-12%, respectively) and supported the lowest aphid populations. Strain composition differed by crop: wheat infections were dominated by PAV-associated single and mixed infections, whereas barley shifted toward MAV-dominated infections with reduced strain diversity. Aphid abundance was positively associated with YDV infection in wheat and barley. Collectively, these results highlight the interacting roles of host susceptibility, strain diversity, and vector dynamics in shaping YDD epidemiology and support integrated cultivar- and vector-based management strategies.
M. Barman, Nikhitha Gangavarapu, Thomas Wilbur Davis et al.· Plant Disease· 0 citations
Barley Yellow Dwarf (BYD), caused by viruses from the Tombusviridae and Solemoviridae families, poses a serious threat to wheat production worldwide. In Ukraine, a major wheat-producing region in Europe, the disease has caused growing economic losses, exacerbated by aphid vectors, susceptible cultivars, and variable environmental conditions. Despite long-term monitoring, the pathogens responsible for recent outbreaks and their molecular characteristics remain insufficiently studied, limiting the development of targeted management strategies. This study aimed to evaluate BYD incidence over 11 years (2014–2024) in the Kyiv region of Ukraine, identify the causal pathogen(s) in the 2019/2020 and 2023/2024 outbreaks, and characterize them at the molecular level. Methods. Annual field surveys were conducted on 4.5 ha of winter wheat plots, monitoring nine cultivars for disease symptoms and collecting leaf, aphid, and weed samples. Grain yield was assessed at maturity using a Sampo-130 combine on 100 m² plots with four replications. Meteorological data were obtained from the Ukrainian Hydrometeorological Center and analyzed for key phenological stages. Serological detection used a double- or triple-antibody sandwich ELISA, and molecular confirmation involved RT-PCR amplification of a 641-bp coat protein gene fragment, followed by Sanger sequencing and the maximum-likelihood phylogenetic analysis. Yield data were analyzed using ANOVA (p < 0.05). Results. Barley yellow dwarf virus-PAV was identified as the sole pathogen in symptomatic wheat, its vectoris Rhopalosiphum padi, and the alternative hosts are Arrhenatherum elatius and Echinochloa crus-galli. Phylogenetic analysis showed 92% nucleotide identity between wheat and aphid isolates, clustering with strains from Ireland, Poland, Turkey, and the Czech Republic. The grass isolate shared 85% identity and formed a separate clade with isolates from the USA, Belgium, and China. In the susceptible cultivar Poliska 90, yield losses reached 69.8% in 2020 and 29.2% in 2024, whereas the resistant standard Lisova Pisnia was minimally affected. Conclusions. Barley yellow dwarf virus-PAV is the primary pathogen causing recurrent epidemics in Ukrainian winter wheat over the 2019/2020 and 2023/2024 growing seasons. The spread of BYD is facilitated by viruliferous aphids, host susceptibility, and favorable environmental conditions.
Soybean (Glycine max L.) is one of the world's most important legume crops, valued for its high protein content and extensive applications in food, feed, and industrial products. However, soybean production is frequently threatened by Soybean mosaic virus (SMV), one of the most destructive viral pathogens affecting crop yield and seed quality. This study aimed to detect and molecularly characterize SMV infecting soybean in Uzbekistan. During the 2023 growing season, leaf samples were collected from 35 soybean varieties exhibiting typical virus-like symptoms, including mosaic, yellowing, stunting, and leaf deformation, from the experimental field of the Institute of Genetics and Experimental Plant Biology of the Republic of Uzbekistan. Total RNA was extracted from symptomatic plants and subjected to RT-PCR using SMV-specific primers targeting the coat protein (CP) gene. A DNA fragment of approximately 756 bp was successfully amplified from infected samples, confirming the presence of SMV. The amplified CP gene was sequenced and analyzed to determine its genetic relationship with previously reported SMV isolates. Phylogenetic analysis showed that the Uzbek isolate TH-UZB1 (GenBank accession no. OQ385206.1) clustered closely with Korean SMV isolates and shared high nucleotide identity with the Serbian isolate NDS_21, indicating a high degree of genetic similarity. The molecular detection and characterization of SMV reported in this study provide valuable information on the occurrence and genetic identity of the virus in Uzbekistan. These findings contribute to a better understanding of the genetic diversity of SMV and provide a scientific basis for disease surveillance, resistance breeding, and the development of effective management strategies for sustainable soybean production.
Tohir Xusanov· Journal of Science and Mathe...· 0 citations
Climatic changes are heavily affecting the sustainability of vegetable crops crucial for food supply worldwide, mainly in subtropical countries. One of the main threats to food security is the spread of diseases caused by plant viruses, favored by irregular rains and extreme temperatures, which reduce crop yield and quality. During a preliminary field survey carried out in two provinces of Angola in 2024, a few symptomatic plants of tomato, habanero pepper, common bean and a wild weed were sampled. These plants generally showed dwarfing, yellowing and leaf curl and were submitted to high-throughput sequencing to detect any viral agent. The evidence of mixed infections of several polyphagous viruses with RNA or DNA genomes, variously affecting the selected plants, was assessed from the sequence analysis and further confirmed for most samples by molecular tests, like (RT)-PCR or qPCR. Emerging polero-, begomo and tobamoviruses were denoted as infecting these plants. A novel, previously unknown carlavirus was also described in a wild weed. Most of those viruses are efficiently mechanically transmitted or airborne vehiculated by insect vectors. Although based on a limited number of samples, this study provides a first insight into the diversity of viruses infecting vegetable crops in Angola. It also highlights the pressing need for a broader monitoring to better understand virus distribution and epidemiology, and suggests the use of virus-free seeds to reduce the potential risk to crop production.
Serafina Serena Amoia, A. Giampetruzzi, Fernando Francisco de Sousa et al.· Viruses· 0 citations
The results indicate that the genetic architecture of corn in response to MaYMV is complex, and that developing immune cultivars may not be achievable using natural sources of genetic variation, but this study provides a foundation for breeding maize with improved tolerance and advances the understanding of host response to MaYMV infection.
Erik W. Ohlson, C. Nacci, Nitika Khatri et al.· bioRxiv· 0 citations
Potato virus S (PVS, Carlavirus sigmasolani) is a regulated pathogen in EU seed potato (Solanum tuberosum L.) production programs. Phylogenetic studies have identified three lineages: ordinary (–O; spread worldwide), and two Andean phylogroups (–A, mainly found in Latin America, Middle East, and East Africa; and –RVC with a limited spread in the Andes region) (Topakaya et al. 2023). Recently, we reported the first complete genome of a PVS-O isolate in Estonia (PV764920; van der Sman et al. 2026). In September 2025, seed lots from 34 potato fields (100 tubers per lot) were analysed using high-throughput sequencing (HTS). Plants were grown out and pooled into ten subsamples for each lot. Total RNA was extracted using a Thermo Scientific KingFisher Flex system with the MagMAX™ Plant RNA Isolation Kit (Applied Biosystems). The subsamples from the same seed lot were subsequently pooled for library preparation using the TruSeq Stranded Total RNA with Ribo-Zero Plant kit (Illumina) and sequenced on an Illumina iSeq100 platform using an iSeq 100 i1 Reagent v2 (300-cycle) cartridge, producing 2 × 75 bp paired-end (PE) reads. Reads were demultiplexed according to the instrument workflow. All bioinformatic analyses were performed in Geneious Prime 2026.0.2. Raw reads were quality trimmed and filtered using BBDuk, then PE reads were merged and duplicate reads were removed using default settings. De novo assembly was carried out with SPAdes. Resulting contigs were screened by BLASTn against the NCBI virus database, revealing 71 contigs, ranging from 297 to 8547 nucleotides in length, with the highest nucleotide identity with PVS in 11 out of 34 libraries. Five complete or near-complete genomes were assembled. Two genomes (GenBank Acc. No. PZ397343-44) represented PVS-A isolates, showing the highest nucleotide identity with the Kazakhstan isolate MN095414 (99%), while three genomes (GenBank Acc. No. PZ397345-47) represented PVS-O isolates showing the highest nucleotide identity (98%) with European isolates PP856220, MF346599, and OL472247. PVS-A was once detected in the same library with PVS-O, and once with PVY and PLRV. In other libraries, PVS-O was detected alone (in seven cases), or together with PVY and PVM (once), or with PVY (once). No other viruses were found. Phylogenetic analysis of PVS genome sequences was performed in MEGA 12 using MUSCLE (1000 iterations), and maximum-likelihood phylogenetic tree reconstruction in RAxML 2.0.1 GTR+G+I model, 1000 bootstrap replicates tree visualized in iTOL, showing clustering of Estonian PVS genomes consistent with BLASTn results (Suppl. Fig. S1). In parallel, seed samples were tested for potato virus A, Y, X, M, S and potato leafroll virus, using RT-qPCR as described in van der Sman et al. (2025). RT-qPCR results confirmed the findings of HTS. PVS incidence ranged from 1% to more than 20%. Our two PVS-A findings originated from the neighbouring fields located in Viljandi county where the seed potato was grown from the seed tubers originated from Germany. Given that Andean PVS-A isolates have been mainly reported in association with material originating from Germany (Bragard et al. 2020), this finding may suggest a possible introduction pathway linked to imported seed material.
Piret van der Sman, Anette Stražev, M. Sõmera· Plant Disease· 0 citations
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