Wheat viruses including wheat streak mosaic virus, Triticum mosaic virus, and barley yellow dwarf virus cost substantial losses in crop yields every year. Although there have been extensive studies conducted on these known wheat viruses, currently, there is limited knowledge about all components of the wheat (Triticum aestivum L.) virome. Here, we determined the composition of the wheat virome through total RNA deep sequencing of field-collected leaf samples. Sequences were de novo assembled after removing the host reads, and BLASTx searches were conducted. In addition to the documented wheat viruses, novel plant and fungal-associated viral sequences were identified. We obtained the full genome sequence of the first umbra-like associated RNA virus tentatively named wheat umbra-like virus in cereals. Moreover, a novel bi-segmented putative virus tentatively named wheat-associated vipovirus sharing low but significant similarity with both plant and fungal-associated viruses was identified. Additionally, a new putative fungal-associated tobamo-like virus and novel putative Mitovirus were discovered in wheat samples. The discovery and characterization of novel viral sequences associated with wheat is important to determine if these putative viruses may pose a threat to the wheat industry or have the potential to be used as new biological control agents for wheat pathogens either as wild-type or recombinant viruses.

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.

Umbravirus-like associated RNAs (ulaRNAs) are a new group of subviral RNAs associated with plants. Little is known about the biology of ulaRNAs. We recently reported wheat umbra-like virus (WULV) from Kansas fields. In this work, we generated a full-length cDNA clone of WULV which systemically infected N. benthamiana. While agroinfiltrated leaves demonstrated severe necrosis, upper leaves were symptomless. We also showed that WULV is capable of infecting wheat in the absence of a helper virus. Furthermore, and through sap inoculation, we demonstrated that WULV is transmissible in the form of free RNA. This is the first report of a mechanically transmissible ulaRNA. Together, these findings contribute to advancing our knowledge of the biology of WULV. Moreover, the construction of the WULV infectious clone provides a valuable research tool for further investigations including the role of WULV in symptom development in interaction with other wheat viruses.

Plant viruses are emerging and re-emerging to cause important diseases in many plants that humans grow for food and/or fiber, and sustainable, effective strategies for controlling many plant virus diseases remain unavailable

The wheat streak mosaic (WSM) complex, primarily caused by wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV), results in significant annual yield losses in the northern plains of the United States. Wheat wild relatives, including Aegilops tauschii , represent valuable resources of genetic diversity, including resistance to pathogens. In this study, we report the first comprehensive phenotypic assessment and genome-wide association study (GWAS) of a geographically diverse panel of 250 Ae. tauschii accessions for WSMV tolerance in single and mixed infections with TriMV. Phenotyping for WSMV symptom severity and quantitative polymerase chain reaction (qPCR)-derived viral titers identified 124 tolerant genotypes in single infections. In double-infection assays, 22 of 39 tested accessions, including both WSMV-tolerant and susceptible genotypes, exhibited tolerance to both viruses. The GWAS revealed that 12 genomic loci were significantly associated with WSMV severity and 8 loci were associated with the viral titer in single infections. Notably, a large effect locus for symptom severity mapped to the long arm of chromosome 5D within lineage two (L2) at 432 Mb. Additional loci in the same region, also identified by the BLINK model, were detected at 430 Mb and 529 Mb. These regions harbor multiple previously reported disease resistance-related genes. These findings suggest that tolerance to WSMV in Ae. tauschii is controlled by multiple quantitative trait loci (QTL), highlighting the need for further validation and functional characterization. The WSMV-tolerant germplasm identified in this study constitutes a valuable genetic resource for incorporation into wheat improvement programs. This work lays the foundation for the functional characterization of WSMV tolerance loci in Ae. tauschii and provides a framework for leveraging genetic diversity for improving virus resistance in wheat through marker-assisted breeding strategies.