Occurrence and high throughput sequencing of viruses in Ohio wheat

Authors: HODGE, BRIAN - The Ohio State University; PAUL, PIERCE - The Ohio State University; Stewart, Lucy

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/8/2020
Publication Date: 4/29/2020
Citation: Hodge, B.A., Paul, P.A., Stewart, L.R. 2020. Occurrence and high throughput sequencing of viruses in Ohio wheat. Plant Disease. 104(6):1789-1800. https://doi.org/10.1094/pdis-08-19-1724-re.
DOI: https://doi.org/10.1094/pdis-08-19-1724-re

Interpretive Summary: Ohio is a leading producer of soft red winter wheat. Many viruses impact wheat production, but there is a lack of contemporary information on the presence, distribution and potential impact of wheat viruses in Ohio and the Midwestern United States. To address this, we surveyed Ohio wheat in 2012, 2016, and 2017 and utilized high throughput RNA sequencing and transect sampling to develop a comprehensive catalog of viruses in Ohio wheat, their genome sequences, and incidences across sampling sites. dentified by high throughput RNA sequencing (HTS) and their incidences in sampling sites across the state. The viruses detected most often included barley yellow dwarf virus (BYDV), cereal yellow dwarf virus (CYDV), wheat streak mosaic virus (WSMV), and wheat spindle streak mosaic virus (WSSMV), which were detected at 67, 55, and 28% of the locations with average incidences of 18, 19, 20, and 49% within fields, respectively. Brome mosaic virus (BMV) and cocksfoot mottle virus (CfMV) were also viruses of potential importance detected in Ohio, being detected at 26 and 17% of the locations, respectively. Statistical analyses indicated that the presence of BYDV, CYDV, WSMV, and WSSMV were associated with the presence of volunteer wheat, supporting recommendations to remove volunteer wheat to reduce virus reservoirs. The results of this study provide a comprehensive framework and reference resource for wheat virus diagnosis, which impacts ability to contain and manage viruses and prerequisite data to improve risk management and management recommendations to growers.

Technical Abstract: Ohio is a leading producer of soft red winter wheat. Many viruses impact wheat production, but there is a lack of contemporary information on distribution and potential impact of wheat viruses. To address this, we created a comprehensive dataset of viruses identified by high throughput RNA sequencing (HTS) and their incidences in sampling sites across the state. Samples were collected from 103 wheat fields in surveys conducted in 2012, 2016, and 2017 and subjected to HTS, RT-PCR, or ELISA to assess virus sequence diversity, prevalence, and incidence within fields. Partial and complete virus sequences were assembled, validated by RT-PCR and Sanger sequenced, and compared to previously known virus sequences. The viruses detected most often included barley yellow dwarf virus (BYDV), cereal yellow dwarf virus (CYDV), wheat streak mosaic virus (WSMV), and wheat spindle streak mosaic virus (WSSMV), which were detected at 67, 55, and 28% of the locations with average incidences of 18, 19, 20, and 49% within fields, respectively. Brome mosaic virus (BMV) and cocksfoot mottle virus (CfMV) were also viruses of potential importance detected in Ohio, being detected at 26 and 17% of the locations, respectively. Logistic regression analyses indicated that the presence of BYDV, CYDV, WSMV, and WSSMV were associated with the presence of volunteer wheat, BYDV and CfMV with monocots as the previous crop, and BMV with the presence of nearby corn fields (p < 0.10). For multiple viruses the variance of virus incidence was higher at the county than the region spatial level and were spatially clustered in at least one location, suggesting that there are location-specific factors influencing virus incidence and clustering. The results of this study provide a snapshot of viruses present in Ohio wheat and provide insights into virus biology, production risks, and potential management strategies.