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ARS Home » Southeast Area » Auburn, Alabama » Soil Dynamics Research » Research » Publications at this Location » Publication #429831
Research Project: Integrated Crop Disease Mitigation through Improved Understanding of Relationships between Genetics, Environment, and Management

Location: Soil Dynamics Research

Title: Data collection and transcriptome analysis of Triticum aestivum samples from Alabama revealed the presence of barley yellow dwarf virus

Author
item LIVINGSTON, RACHEL - Auburn University
item MAYFIELD, MICHAEL - Auburn University
item Zhao, Chaoyang
item POTNIS, NEHA - Auburn University
item STRAYER-SCHERER, AMANDA - Auburn University
item MARTIN, KATHLEEN - Auburn University

Submitted to: Frontiers in Agronomy
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/21/2025
Publication Date: 12/8/2025
Citation: Livingston, R.M., Mayfield, M., Zhao, C., Potnis, N., Strayer-Scherer, A., Martin, K.M. 2025. Data collection and transcriptome analysis of Triticum aestivum samples from Alabama revealed the presence of barley yellow dwarf virus. Frontiers in Agronomy. 7:1721047. https://doi.org/10.3389/fagro.2025.1721047.
DOI: https://doi.org/10.3389/fagro.2025.1721047

Interpretive Summary: Barley yellow dwarf (BYD) is a major cereal disease, yet Alabama-specific sequence data confirming the viruses involved have been lacking. This gap hinders timely diagnosis and informed management decisions for growers and researchers. In April 2023, we collected symptomatic leaf samples from four winter wheat cultivars grown in Alabama and performed total RNA extraction followed by high-throughput sequencing. Bioinformatic analysis was used to detect BYD-associated viruses and other organisms present in the samples. Most sequences were host-derived, with bacterial and fungal reads commonly observed across cultivars. One cultivar exhibited a strong signal for barley yellow dwarf virus (BYDV), while the others showed only weak viral signals. All raw sequencing data and metadata are publicly available via NCBI BioProject PRJNA1250571. This dataset represents the first publicly accessible RNA resource from Alabama wheat exhibiting BYD-like symptoms and provides a foundation for BYDV confirmation, preliminary variant assessment, and improved disease surveillance and management in regional wheat production.

Technical Abstract: Barley yellow dwarf (BYD) is a globally important cereal disease caused by RNA viruses in the genera Luteovirus and Polerovirus. We generated metatranscriptomic datasets from four Alabama winter wheat (Triticum aestivum) cultivars (GA 161, GA GORE, 26R33, AGS4043) exhibiting BYD-like symptoms. Symptomatic leaf samples collected in 2023 underwent total RNA extraction, ribosomal RNA depletion, and paired-end Illumina sequencing, yielding 38.9-47.2 million raw reads per sample. Kraken2 profiling indicated that the majority of reads originated from host, bacterial, or fungal sources. Cultivar 26R33 showed a strong Luteovirus signal, with 48,633 reads assigned, while the other cultivars showed minimal Luteovirus presence. No Polerovirus-classified reads were detected in any sample. De novo assembly and contig-level annotation corroborated the read-level classifications. These publicly available datasets establish a baseline for barley yellow dwarf virus (BYDV) detection and variant analysis in Alabama wheat, and offer valuable resources for exploring host-pathogen interactions. Raw reads and metadata are accessible via NCBI BioProject PRJNA1250571.