High-Throughput Oxford Nanopore Sequencing Unveils Complex Viral Population in Kansas Wheat: Implications for Sustainable Virus Management
Wheat viruses are major yield-reducing factors, with mixed infections causing substantial economic losses. Determining field virus populations is crucial for effective management and developing virus-resistant cultivars. This study utilized the high-throughput Oxford Nanopore sequencing technique (O...
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| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-01-01
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| Series: | Viruses |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1999-4915/17/1/126 |
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| Summary: | Wheat viruses are major yield-reducing factors, with mixed infections causing substantial economic losses. Determining field virus populations is crucial for effective management and developing virus-resistant cultivars. This study utilized the high-throughput Oxford Nanopore sequencing technique (ONT) to characterize wheat viral populations in major wheat-growing counties of Kansas from 2019 to 2021. Wheat leaves exhibiting virus-like symptoms were collected, total RNA was extracted, and cDNA libraries were prepared using a PCR-cDNA barcoding kit, then loaded onto ONT MinION flow cells. Sequencing reads aligned with cereal virus references identified eight wheat virus species. <i>Tritimovirus tritici</i> (wheat streak mosaic virus, WSMV), <i>Poacevirus tritici</i> (Triticum mosaic virus, <i>TriMV</i>), <i>Bromovirus BMV</i> (brome mosaic virus, <i>BMV</i>), as well as <i>Emaravirus tritici</i>, <i>Luteovirus pavhordei</i>, <i>L. sgvhordei</i>, <i>Bymovirus tritici</i>, and <i>Furovirus tritici.</i> Mixed infections involving two to five viruses in a single sample were common, with the most prevalent being WSMV + TriMV at 16.7% and WSMV + TriMV + BMV at 11.9%. Phylogenetic analysis revealed a wide distribution of WSMV isolates, including European and recombinant variants. A phylogenetic analysis of <i>Emaravirus tritici</i> based on RNA 3A and 3B segments and whole-genome characterization of <i>Furovirus tritici</i> were also conducted. These findings advance understanding of genetic variability, phylogenetics, and viral co-infections, supporting the development of sustainable management practices through host genetic resistance. |
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| ISSN: | 1999-4915 |