Wheat Virus Identification Within Infected Tissue Using Nanopore Sequencing Technology.

Area of Science:

• Plant pathology
• Virology
• Genomics

Background:

• Viral diseases significantly limit wheat production and are challenging to diagnose early.
• Traditional methods like immunological assays have limitations in sensitivity and antibody availability.
• Existing resistance genes, such as Wsm2, may be overcome by emerging viral variants.

Purpose of the Study:

• To evaluate Oxford Nanopore sequencing (ONT) as a diagnostic tool for wheat viruses.
• To identify viral agents in wheat plants exhibiting WSMV-like symptoms.
• To investigate potential new variants of Wheat streak mosaic virus (WSMV) that could impact resistance.

Main Methods:

• cDNA cloning and Sanger sequencing were initially used for WSMV detection.
• Single-strand cDNA from infected wheat tissue was sequenced using Oxford Nanopore sequencing (ONT).
• Deep coverage sequencing was employed to analyze full-length WSMV genomes and identify variations.

Main Results:

• ONT successfully confirmed the presence of WSMV, Triticum mosaic virus (TriMV), and Barley yellow dwarf virus (BYDV).
• High Plains wheat mosaic virus (HPWMoV) was detected in one sample.
• WSMV variants were identified, showing genetic divergence from the reference strain and potentially overcoming Wsm2 resistance.

Conclusions:

• ONT provides a more accurate and comprehensive method for identifying causal viral agents in wheat.
• The technology offers sufficient resolution to detect viral variants, including those that may challenge existing resistance mechanisms.
• This advancement aids in understanding wheat viral disease dynamics and developing resistant crop varieties.