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A new molecular seed assay to predict Ustilago nuda field infection levels

Summary

Scientists developed a new DNA-based test to detect a fungus that infects barley seeds and causes crop disease. This test is faster and more accurate than the current method of manually inspecting seeds under a microscope. By using this new test, farmers can better decide which seeds need treatment, reducing unnecessary use of pesticides while still preventing disease outbreaks in their fields.

Background

Seed health tests are essential for preventing the spread of seedborne pathogens, but detecting internal pathogens like Ustilago nuda (which causes loose smut in barley) is challenging because symptoms only appear during ear development. Current detection methods rely on visual inspection of embryos or field observations, which are laborious and often unreliable.

Objective

To develop a multiplex qPCR method for detecting Ustilago nuda in bulk milled barley seeds that better predicts field infection levels than the current embryo test. The study aimed to correlate laboratory detection results with observed field infections to establish reliable tolerance thresholds for seed certification.

Results

The qPCR method showed 22% higher correlation with field infections compared to the embryo test. The qPCR method correctly identified all six seed lots as above or below the field tolerance threshold with perfect sensitivity and specificity (1.0), while the embryo test produced false negatives by missing infections in two seed lots that exceeded field tolerance thresholds.

Conclusion

The multiplex qPCR method provides a more accurate, scalable, and practical alternative to visual embryo inspection for detecting U. nuda in barley seeds. Integration of this method into seed certification processes would improve targeted seed treatments, reduce unnecessary pesticide applications, and strengthen integrated pest management strategies.
  • Published in:Scientific Reports,
  • Study Type:Experimental Research Study,
  • Source: 10.1038/s41598-025-18544-3, PMID: 41053118
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