Molecular detection of Ustilago nuda in barley seeds and corresponding field infection levels

Agricultural policies aim to reduce synthetic plant protection products (PPPs), including prophylactic seed treatments. A broader use of untreated seed would help limit synthetic PPP applications. Currently, seed is certified through the visual detection of seed-borne diseases, including loose smut (Ustilago nuda) of barley (Hordeum vulgare). U. nuda infection is asymptomatic in seeds and plants until its teliospores develop at barley heading. PCR-based molecular detection of U. nuda can help streamline the certification process for untreated seed and improve its accuracy and precision. We developed a multiplex qPCR protocol that targets U. nuda and H. vulgare DNA. The new molecular assay and a visual detection method using extracted embryos were performed to analyze seed samples with varying rates of infection. The resulting disease levels were then evaluated in field. Based on the 2022 data, U. nuda field infections show a stronger positive correlation with the qPCR results than those from the visual analysis of embryos. The experimental results enable us to propose a threshold value of U. nuda/H. vulgare DNA to delineate healthy and diseased seeds. Future research with additional samples from practice is needed to validate the proposed threshold under diverse environmental conditions. Molecular methods in seed health testing could aid in the wider adoption of sowing untreated seed and reduce synthetic PPP application.