Scientists at the Agricultural Research Service (ARS) have developed a new genomics-based disease surveillance platform that could significantly strengthen how crop pathogens are detected and tracked, with clear implications for potato production and seed health systems.

Developed by ARS researchers in Corvallis, Oregon, in collaboration with Oregon State University, the PathogenSurveillance platform is an open-source software pipeline designed to rapidly analyze DNA sequences and identify known or novel microbial variants. The system is intended to support real-time responses to emerging and re-emerging plant pathogens and pests across agricultural systems.

According to ARS, the automated pipeline enables genome-based biosurveillance that can be deployed quickly and used by laboratories with limited computational expertise. This lowers barriers for routine monitoring and outbreak investigation — a key challenge in crops such as potatoes, where early detection of evolving pathogens is critical to limiting spread through seed and supply chains.

“This genomics pipeline revolutionizes plant health, allowing us to identify any microbe, pest, or pathogen in just minutes-to-hours once there is a genome sequence,” said Nik Grunwald, research plant pathologist at the ARS Horticultural Crops Disease and Pest Management Research Unit in Corvallis. “The genomic pipeline can be used for real-time biosurveillance of known, or unknown, pathogens relatively quickly, which lessens the barrier to adoption and use of PathogenSurveillance drastically.”

Because the platform is fully sequence-based, it allows scientists to track how pathogen populations evolve over time and geography. This capability is particularly relevant for crops affected by fast-changing disease pressures, where new strains or variants can undermine existing control strategies.

Grunwald explained that samples are processed through local laboratories before genomic data is uploaded into the system for identification and comparison. “Variation in genomes can thus be monitored over time and space by comparing genomes,” he said.

The platform supports analysis of one to several hundred samples simultaneously and is designed for organisms with small-to-modest genome sizes, including bacteria, fungi, insects, and nematodes. Output is presented through intuitive visualizations and interactive reports, enabling rapid interpretation by diagnosticians and researchers.

“This will be a benefit to researchers, disease clinics, and diagnosticians in their work to identify clonal, or other types of variants,” Grunwald added, citing high-profile plant disease examples such as UG99 stem rust and sudden oak death.

For the potato industry, such capabilities could enhance disease surveillance programs, improve response times to outbreaks, and support more robust phytosanitary decision-making — particularly as international trade, climate pressure, and pathogen mobility continue to increase.

ARS is the U.S. Department of Agriculture’s chief in-house scientific research agency and focuses on developing practical solutions to agricultural challenges affecting U.S. production systems.