ARS, Cepheid Team to Make Plant Disease Diagnosis Faster, Easier and More Accurate

When it comes to fighting crop diseases, field surveillance also has its place on the front lines of farming. That's why Agricultural Research Servicescientists and Cepheid, a Sunnyvale, Calif., company, are collaborating on tests of portable, DNA-based devices that will identify plant disease organisms in less than 60 minutes versus days or weeks by traditional methods.

Rather than await results from diagnostic labs using such methods, for example, Extension Service agents could make on-site, "real-time" recommendations on how best to curtail a crop disease outbreak before it spreads further. Another foreseeable use is checking perishable plant materials at ports of entry for exotic plant disease organisms that could imperil domestic crops, notes Norm Schaad, with ARS' Exotic Diseases-Weed Science Research Unit, Frederick, Md.

Along with ARS lab associates Reid Frederick and Vern Damsteegt, Schaad is collaborating with Cepheid under a cooperative research and development agreement (CRADA) with ARS. Cepheid's portable Smart Cycler unit, which connects to a laptop computer, uses polymerase chain reaction (PCR) to replicate a target pathogen's DNA--its unique genetic fingerprint.

The ARS scientists are using their expertise in bacterial, fungal, and viral genetics to design primers and probes targeting specific DNA sequences of several major plant pathogens. The primer’s main job is to bind with a pathogen’s DNA--if present in a leaf sample, for example--and prepare it for PCR amplification on the testing unit. The amplified DNA also binds with the probe, emitting a flourescent signal at the end of each PCR amplification cycle that’s measured and displayed on the computer.

For bacteria, users need only immerse infected tissue specimens in water for 20 minutes before placing a microliter sample of it into one of the unit's 16 reaction chambers--no DNA extraction is necessary.

The ARS scientists will share data from lab and field tests of the Smart Cycler using ARS primer/probes for Pierce’s disease, citrus canker, watermelon fruit blotch, bacterial wilt, brown rot of potato, potato ring rot, Karnal bunt, soybean rust, plum pox and other diseases. Under the CRADA, Cepheid has first rights to commercialization of primers and probes for these diseases.

ARS is the U.S. Department of Agriculture's main scientific research agency.