New Instrument Expands Arkansas Plant Health Clinic’s Research and Diagnostic Capabilities

Arkansas Plant Health Clinic Director Sherrie Smith (left) stands with Alejandro Rojas, Assistant Professor of Plant Pathology, and Program Associate Jason Pavel.

Fred Miller

Arkansas Plant Health Clinic Director Sherrie Smith (left) stands with Alejandro Rojas, Assistant Professor of Plant Pathology, and Program Associate Jason Pavel.

A new diagnostic instrument at the U of A System Division of Agriculture’s Arkansas Plant Health Clinic is helping expand its research and detection capabilities.

Alejandro Rojas, assistant professor of soil pathogenic pathology and ecology at the Arkansas Agricultural Experiment Station, a research arm of the Department of Agriculture, is using qPCR diagnostic instruments to focus on specialized crops. phytophthora Seeds as stepping stones to study more plant pathogens.

“The idea for this project was to start building resources in diagnostic labs to help us better identify them. phytophthora Species that cause disease,” said Rojas, who teaches in the Department of Entomology and Plant Pathology at the Dale Bumpers College of Agriculture, Food and Life Sciences. More common for growers, we’ll dig a little deeper into them. “

The device will also improve the diagnostic capabilities of the Arkansas Plant Health Clinic, a diagnostic services arm of the division’s Joint Extended Services.

new equipment

qPCR — Quantitative Polymerase Chain Reaction — The instrument uses a process similar to the COVID-19 diagnostic test. The machine rapidly replicates extracted DNA, detects plant pathogens, and distinguishes between species when researchers add specific primers (short single-stranded DNA sequences).

Diagnostic clinics have also acquired isothermal amplification tools that use crushed plant material and run cycles determined by scanned barcodes to rapidly replicate and detect DNA of specific pathogens. A positive or negative sign indicates the result.

The qPCR instrument takes a little longer than the Amp, but it provides more specific information about plant pathogens, says Rojas.

Traditional methods can only give positive or negative readings. phytophthora, But higher sensitivity can lead to more false positives, Rojas said. For samples of critical concern, DNA must be extracted and sent to an approved external lab for review of the results. This may eventually change with new features.

“With access to this kind of equipment, hopefully in the future, we will be able to do all the processes here and see the samples,” says Rojas.

Arkansas Plant Health Clinic is not yet licensed to validate samples. Phytophthora ramorum (species of major concern), but it plans to file one.

Substantial service

The qPCR instrument and its detailed results help diagnosticians to provide better guidance to producers.

“What species (of phytophthora“It could be useful,” said Sherry Smith, director of the Arkansas Plant Health Clinic. phytophthora than another. “

Differentiating species is important in knowing how best to help growers, Smith said.

Jason Pavel, a program associate at the Plant Health Clinic, has noticed a reduction in the time it takes to perform tests using the amplifier.

“The machine itself takes 20 to 30 minutes, depending on the type of pathogen being tested,” says Pavel. It saves him time when other methods can take hours or even overnight to produce results.

The Plant Health Clinic has discovered an amp test for rosette virus in roses. Xylella Most useful ever.

“The method we were using, a molecular method to detect rosette viruses in roses, took a full day and a half to perform the procedure, so we love the amp machine,” Smith said. Said. Right now the tests take less than an hour to run.

research focus

phytophthora The seed, a type of water mold, causes many plant diseases, including late blight (the cause of the potato famine in Ireland), buckeye rot, and the sudden death of oak, Smith said.

When late blight hits crops, or when a clinic gets a sample, it’s usually too late for treatment, Smith said. should be detected early.

Growers can reduce the risk by planting resistant varieties, Smith said.

Rojas gave much of his attention to phytophthora, His research may lead to other disease prevention mechanisms.

Many research questions can be answered with the new device, Rojas said. For example, you can investigate the presence of pathogens in different soil types and discover recommendations for improved management.

The new resource will also open up more opportunities for ecological and epidemiological research, according to Rojas.

One of Rojas’ graduate students is developing a diagnostic test for taproot decay, a soybean disease, Rojas said.Another student is also working on culture phytophthora This allows researchers to study the species more thoroughly.

The Arkansas Plant Health Clinic is part of a nationwide network of clinics, Rojas said. And it offers both research and expansion benefits.

“If another lab uses a method, we might adapt it,” Rojas said. “And[the clinic]can use it to start serving growers.”

The purchase of the qPCR equipment was supported by funding from the USDA Specialty Crop Block Grant Program and support from the agriculture sector through the Infrastructure Fund. An emergency mini-grant from The Southern Plant Diagnostic Network helped purchase isothermal amplification tools.

The team behind the grant includes Keiddy Urrea-Morawicki, former diagnostician at the Rojas, Smith and Arkansas Plant Health Clinic, and director of the department of agriculture and the Department of Entomology and Plant Pathology at the Dale Bumpers College of Agricultural. It included Ken Korth. , food and life sciences.

For more information about the Agricultural Research Division, visit the Arkansas Agricultural Experiment Station website at Follow @ArkAgResearch on Twitter. For more information on the agriculture sector, visit Follow @AgInArk on Twitter. For Arkansas extension programs, contact your local Cooperative Extension Service agent or visit

About the agricultural sector: The mission of the University of Arkansas Systems Agriculture Division is to strengthen agriculture, communities, and families by linking sound research with the adoption of best practices. Through the Agricultural Experiment Station and Joint Extension Service, the agricultural sector conducts research and extension work within the country’s historic land grant education system. The Department of Agriculture is one of 20 entities within the University of Arkansas system. It has offices in all 75 Arkansas counties and faculties on five system campuses. The University of Arkansas School of Agriculture recognizes race, color, sex, gender identity, sexual orientation, national origin, religion, age, disability, marital or veteran status, genetic information, or other legally protected status. and is an affirmative action/equal opportunity employer.

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