New equipment expands research, diagnostic capabilities at Arkansas Plant Health Clinic

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Sherri Smith, left, director of the Arkansas Plant Health Clinic, stands with Alejandro Rojas, assistant professor of plant pathology and program associate.

Fred Miller

Sherri Smith, left, director of the Arkansas Plant Health Clinic, stands with Alejandro Rojas, assistant professor of plant pathology and program associate.

At the U of A System Division of Agriculture’s Arkansas Plant Health Clinic, new diagnostic tools are helping to expand its research and discovery capabilities.

Alejandro Rojas, assistant professor of soil-borne pathology and ecology at the Arkansas Agricultural Experiment Station’s Division of Agricultural Research, uses a qPCR diagnostic tool in specialty crops and Phytophthora as a stepping stone for the investigation of many plant pathogens.

“The idea of ​​the project was to start building resources in the diagnostic laboratory, so that we can identify those better. Phytophthora disease-causing species,” said Rojas, who teaches in the Department of Entomology and Plant Pathology in the Dale Bumpers College of Agriculture, Food and Life Sciences. “And two, by doing that, we can see what problems there are. They are very common to gardeners and go into those a little deeper.

The equipment will enhance the diagnostic capacity of the Arkansas Plant Health Clinic, Division of Cooperative Extension Services’ Diagnostic Services Unit.

The new device

The qPCR – Quantitative Polymerase Chain Reaction – tool uses the same process as the Covid-19 diagnostic test. The machine quickly replicates the extracted DNA, detects plant pathogens and, when the researchers add specific primers, differentiates between these species – short single DNA sequences.

The diagnostic clinic has acquired an isothermal amplification device that uses crushed plant material and runs cycles determined by a scanned barcode to rapidly replicate and identify the DNA of a specific pathogen. A positive or negative sign indicates the result.

The qPCR tool takes a little longer than the amplifier, but provides more specific information about plant pathogens, Rojas said.

Traditional methods only give a positive or negative reading Phytophthora, But sensitivity can lead to more false positives, Rojas said. For more serious samples, DNA must be extracted and sent to a licensed outside lab to confirm the results. That may eventually change with new skills.

“Having equipment like this, in the future, hopefully, we can do all the procedures here and confirm the samples,” said Rojas.

The Arkansas Plant Health Clinic is not yet licensed to confirm if it is a sample. Phytophthora ramus (species of major concern), but plans to apply.

Improved service

The qPCR tool and its detailed results help diagnosticians provide better guidance to growers.

“This new machine will distinguish which species PhytophthoraIt is, it can be useful, “said Sherry Smith, director of the plant health clinic of Arkansas. “Basically, regardless of the species, the treatment is the same, but there are some crops that are more resistant to one. Phytophthora than the other.”

Differentiating between varieties is important to knowing how to best help growers, Smith said.

Jason Powell, a program associate at the Plant Health Clinic, has noticed a reduction in time when running tests with the magnifying machine.

“The machine itself takes 20 to 30 minutes, depending on the pathogen we’re testing. Some other methods can take a few hours to wait for results overnight, so it saves time,” Pavel said.

The Plant Health Clinic has acquired rosette virus and amplifier tests Xylella By far the most useful.

“We like the amplification machine because the method we use, the molecular method to identify the pink rose virus, took a good day and a half to do the process,” Smith said. The test now takes no more than an hour to complete.

Research focus

Phytophthora The species, water mold, causes many plant diseases, including late blight — the cause of the Irish potato famine — bucky rot and sudden oak death, Smith said.

By the time late blight infects the crop or the clinic receives the sample, it’s often too late for treatment, Smith says. Some chemicals can treat the disease, but it must be caught early to be effective.

Producers can reduce the risk by planting resistant cultivars, Smith said.

Rojas focuses most of his attention. Phytophthora, And his research may lead to other immune systems.

According to Rojas, many research questions can be answered with the new tools. For example, by studying the presence of pathogens in different soil types, you can get improved management recommendations.

The new resources open up more research opportunities in ecology or epidemiology, Rojas said.

One of Rojas’ graduate students is developing a diagnostic test. taproot failure, a disease in soybeans, said Rojas. Another student is also doing cultural work. Phytophthora Samples from the clinic so that the researchers can examine the species in depth.

The Arkansas Plant Health Clinic is part of a nationwide network of clinics, Rojas said. And that provides both research and extension benefits.

“Any method that another lab is using, we have an opportunity to tweak it,” Rojas said.

Purchase of the qPCR equipment was supported by funding from the US Department of Agriculture’s Special Crop Block Grant program and infrastructure funds from the Department of Agriculture. An emergency small grant from the Southern Plant Research Network helped purchase the isothermal amplification equipment.

The team behind the grant includes: Rojas, Smith, Keidy Urrea-Morawicki, former diagnostician at the Arkansas Plant Health Clinic and head of the Department of Entomology and Plant Pathology at the Ken Court Department of Agriculture and the Dale Bumpers College of Agriculture, Food and Life Sciences.

To learn more about the Department of Agricultural Research, visit the Arkansas Agricultural Experiment Station website: aaes.uada.edu. Follow on Twitter at @ArkAgResearch. Visit to know more about agriculture department uada.edu. Follow us on Twitter at @AgInArk. To learn about Arkansas Extension programs, contact or visit your local Cooperative Extension Service agent www.uaex.uada.edu.

About Agriculture Department:- The mission of the University of Arkansas Department of Agricultural Systems is to strengthen agriculture, communities and families by connecting trusted research with best practices. At the Agricultural Experiment Station and Cooperative Extension Service, the Division of Agriculture conducts research and extension work within the nation’s historic land grant education system. The Department of Agriculture is one of 20 departments at the University of Arkansas. It has offices in 75 counties in Arkansas and faculty on five system campuses. The University of Arkansas Department of Agriculture provides all of its extension and research programs and services without regard to race, color, sex, gender identity, sexual orientation, national origin, religion, age, disability, marital or veteran status, genetic information or consideration. Any other legally protected, affirmative action/equal opportunity employer.

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