Arkansas Clean Plant Center leads global effort to wipe ‘phantom agents’ from pathogen regulatory lists

FAYETTEVILLE, Ark. — Wiping “phantom agents” from a list of suspected plant pathogens would improve agricultural efficiency and food security by updating regulations on international shipment of pathogen-free plant materials destined for countries where they are needed.

Phantom agents are suspected pathogens that have been reported in scientific literature going back to the early 1900s with no real evidence they exist, according to Ioannis Tzanetakis, professor of plant virology for the Arkansas Agricultural Experiment Station and director of the Arkansas Clean Plant Center. The experiment station is the research arm of the University of Arkansas System Division of Agriculture.

The Arkansas Clean Plant Center led the efforts of a team of 185 agricultural scientists from more than 40 countries that test for plant pathogens. They are calling for the removal of more than 120 phantom agents from regulation lists because they are outdated and impede access to plant materials clean of pathogens. Clean plants are needed for the sustainable production of crops.

India, for example, is the second-largest producer of fruits and vegetables in the world, but its lack of disease-free propagation material limits its yield potential, Tzanetakis said.

Most of these phantom agents were described before modern molecular techniques, and there are no samples or genome sequences available to study them. Despite the lack of evidence of their existence, the suspected pathogens made their way into international regulations that control the shipment of plant materials.

The result, Tzanetakis said, is a confusing mix of real and phantom agents on regulatory lists that must be ruled out by the sender before plants can be shipped from country to country.

“We have tried to clean the list of regulated pathogens to make this process much more mainstream,” Tzanetakis said. “What we call phantom agents are names where there’s not really any knowledge of what they are, nor are there any places on this planet where you can go pick this plant and say it is infected with agent X.”

In a Plant Disease article recently published by the American Phytopathological Society, Tzanetakis and a broad host of co-authors identify phantom agents in eight crops that still appear on regulated pathogen lists even though there is no way to accurately test for them.

The article is titled “Streamlining Global Germplasm Exchange: Integrating Scientific Rigor and Common Sense to Exclude Phantom Agents from Regulation.”

“With today’s technology, if an indicator plant shows symptoms, it would undergo analysis by high-throughput sequencing, also known as HTS,” Tzanetakis explained. “If this process identifies a novel agent, it’s unlikely to be attributed to a phantom. Instead, it would be recognized as a new pathogen of the host. As a result, phantom agents tend to persist indefinitely.”

High-throughput sequencing is a scientific method that allows researchers to quickly sequence DNA from a large numbers of samples and/or organisms simultaneously.

Start clean, stay clean

The Arkansas Clean Plant Center, or ACPC for short, is the newest center for berries in the National Clean Plant Network. The network, also known as the NCPN, was created to protect U.S. specialty crops from the spread of economically harmful plant pests and diseases. The U.S. Department of Agriculture funds the NCPN, which includes scientists, educators, state and federal regulators, nurseries and growers who work together to make sure plant propagation material is clean and available.

Labs like the Arkansas Clean Plant Center conduct testing to identify and verify the presence of plant pathogens like those on regulatory lists. The ACPC also provides “clean-up” services to ensure that plant material is the best quality possible before providing it to nurseries, breeding companies and growers.

Tzanetakis said cleaning plant material might be responsible for the elimination of some of the pathogens on the list of phantom agents. Suspected pathogens could also be caused by either a single or multiple viruses now known under a different name, or possibly even eliminated through resistance in modern cultivars.

For example, among the list of phantom agents is “Strawberry band mosaic virus,” something described as a disease once in Hungary in the 1960s on an old cultivar by its display of symptoms based on a single picture present in a publication.

“Given the limited information provided in the single report, the agent cannot be studied further,” Tzanetakis and his co-authors noted.

The ACPC lab is one of only two in the National Clean Plant Network with in-house HTS capabilities, which streamlines the testing and clean-up processes for breeding lines that improve quality control in pathogen testing.

The goal, Tzanetakis said, is to improve crop production and ensure that farmers have access to high-quality, disease-free plants without unnecessary obstacles.

“Those regulations are in place even though we have so many better tools to test for a disease,” Tzanetakis said.

New tools in the toolbox

Tzanetakis said that NCPN labs like the Arkansas Clean Plant Center are designed to test for and eliminate viruses from plants.

Once the plants are “clean” — that is, free from systemic pathogens like viruses — the ACPC maintains “G1” — Generation 1 — materials to offer “the highest level of protection against re-infection by systemic pathogens,” Tzanetakis added.

“This ensures the long-term maintenance of G1 materials, providing breeders and stakeholders with confidence in the quality and integrity of their advanced selections,” Tzanetakis said.

Along with HTS-based virus diagnostic tools and robotics for nucleic acid extraction, Tzanetakis noted that the ACPC is also staffed by a team of experts.

The collective experience, facilities, equipment and staff, Tzanetakis said, add up to “smooth virus elimination operations, offering solutions for selections that are difficult to propagate in vitro, while also keeping pace with and tailoring new protocols for virus elimination.”

To learn more about the Division of Agriculture research, visit the Arkansas Agricultural Experiment Station website. Follow us on X at @ArkAgResearch, subscribe to the Food, Farms and Forests podcast and sign up for our monthly newsletter, the Arkansas Agricultural Research Report. To learn more about the Division of Agriculture, visit uada.edu. Follow us on X at @AgInArk. To learn about extension programs in Arkansas, contact your local Cooperative Extension Service agent or visit uaex.uada.edu.

About the Division of Agriculture

The University of Arkansas System Division of Agriculture’s mission is to strengthen agriculture, communities, and families by connecting trusted research to the adoption of best practices. Through the Agricultural Experiment Station and the Cooperative Extension Service, the Division of Agriculture conducts research and extension work within the nation’s historic land grant education system.

The Division of Agriculture is one of 20 entities within the University of Arkansas System. It has offices in all 75 counties in Arkansas and faculty on five system campuses.

The University of Arkansas System Division of Agriculture offers all 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 any other legally protected status, and is an Affirmative Action/Equal Opportunity Employer.

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Media Contact: John Lovett
U of A System Division of Agriculture
Arkansas Agricultural Experiment Station
(479) 763-5929
jlovett@uada.edu