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

By John Lovett
University of Arkansas System Division of Agriculture
Arkansas Agricultural Experiment Station

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.

PHANTOM AGENTS — Scientists around the globe have called for reform in testing some regulated pathogens because there is no way to accurately test for them. (U of A System Division of Agriculture photo)

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 They are calling for the removal of more than 120 phantom agents from regulation lists because they are outdated and impede access to plant materials clean of pathogens.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.

REFORM CALL —  Ioannis Tzanetakis is professor of plant virology for the Arkansas Agricultural Experiment Station and director of the Arkansas Clean Plant Center. (U of A System Division of Agriculture photo)

“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.

Arkansas to lead $5 million grant-established center to advance robotics in poultry processing

By Fred Miller
U of A System Division of Agriculture

FAYETTEVILLE, Ark. — Researchers in Arkansas and two other states will be using a $5 million grant to increase use of artificial intelligence and robotics in chicken processing to reduce waste in deboning and detect pathogens.

COLLABORATION — The Center for Scalable and Intelligent Automation in Poultry Processing, established by a $5 million USDA-NIFA grant, aims to adapt robotic automation to the poultry processing industry. (U of A System Division of Agriculture photo)

The grant from the U.S. Department of Agriculture’s National Institute of Food and Agriculture will establish the Center for Scalable and Intelligent Automation in Poultry Processing. The center, led by the University of Arkansas System Division of Agriculture, will join researchers from five institutions in three states in efforts to adapt robotic automation to chicken meat processing.

Project director Jeyam Subbiah said the Arkansas Agricultural Experiment Station, the research arm of the Division of Agriculture, will receive $2.2 million from the grant primarily to focus on food safety automation for poultry processing plants. The grant is for four years.

Subbiah is a professor and head of the food science department for the Division of Agriculture and the Dale Bumpers College of Agricultural, Food and Life Sciences at the University of Arkansas.

The Georgia Institution of Technology, better known as Georgia Tech, is a major partner in the project, Subbiah said. $2.1 million of the grant will go to Georgia Tech to focus on automating the processing lines that turn chickens into meat.

The remaining grant money will be divided between Julia McQuillan, Willa Cather professor of sociology at the University of Nebraska-Lincoln, and Brou Kouakou, associate dean for research at Fort Valley State University in Georgia.

Jeff Buhr, a USDA Agricultural Research Service scientist, will contribute his expertise in broiler physiology to guide robotic deboning of meat, Subbiah said.

Georgia is the nation’s top broiler producer. Arkansas is number 3, according to 2021 figures from USDA.

Meeting the challenge

The recent impetus to automate chicken processing began with the COVID-19 pandemic, Subbiah said. The illness spread quickly among workers on the processing line. Since the worst of the pandemic, the poultry industry, like many others, has been having trouble hiring enough workers.

“Poultry processing lines began 70 to 80 years ago,” Subbiah said. “Since then, there have been only incremental changes in technology. Today, there’s a need for transformative change.”

Robotic hands are not adept at holding a chicken, he said. New technology is needed to prevent dropping slippery meats. Separating the carcasses into cuts of meat is also tricky.

“It’s hard enough to teach people how to use a knife with precision,” said Dongyi Wang, assistant professor of biological and agricultural engineering for the Arkansas Agricultural Experiment Station. “Robotics are fit for repetitive tasks but don’t do well with the precision needed to cut up chicken products.”

For example, he said humans could feel when a knife hits a bone. In contrast, existing automation in poultry processing, like deboners, wastes a lot of meat.

“Human deboners leave about 13 percent of meat on the bones,” Subbiah said. “Automated deboners leave 16 to 17 percent. On an industrial scale, that’s a significant loss in value. We will use artificial intelligence and virtual reality to improve precision and reduce wastage.”

Automation can relieve labor shortages, Subbiah said. It also allows plants to locate in rural areas with a smaller labor force but nearer poultry houses and with lower property costs.

Initially, people working remotely may help advance robotic processing. Subbiah envisions workers logging on from home with virtual-reality goggles and haptics gloves to control robots located miles away.

While working remotely, the labor force will teach artificial intelligence how to cut up chickens of varying sizes and shapes.

“Automated machines right now are programmed to debone or cut up chickens based on an average size and shape. But no chicken is that size or shape,” Subbiah said. “Robot-wielded knives cut meat poorly. The machines have to learn how to adjust to the reality of random sizes and shapes.”

Research team

Arkansas’ research will involve scientists from at least three departments:

• Subbiah, Kristen Gibson and Philip Crandall from the department of food science — Gibson is also affiliated with the Center of Excellence for Poultry Science

• Casey Owens and Tomi Obe from the department of poultry science and the Center of Excellence for Poultry Science

• Dongyi Wang and Yanbin Li from biological and agricultural engineering — Wang also has an appointment in food science, and Li is affiliated with the Center of Excellence for Poultry Science

The primary focus of Arkansas Agricultural Experiment Station researchers will be to automate food safety practices. Subbiah said they will develop robots that monitor processing lines for pathogens like Salmonella and maintain clean and safe spaces and equipment.

Wang and Subbiah will also develop hyperspectral imaging to detect plastics in chicken meat, Subbiah said. Wang will also develop a mobile robot that is equipped with a biosensor invented by Li to produce a biological map of the facility. The “biomap” will be used to evaluate the efficacy of sanitation.

Where the biomap indicates potential hot spots, the robot will automatically collect swabs to test for bacteria. Gibson and Obe will analyze the biomap and develop strategies to enhance food safety.

Owens and Crandall will conduct outreach activities to extend new knowledge and technology to the industry. 

Georgia Tech’s participating scientists are all faculty of the Georgia Tech Applied Research Corporation:

• Doug Britton, manager of the Agricultural Technology Research Program

• Colin Trevor Usher, senior research scientist and branch head of robotics systems and technology, Agricultural Technology Research Program

• Ai-Ping Hu, principal research engineer, Agricultural Technology Research Program

• Konrad Ahlin, research engineer, Intelligent Sustainable Technologies Division

• Michael Park, research engineer, Intelligent Sustainable Technologies Division

• Benjamin Joffe, research scientist, Intelligent Sustainable Technologies Division

• Shreyes Melkote, the Morris M. Bryan, Jr. Professorship in Mechanical Engineering, associate director of the Georgia Tech Manufacturing Institute and executive director of the Novelis Innovation Hub

Collaborative research

“We are thrilled to partner with our colleagues here in the Division of Agriculture, as well as our colleagues at Georgia Tech and the other participating institutions on this exciting project,” said David Caldwell, head of the Division of Agriculture’s poultry science department and director of the Center of Excellence for Poultry Science.

“We expect the findings from these coordinated research projects will be impactful for our stakeholders in the commercial poultry industry here in Northwest Arkansas and throughout the entire industry,” Caldwell said. “This project will help keep moving technology forward in processing and food safety of poultry.”

Britton said his team was very excited to work on this project with the University of Arkansas System Division of Agriculture, Fort Valley State University, and the University of Nebraska-Lincoln.

“The ultimate goal is to drive transformational innovation into the poultry and meat processing industry through automation, robotics, AI, and VR technologies,” Britton said. “Building on years of work in the GTRI Agricultural Technology Research Program, we are pleased to see that the USDA-NIFA has chosen this team to continue these efforts.”

Hu said, “GTRI is excited to work on such an impactful project with our fellow institutions. The last few years have highlighted the need for new technological innovations in the meat and poultry production space, which we plan to address through robotics, virtual reality, and artificial intelligence.”

McQuillan, from the University of Nebraska-Lincoln, said it was exciting to be part of a multi-institutional team discovering innovative ways to improve poultry processing through automation. “As a social scientist who has studied work and health challenges and who is starting to work with extension faculty in Rural Prosperity Nebraska, this project provides great new opportunities,” she said.

McQuillan will study the effects of robotics on poultry industry laborers and how they perceive the technology.

“We hope eventually to bring new owner-operated businesses to rural areas,” McQuillan said. “Collaborating with food scientists, computer scientists, extension faculty and robotics engineers provides amazing opportunities to understand the meanings of innovations for entrepreneurs, workers, and other stakeholders, and to advance fundamental theories about science, technology, and society in sociology.”

Kouakou, from Fort Valley State University, will investigate the application of technology developed in this project to other meat processing industries. He said he was excited about working with this team of collaborators.

“Our state-of-the-art meat processing plant at the Georgia Small Ruminant Research and Extension Center on campus will serve as a resource to extend the technology developed by the Center for Scalable and Intelligent Automation in Poultry Processing to red meat species,” Kouakou said. “This research will greatly benefit our students and processors to observe artificial intelligence in meat processing.”

To learn more about Division of Agriculture research, visit the Arkansas Agricultural Experiment Station website: https://aaes.uada.edu/. Follow us on Twitter at @ArkAgResearch and on Instagram at @ArkAgResearch. To learn more about the Division of Agriculture, visit https://uada.edu/. Follow us on Twitter at @AgInArk.