Features Diseases
Fighting potato wart via genomics and molecular tools

Potato wart is a yield-limiting, soil-borne disease that disfigures infected tubers, making them unmarketable. On top of that, the pathogen is really difficult to eradicate once it enters a field. Along with strict phytosanitary measures, Canada is tackling this threat through both potato breeding and potato wart research. And both research efforts are tapping into the power of genomics and molecular tools to speed advances.

Potato wart basics

“Potato wart is caused by a fungus called Synchytrium endobioticum. The fungus infects potatoes and causes cauliflower-like formations and warty growths on the tubers,” explains Hai Nguyen, a research scientist with Agriculture and Agri-Food Canada (AAFC) at the Ottawa Research and Development Centre (ORDC). His current research focuses on molecular and genomic studies of the potato wart pathogen and other related fungi. 

Nguyen notes that Synchytrium endobioticum needs a host potato plant in order to grow and complete its life cycle. Inside its host, the fungus forms resting spores, which are released into the soil as the diseased plant dies and decays. The resting spores can remain infectious for decades, waiting for cool, moist conditions and another potato plant so they can start their next infection cycle.

Potato wart is a regulated pest in many countries, including Canada and the United States. It is not a threat to food safety or human health, but it can have very damaging impacts on potato production and exports.

“Potato wart can cause severe yield reductions, which can make land unsuitable for potato production for a long period of time as the spores can remain dormant in a field for more than 40 years. Also, if potato wart is present, it can impact the trade [not only of potatoes but also] of other commodities associated with soil such as root crops or other plants that will be replanted,” explains David De Koeyer. He is a potato breeder and geneticist at AAFC’s Fredericton Research and Development Centre (FRDC).

“The fungus can be present but undetected in the soil for many years or even decades before visible signs are observed on the tubers. During that period of time, a farm can unknowingly expose itself to the potato wart pathogen through the replanting of potatoes from infested fields to new locations, and there is a risk of moving the pest to other farms,” notes De Koeyer. Officials at the Canadian Food Inspection Agency (CFIA) add that replanting of infected potato tubers poses the highest risk for pathogen spread, while movement of infected soil and potato waste also pose a risk when mitigation measures are not in place to control the risk of pathogen spread.

“So, potato wart is difficult to detect, it is difficult to manage, and it has a lot of implications economically,”  says De Koeyer.

Potato wart in Canada

The disease is thought to have originated in potatoes grown in the Andes of Peru and to have arrived in the United Kingdom around the 1880s and spread from there. Nguyen summarizes the history of potato wart in Canada, drawing mainly from a 1993 article by M.C. Hampson, a former AAFC research scientist.

Nguyen divides Canada’s potato wart history into three periods. “The first period covers the early 1900s to the 1950s. It begins with the introduction of potato wart into Newfoundland around 1900. The disease was thought to have come from seed potatoes from the United Kingdom. In 1909, an English botanist, who worked at the experimental farm in Ottawa, received diseased tubers from Newfoundland. He confirmed the disease was potato wart. He then helped to work on legislation to prevent entry of potato wart into mainland Canada from Newfoundland and other countries where the pest was reported. He also made a bulletin and distributed it to increase awareness of the disease.”

Over the next few decades, the disease spread in Newfoundland. By the 1920s, wart-resistant potato varieties were being imported from England for use in Newfoundland. However, by the 1940s, new races, or ‘pathotypes,’ of potato wart emerged, overcoming the resistance genes in those varieties.

Nguyen sees the second period as starting after Newfoundland joined Canada in 1949 and ending in the 1990s. During that period, Canadian scientists conducted surveys to determine potato wart’s distribution, confirming that it was widespread in Newfoundland primarily in home gardens. They also experimented with different control measures such as chemical eradication, but no eradication methods were successful.

De Koeyer notes that, starting in the 1950s, AAFC worked on developing potato varieties with resistance to the potato wart pathotypes in Newfoundland. From the late 1950s up until 1998, these breeding activities took place at the St. John’s Research and Development Centre. The St. John’s RDC established an infested field location at its Avondale sub-station in Newfoundland for evaluating wart resistance levels in the breeding lines.

According to Nguyen, the third period starts when potato wart was first detected in Prince Edward Island (P.E.I.) in 2000. As the CFIA website explains, this detection resulted in the closure of the U.S.–Canada border for all fresh P.E.I. potatoes, including seed and table stock, for six months. At that time, the Potato Wart Domestic Long Term Management Plan was also put in place. The Plan outlines the mandatory minimum survey, testing and surveillance activities required to mitigate the risk of spread of potato wart outside of the restricted areas in P.E.I. In addition, in 2021, CFIA enhanced its National Surveillance Program with additional soil samples taken in every seed potato-producing region of Canada. The Canadian surveys have not detected the disease beyond Newfoundland and Labrador (NL) and P.E.I.

“This post-2000 period also marks the development of molecular technologies and genomics to help us deal with the disease. Those technologies just didn’t exist in the first two periods,” says Nguyen. He is one of the AAFC researchers working together with CFIA scientists and with collaborators in the Netherlands on potato wart genomic/molecular research.

As of 1998, FRDC has taken on the task of breeding wart-resistant potato cultivars. However, the evaluations of breeding lines for wart resistance levels are still done at the Avondale sub-station, under a memorandum of understanding between AAFC and CFIA, ensuring the safe containment of diseased materials.

Over the years, AAFC has released several wart-resistant potato varieties suited to the needs and preferences in NL. And these days, it is stepping up its efforts to breed resistant varieties of market interest for P.E.I. as well.

Hai Nguyen, whose research includes molecular and genomic studies of the potato wart pathogen.
Photo courtesy of Hai Nguyen, AAFC.

Resistance breeding for P.E.I.

Synchytrium endobioticum pathotypes are identified using a standardized set of potato lines, referred to as differential hosts. Based on the symptoms expressed by each of the lines when inoculated with a particular isolate of the pathogen, that isolate can be identified as a specific pathotype.

“Currently in the world, over 40 pathotypes of the potato wart pathogen have been discovered. In Canada, only three have been found,” says De Koeyer. Pathotypes 2, 6 and 8 have been found in NL while only pathotypes 6 and 8 have been detected in P.E.I.

He notes, “CFIA approves resistant varieties for use in restricted fields in P.E.I. as part of the Potato Wart Domestic Long Term Management Plan. At present, five varieties – Althea, Frontier Russet, Goldrush, HiLite Russet and Prospect – are the only ones on that approved list for the wart pathotypes in P.E.I. Some other varieties are currently being assessed for resistance.”

According to De Koeyer, breeding potatoes for wart resistance comes with many challenges. One fundamental challenge is the complexity of potato genetics. “It takes a big effort to incorporate wart resistance into a potato that also has all of the other traits needed by [growers and processors]. The companies have standards that need to be met, and consumers have standards for what they want to eat,” he says. 

In addition, identifying wart-resistant potato varieties is a time-consuming process involving multiple rounds of testing and requiring trained staff. And, since potato wart is a regulated pest, resistance testing has to be done either in Newfoundland where the disease is endemic or in a very highly contained laboratory. 

As well, the potato wart pathotype composition in P.E.I. needs to be monitored to ensure that the resistance screening efforts are working with the relevant pathotypes. The low levels of pathogen infestation on P.E.I. also pose a scientific challenge for confirming the pathotypes present in some cases. 

AAFC is enhancing its wart-resistance breeding efforts for P.E.I. in a number of ways, including increasing its potato wart-related capacity in NL. “We’ve been rejuvenating our Avondale testing site by increasing the available research area to approximately five acres, providing dedicated equipment for plot management, storage facilities and fencing to keep the moose out and so on,” says De Koeyer. 

“We’re also working with industry to look at a greater scope of varieties, especially those that are most important to P.E.I. And we’re looking at complementary or improved methods for testing breeding lines for resistance to potato wart such as using molecular markers linked to the resistance and indoor testing under controlled conditions. Indoor testing in Newfoundland will be initiated when renovations to the St. John’s RDC are completed.” 

AAFC also works with a collaborative grower in Newfoundland who has a small, infested area where a few varieties can be screened. “The field is very heavily infested with potato wart so we get a good screening, but it is very small scale.”

Wart resistance genes

“We are working to characterize the different sources of resistance in our potato germplasm pool. We’ve had a long history of working on potato wart so we’ve been using our historical data as well as molecular markers to look for resistance sources,” says De Koeyer.

“We have confirmed that we have multiple sources of wart resistance available in Canada. Some of them seem to be similar to those that have been previously reported in the scientific literature, but other sources are novel.”

He adds, “It is quite an endeavour to characterize new sources of resistance.” That work includes developing large populations of different potato lines, evaluating the resistance level of each genotype and associating the resistance with variant forms of specific DNA sequences using genomic analysis. “So, there is certainly a lot more research to do. But it is promising in that we have different types of resistance sources in different market categories.” 

AAFC is also working on markers for screening breeding materials for resistance genes. “We have markers from the literature and collaborations for testing the markers. Some of these markers are effective in varying degrees for the pathotypes we have in Canada, and we’re using those to screen for resistance genes in our breeding material and some Canadian varieties,” he says. 

“This work is still at a preliminary stage, but it seems that the results from the marker data are not universally good at predicting resistance [in Canadian potato lineages].” 

A marker is a sequence of DNA associated with a particular gene, but it may not actually be part of the gene. So sometimes a marker may predict the gene’s presence when the gene isn’t actually there. Developing more robust markers suited to Canadian potato germplasm was recommended by the International Advisory Panel on potato wart disease management in P.E.I. in their December 2022 report and is also a priority for AAFC research.

David De Koeyer, AAFC potato breeder and geneticist.
Photo courtesy of Camille Coulombe, AAFC.

Improving pathotyping methods

In Canada, CFIA is responsible for determining the pathotypes of potato wart isolates because it has the biosecurity facilities, procedures and trained staff essential for this work. “At AAFC, once we build up our capacity at the St. John’s RDC, we hope to help Canada with this pathotyping work,” says Nguyen.

A molecular pathotyping system could be an alternative to the time-consuming, labour-intensive current pathotyping system, which relies on the plants’ phenotypical reactions – their physical responses – to the pathogen. “The currently used pathotyping system was conceived before all of the genomics and molecular tools we have now,” says Nguyen. “The idea of a molecular pathotyping system has been around for at least 10 years, but no one has been able to pull it off very successfully.”

Nguyen and his research group at ORDC have done some work towards developing a tool for molecular pathotyping. To develop it, they sequenced the whole genomes of potato wart isolates that have been pathotyped traditionally. Then they used machine learning techniques to identify patterns across the whole genome associated with the different pathotypes, and they used those patterns to predict probable pathotypes in other isolates.

“This approach shows promise because it looks at the entire genome, and it doesn’t rely on any preconceptions about what genes or what areas of the genome are responsible for infection. So, it might work with our current phenotypic pathotyping system,” he says.

“However, I think this approach can also be modified to work with a gene-based pathotyping system.” He thinks the best option would be to transition to such a gene-based system. “There have been conversations in the scientific community that we need to figure out a better pathotyping system, and that is what we’re working on now.”

Wart genomics and molecular tools

In recent years, AAFC, CFIA and their Dutch collaborators have made progress on various potato wart-related molecular tests. For example, they developed one of the first molecular tests for the pathogen, which can detect whether the pathogen is present in a sample. Then this research collaboration developed molecular tests that can detect quantities of the pathogen, based on the amount of its DNA in the sample. And most recently, they have created tests to help detect if resting spores remain viable.

Although these molecular tests are faster and easier than traditional methods like bioassays and microscopic examinations, Nguyen cautions that even these molecular tests can sometimes give false positives and false negatives, and they also depend on good sampling techniques to give accurate results.

Over the past decade or so, AAFC, CFIA and their Dutch colleagues have also done quite a bit of work to characterize the genomes of different Synchytrium endobioticum isolates of different pathotypes and from different locations. 

“This fungus is a challenging organism to sequence and work with because it needs a host to grow. So, there are problems with getting enough potato wart DNA and with the purity of the wart DNA for sequencing,” explains Nguyen. The initial stage of their research was mainly focused on dealing with these basic hurdles so they could have sufficient, pure Synchytrium endobioticum DNA to work with. 

More recently, their progress has accelerated. For example, Nguyen was part of a team that sequenced and characterized the genomes of two Synchytrium endobioticum isolates, one from P.E.I., and the other from the Netherlands. In their 2019 paper, the researchers compared those genomes to the genomes of other related fungi. Their work shed new light on important aspects of Synchytrium endobioticum’s biology at the molecular level, including how it might cause infection.

Then, in a 2023 paper, the researchers sequenced and characterized many more isolates of the pathogen, including recent isolates from P.E.I. and an international collection of historical and recent isolates from the Netherlands and other countries. This work has increased scientific understanding of the pathogen’s diversity and its migration pathways.

“[As part of this research] we built a website where we are able to use the molecular variation to try to track and trace the different strains that we find,” notes Nguyen. Not only does this interactive web tool allow the team to share the data from this paper, but other researchers can also contribute to expanding this track-and-trace effort. (Although the tool includes regional locational information, it never refers to specific potato fields).

His current potato wart research focuses on further improving the genome data available for Canadian isolates by sequencing more Canadian samples, mainly isolates of pathotypes 6 and 8.

Such genomic data provides the foundation for development of more advanced molecular tools. “For instance, using the genome data, AAFC, CFIA and our Dutch collaborators have been working on a new molecular tool to enhance the capture of the pathogen’s DNA,” he explains.

“The technique, called ‘target enrichment’, is particularly useful in environmental samples where there is also DNA from other organisms and where there may not be a lot of DNA from the pathogen either. In a nutshell, the tool allows you to characterize the pathogen’s full genome even though there is a low amount of DNA or the DNA is very low quality.”

He notes, “This tool could be helpful one day, for example, in enabling us to characterize the pathotypes even in samples with low amounts of the pathogen and perhaps [identifying the pathotype faster] and at a lower cost.”

Nguyen says this new tool is just one example of a whole suite of molecular tools that could be developed. “No tool is a silver bullet, but having more tools gives us more options.”

More research, more hope

Nguyen and De Koeyer both emphasize that potato wart is a challenging issue, but advances in genomics and molecular tools offer exciting possibilities in the battle against the disease.

“Resistant potato varieties aren’t a silver bullet, but they do play an important role in the management of this disease. They have proven very effective in other countries,” says De Koeyer.

“I feel that DNA markers and genomics technology will make development of varieties with durable wart resistance even more efficient and effective. I think it will be important to put together multiple resistance genes to make a variety’s resistance more durable.”

Similarly, potato wart genomic studies have the potential to provide further help in managing the disease. “We hope that with more genomic data and more genomic insights into concepts like the differences between the pathotypes, we can understand more about the essential pathways and essential genes in the pathogen’s infection process or its general life cycle. From there, we could look at different strategies to detect it from a different angle such as its biochemistry,” Nguyen says.

“And, if we know something about the genes involved in carrying out its life cycle, maybe we can find something that could disrupt its life cycle. Such methods might only suppress the pathogen, but if you have a multipronged strategy, then you might be able to suppress it enough that the risk is virtually next to zero.” 

Although there is much research still to be done, there is also the growing hope of substantially curbing the threat of potato wart in the years ahead.