Aphanomyces: The Hunt for Resistance - Pulse Research
July 03, 2019
Aphanomyces root rot is an incredibly tough disease to crack. Since its discovery on the Canadian Prairies, Aphanomyces euteiches has become a major limiting factor for pea and lentil production.
Yield losses vary from year to year depending on moisture conditions, but some estimates peg losses at 50% or higher in cases of severe infestation.
When it comes to Aphanomyces euteiches, infestation means that resting spores can survive in the soil for decades, providing a constant source of inoculum that is ready and waiting for the ideal conditions to attack.
Part of Saskatchewan Pulse Growers’ (SPG) strategic plan is to reduce the agronomic constraints that prevent pulse producers from achieving the highest possible yields and grades. That is why SPG funds this research into Aphanomyces root rot resistance.
By now, most pulse growers on the Prairies know the story:
- Aphanomyces euteiches was first identified in Saskatchewan in 2012
- It affects mainly peas and lentils
- It is “triggered” in wet years and can still show up in dry ones
- Once in a field, it is a permanent problem
- Chemical controls are weak
- Resistant pea and lentil varieties are not yet available
That last item is something plant pathologists, like Dr. Sabine Banniza, and plant breeders, like Dr. Tom Warkentin, have been steadily working on for years at the Crop Development Centre at the University of Saskatchewan. They know just as well as others how complex the problem is and how urgently solutions are needed.
“It is important that we find genetic solutions since chemical control is marginal,” says Warkentin, adding that the only real option growers have now is to observe prohibitively long rotations, at least six years, between susceptible crops.
So why is it so tough to find sources of resistance and breed that into adapted pea and lentil varieties? Part of it comes down to the complexity of the disease itself, and part of it is the complex nature of resistance mechanisms.
Puzzle Upon Puzzle
To achieve the goal of Aphanomyces-resistant cultivars, researchers need to do three things. First, identify the disease pathotypes they are dealing with – that is, what specific variations, or strains, of Aphanomyces euteiches exist in the soil here. Second, identify pea and lentil germplasm that have resistance to those disease strains. Third, they need to transfer that resistance into pea and lentil germplasm, which can then be incorporated into pea and lentil breeding programs.
It sounds straight forward, but it is a painstaking process where tens of thousands of plants are evaluated through experiments designed to not only identify disease-causing pathotypes and sources of resistance, but also to develop methods and techniques to help researchers move that resistance into new pea and lentil breeding lines more efficiently and evaluate the results more quickly.
With funding from SPG, Banniza and Warkentin are working together on a number of research projects aimed at finding some answers.
The first task is to identify the disease pathotypes, which vary in virulence, meaning some are better than others at taking out plants. The bad news? “We primarily have the virulent pathotype in Saskatchewan and Alberta,” says Banniza.
Peas showing signs of root rot stress early in the growing season.
So far, Banniza and her team have determined that the vast majority of strains from Saskatchewan and Alberta belong to the highly aggressive pathotype I, whereas only 12% belonged to the less aggressive pathotype III.
They also found that the isolate used by the United States Department of Agriculture (USDA) for pea germplasm screening is less aggressive than many of the Saskatchewan isolates. “That is important to know because it tells me that any ‘partially resistant’ pea or lentil lines
identified at the USDA need to be evaluated here with Saskatchewan isolates to ensure that resistance really works before starting to breed with it,” says Banniza.
“Aphanomyces root rot is similar to clubroot in its complexity,” she says. Canola growers have experienced resitance break down with new clubroot resistant cultivars, as a different strain of the disease has gained dominance. “Nobody knows how durable Aphanomyces resistance is because nobody has put out resistant peas yet,” says Banniza. “We suspect it can break down quickly if not used properly, but we do not know for sure.”
The traditional way to screen germplasm for Aphanomyces root rot resistance is a process called pathogenicity testing. This involves exposing plant material to disease-causing strains to see what lives or dies, in an effort to find resistant germplasm to use in breeding programs.
In one SPG-funded study Banniza and her team were able to design molecular markers in peas that are specific to the Canadian situation to help speed the selection process.
“Resistance to Aphanomyces root rot is not complete and it is controlled by many genes,” explains Banniza.“Tracing all of those genes through the breeding programs is difficult using traditional pathogenicity testing because resistance is quantitative, so the differences between different [plant] lines may be very small, but as you combine those little differences, they become bigger. The molecular markers are like tags on many of those genes, so you search for those pea lines with the highest number of tags.”
Combining the new molecular markers with pathogenicity testing makes the screening process more robust, allowing the team to screen more germplasm samples, and screen them quicker than they would have been able to through traditional pathogenicity testing.
Breeding Resistant Peas and Lentils
Banniza and Warkentin tested plant germplasm from all over the world searching for sources of resistance. It is a challenge though, because breeders need to marry two things into one plant, disease resistance and good performance in Canadian conditions.
“Basically, we started out with two resources,” says Warkentin. “One, peas from elsewhere that have partial resistance to Aphanomyces euteiches, but are not in themselves high yielding in Saskatchewan, and two, our own pea varieties that are high yielding in Saskatchewan, but susceptible to Aphanomyces euteiches.”
In the case of peas, Banniza and Warkentin have made some important gains. “Our colleagues in France and the United States identified partial resistance, which we are breeding into Canadian pea varieties,” says Warkentin.
They then embarked on an intensive backcrossing program using rapid generation technology (RGT) to move the sources of resistance into selected pea varieties. “RGT is growing plants under conditions where they stay miniature,” explains Warkentin. “It allows them to
mature faster, in about two months instead of three, and they can be grown in crowded conditions for faster breeding. It is only used in the highest priority crosses as it is too labour intensive for everything.”
After three years, they were successful in getting resistant genes or gene regions into the backgrounds of four green and two yellow peas. Further breeding and pathogenicity testing needs to be done before resistant pea varieties can be entered into the variety registration process that is required before making them available to farmers. “I think it will still be another five years until growers have seeds in their hands,” says Banniza.
On the lentil side, it has not been quite as smooth. “We could not find resistance in cultivated lentils,” says Banniza. “So we started testing wild lentil and found good partial resistance in Lens orientalis. This can probably be crossed with cultivated lentils without any problems.”
This is just the start for lentils, she says, explaining that the molecular marker platform developed for peas still needs to be developed for lentils.
“We have developed a solid indoor screening technique, we have a better understanding of the pathogen population, we have developed an efficient breeding platform for pea and are getting closer to having materials that could be tested as varieties and then registered, and we have found good partial resistance in wild lentil relatives, so we can start working on that now, too,” says Banniza.