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Proactive pathogen defences

Researchers have been stumped by pathogens plaguing the agricultural community for years.


May 23, 2014
By Amy Petherick

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They know these microbes are out there, see the effects causing farmers distress, and have helped develop products to help manage these effects. But they really haven’t understood what makes these organisms tick. Now they’re getting closer.

Next-generation genome sequencing has opened a window into the world of the very small, allowing scientists access to unfathomable amounts of information. More than they could process at first. New systems of data management are emerging however, and that’s helping. When Barry Saville, a professor and researcher at Trent University, started working in the field of molecular research, it took months just to discover small segments of DNA code and even longer to understand what it meant. But using today’s technology is advancing his knowledge of field crop diseases – such as corn smut and wheat rusts – in an exponential way, which is changing the way he thinks about crop protection.

“Farmers have transgenics that they’re dealing with and they know how these work,” says Saville. “If a plant can express a bacterial toxin like Bt, why not have it express something that can stop fungal growth?” he asks.

Fungal diseases are very familiar to Saville, who began working with corn smut after learning how easily manipulated the organism’s DNA is. Corn smut is also a biotroph, which means it has to get its food from a plant by keeping that plant alive. “These disease-causing fungi produce proteins that go into the plant and reprogram plant cells so that the plant feeds the fungus,” Saville says. As it happens, Saville believes he may now be able to identify some of the genetic codes that lead to the formation of these proteins. He is learning these codes can look the same in other biotrophs, such as wheat leaf rust and maybe even UG99, which has him excited about developing new kinds of genetic disease resistance.

“There is a system in the cells of humans, plants and fungi that shut down genes that might be viruses or other bad things, called RNA interference,” says Saville. “The idea is to use this system in the fungi against the fungi. For example, we could alter plants using a disarmed virus so they produce an RNA
taken up by the fungus, for example wheat leaf rust, or wheat stem rust, or UG99, and that RNA would stop the growth of the fungus.” Saville goes on to explain that now that researchers know the codes for the fungal proteins that alter the plants, these codes can be the targets of this approach, when these genes are turned on, they will produce a molecule that is like one half of a zipper and the RNA introduced will be the other half of the zipper. When the zipper is closed, the resulting molecule is destroyed by the fungus’ own defence systems and the gene is shut down stopping the fungus’s ability to feed on the plant. “The virus is on a suicide mission,” Saville says. “The fungus takes it up and that RNA blocks the ability of the fungus to continue infecting.”

Saville has only recently begun toying with the idea of testing the method on corn smut in a greenhouse environment and any practical application is years into the future. But he says the basic research of confirming the identity and function of these vectors is what makes future applications possible.

Tom Graefenhan is a research scientist with the Canadian Grain Commission (CGC) in Winnipeg, Man., who also studies pathogens using next generation technology. But Graefenhan’s interest is potential impact to end-use quality and market access of Canadian grains, not just agronomy applications. Since the CGC provides foreign buyers with letters of assurance guaranteeing shipments are free of potentially harmful microorganisms regulated in their country, Graefenhan has to be well aware of all the fungi, yeasts and bacteria which culture on seed. In cereals, this includes 100,000 to one million colony-forming units representing hundreds of different species per gram of seed.

“Every single seed is a microcosm for these organisms; it’s their planet,” he says. “Numbers of colony-forming units depend a lot on the environmental conditions a seed was grown in, and Canada tends to have more microbes compared to an Australian climate which is very hot, very dry.”

Without the right tools, finding detrimental species in the microflora of any given wheat, rye or barley sample is very much like trying to find a needle in a haystack. Even worse, Graefenhan says traditional monitoring methods required researchers to grow cultures on artificial media for identification and some fungi are so highly adapted to their hosts, they wouldn’t grow in the lab.

“We knew they were there but we couldn’t look at them,” he says. “With these DNA methods, you can take the raw grain, wash the microbes off those seeds, and the DNA technology gives us the ability to identify single molecules.”

In the same way fingerprints can identify an individual, little pieces of genetic code can tell Graefenhan what species of fungi were living in a seed sample. More importantly however, these codes also can tell him what the fungi was likely doing on that seed and if it would impact end use grain products (such as in sourdough fermentation or barley malting).

“These are things you cannot tell just by looking at the fungus through a microscope,” he says. “It may take us decades to decode the genomes of all these microorganisms, but once we have this information, then we can look for all kinds of characteristics, good and bad.”

Albert Tenuta, field crop plant pathologist with the Ontario Ministry of Agriculture and Food, says knowing more about pathogens is a necessary step in defending against them in the future, because it’s only getting harder to protect our food sources from them.

“Knowing what is out there can allow us to better target our genetic breeding efforts to anticipate those changes,” says Tenuta. “If we have a good understanding of a pathogen’s genetic make up, that can allow us to test germplasms to best protect against them.” Studies have been published for two decades describing which varieties hold up best against pathogens of all sorts, both in the field and through a variety of food processing methods, but explanations of these observances have been limited, to the dismay of few. As long as the result was consistent, answering “How?” hasn’t always been a priority. But Tenuta warns that these days may be over as pathogens evolve.

“With leaf rusts for instance, we often see resistance only last two or three years in the field because the pathogen has adapted to bypass the resistance breeders have developed,” he says. “We’ve done a wonderful job both from a breeding aspect and a management aspect, in reducing our risk over time, but things always change and knowing what is coming in the future is important in terms of planning our defences.”