Using baker’s yeast, the researchers discovered that the plant hormone strigolactone activates fungal genes and proteins associated with phosphate metabolism, a system that is key to growth.

“As we begin to understand how plants and fungi communicate, we will better understand the complexities of the soil ecosystem, leading to healthier crops and improving our approach to biodiversity,” said Shelley Lumba, lead author and assistant professor in the department of cell and systems biology at the University of Toronto.

In the soil, plant roots engage with fungi in a silent molecular “language” to direct their structure. When plants release strigolactones, they signal fungi to attach to their roots, providing phosphates — the fuel plants need to grow, and a major component of most fertilizers — in exchange for carbon.

For the study, Lumba and her fellow researchers investigated why and how fungi respond to strigolactones. Eighty per cent of plants rely on this symbiotic relationship, and enhancing this interaction with beneficial fungi could yield hardier crops, reduce fertilizer use and minimize phosphate runoff into waterways.

In other cases, disease-causing fungi can exploit chemical cues to infect crops, sometimes wiping out entire harvests. Understanding this chemical language could help block such pathogens.

Due to the complexity of the soil ecosystem, scientists couldn’t identify the specific chemicals that encourage beneficial fungi, or the effects of these signals, until now. Lumba and her team cracked the code with baker’s yeast, a quieter fungus that has been domesticated by humans for millennia.

The researchers treated yeast with strigolactones and observed which genes were turned off and on in response. They found that this chemical signal increased the expression of genes labelled “PHO” that are related to phosphate metabolism. Further analysis showed that strigolactones function through Pho84, a protein on the surface of yeast that monitors phosphate levels, activating a cascade of other proteins in the phosphate pathway.

The researchers determined that plants release strigolactones when starved for phosphate, signalling the yeast to change its phosphate uptake.

They found the phosphate response signal holds true not only for domesticated fungi like baker’s yeast but also for wild fungi, specifically the detrimental wheat blight fusarium graminearum and the beneficial symbiotic fungus serendipita indica.

Scientists can use this straightforward method to systematically identify plant-derived small molecules that communicate with fungi. Enhancing the interaction with beneficial fungi could lead to advances in agriculture and mitigate pollution and food insecurity.

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They found that the resistance, which was first detected in Ontario in 2010, has spread thanks to two mechanisms:

• Pollen and seeds of resistant plants are dispersed by wind, water and other means.
• Resistance has appeared through the spontaneous emergence of resistance mutations that then spread.

Researchers found evidence of both mechanisms by comparing the genomes of herbicide-resistant waterhemp plants from midwestern farms in the United States with the genomes of plants from southern Ontario.

“We used modern methods of genome analysis to look at the genetic similarity of different populations of these plants,” explains Julia Kreiner, a PhD candidate in the Department of Ecology & Evolutionary Biology (EEB) in U of T’s Faculty of Arts and Science and lead author of a study published in October in Proceedings of the National Academy of Sciences.

“To our surprise, we found that the genomes of some resistant plants in Ontario were nearly identical to those in very distant U.S. plants. This was evidence that the Ontario plants were very closely related to the U.S. plants and suggests that the former came from seeds that were just picked up from one field and dropped in another.”

While Kreiner and her collaborators did not determine exactly how the seeds were physically transported, this propagation, known as gene flow, is typically accomplished in different ways. Seeds can be carried by water, or in the digestive tracts of animals, or from field to field by way of farm equipment. As well, with a wind-pollinated plant like common waterhemp, genes can also be spread via wind-borne pollen.

The same DNA analysis identified some resistant plants that did not genetically match any other plants suggesting they appeared through the independent emergence of a genetic mutation conveying resistance.

Researchers were surprised to discover both mechanisms at play.

“We have two regions, Walpole Island and Essex County in southwestern Ontario, where waterhemp populations evolved resistance,” says Stephen Wright, a professor in ecology and evolutionary biology at University of Toronto and a co-author of the study.

“Because of their proximity, our expectation was that they would have shared the same origin of resistance. But our results suggest different origins — from the movement of seed from a source population in the U.S., as well as independent evolution of resistance in a local population.”

In addition to the University of Toronto cohort, co-authors included weed scientists from the University of Illinois and the University of Guelph Ridgetown Campus; and genome and developmental geneticists at the Max Planck Institute for Developmental Biology in Germany.

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The study, by an international team of researchers led by University of Toronto assistant professor Adam Martin, used data from the U.N.’s Food and Agricultural Organization (FAO) to look at which crops were grown where on large-scale farmlands from 1961 to 2014.

They found that within some regions crop diversity has actually increased — in North America for example, 93 different crops are now grown compared to 80 back in the 1960s. The problem, Martin says, is that on a global scale we’re now seeing more of the same kinds of crops being grown on much larger scales.

In other words, large farms in Asia, Europe, North and South America are beginning to look the same.

“What we’re seeing is large monocultures of crops that are commercially valuable being grown in greater numbers around the world,” says Martin, who is an ecologist in the Department of Physical and Environmental Sciences at University of Toronto — Scarborough.

“So large industrial farms are often growing one crop species, which are usually just a single genotype, across thousands of hectares of land.”

Soybeans, wheat, rice and corn are prime examples. These four crops alone occupy just shy of 50 per cent of the world’s entire agricultural lands, while the remaining 152 crops cover the rest.

It’s widely assumed that the biggest change in global agricultural diversity took took place during the so-called Columbia exchange of the 15th and 16th centuries where commercially important plant species were being transported to different parts of the world.

But the authors found that in the 1980s there was a massive increase in global crop diversity as different types of crops were being grown in new places on an industrial scale for the first time. By the 1990s that diversity flattened out, and what’s happened since is that diversity across regions began to decline.

He hopes to apply the same global-scale analysis to look at national patterns of crop diversity as a next step for the research. Martin adds that there’s a policy angle to consider, since government decisions that favour growing certain kinds of crops may contribute to a lack of diversity.

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