Genetic discoveries open door to better control of costly soybean disease

In a relatively short time, soybeans have risen to become one of the world's most important food crops. Global soybean production now exceeds 230 million tonnes a year, more than 14 times what it was less than 50 years ago. It's estimated that more than six percent of the world's arable land is now used for soybean cultivationFootnote 1.

Much of the rising popularity of soybeans can be attributed to their nutritional qualities, including a high protein content that makes them an attractive livestock feed. As well, because they also contain lots of fibre, are rich in calcium and magnesium, contain no cholesterol and are very low in the saturated fats, more and more people use soybeans as a substitute for meat in their diets. Tofu, of course, is made from soybeans.

Economic importance

Soybeans are an increasingly important crop in Canada as well. In 2012, Canada produced over 4.9 million tonnes of soybeans, grown on more than 1.7 million hectares of land in Ontario, Quebec, Prince Edward Island and ManitobaFootnote 2. Canadian soybeans are known for their high quality, and Canada's soybean exports are now valued at more than $1 billion a year.

These are the kinds of numbers that Agriculture and Agri-Food Canada (AAFC) research scientist Dr. Mark Gijzen keeps in the back of his mind as he applies the science of genomics to solving one of the most serious problems facing soybean growers in Canada and around the world — a fungus-like organism known as soybean root rot. The disease is costing Canadian growers as much as $50 million a year. Around the world, losses from the soybean root rot are estimated at as much as $2 billion.

With the support of funding through the Government of Canada's Genomics Research and Development Initiative (GRDI), Dr. Gijzen and his team are studying how the soybean plant and the pathogen that causes the disease — Phytophthora sojae, or just P. sojae — interact at the molecular level.

Understanding plants' immune systems

"Just like people, plants have immune systems and, like people, some soybean plants are more immune to disease than others," says Dr. Gijzen. "So, for the past 50 or 60 years, soybean breeders have concentrated on using plants that have shown a resistance to soybean root rot in developing new cultivars. This works, but only for awhile. The pathogen has the ability to mutate into new strains that are able to overcome the plant's resistance — so, it's an ongoing struggle."

Due to the importance of soybeans in so many countries, it's also an international struggle, and thanks to the genomics research capacity established in Canada through the GRDI, Dr. Gijzen has been able to engage in information-sharing sharing collaborations with researchers in the U.S., China and the United Kingdom.

Dr. Gijzen's research has made substantial contributions to this international effort. "Among other things, we've been able to identify many of what are known as 'avirulence factors' in the genomes of specific strains of the pathogen," says Dr. Gijzen. “Avirulence factors are important because soybean resistance genes have learned to use them as cues to activate immune responses that stop the disease — but mutations to these avirulence factors can allow P. sojae to avoid detection by the plant's resistance genes and succeed in infecting the plant.”

Taking it into the field

Based on Dr. Gijzen's findings, a new diagnostic test is expected to be available commercially in the near future that will allow plant breeders to identify at least one strain of P. sojae in the soil. Tests to identify additional strains are expected to follow.

"These tests can be done quickly, right in the field, with inexpensive equipment," says Dr. Gijzen. "Knowing which pathogens are in the soil — because we know more about which of the soybean's resistance genes they are designed to attack — growers can plant soybean cultivars with a different set of resistance genes that the pathogen may not be able to attack successfully."

Filling in the blanks

The Director of Oregon State University's Centre for Genome Research and Biocomputing, Professor Brett Tyler, is enthused and impressed with the results Dr. Gijzen's team is getting. "We've had a really productive collaboration with Mark," says Dr. Tyler. "Genome sequences are only useful when you know what specific genes do and where they're located. Mark's group has done a great job in helping to identify the avirulence genes in the pathogen and how they work — a lot of information we didn't have and that is an essential part of developing new strategies for building resistance in soybeans."

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