Marking and shuffling isn’t just for card sharks. Companies are using these biotech tools in a high stakes game to help move new traits to market faster

So far, soybean cyst nematode or SCN-resistant soybean varieties have been developed using traditional breeding procedures. But biotechnology is still part of the story because options from the biotechnology toolbox shorten the breeding and development process.

One of the most common tools used by plant breeders is called gene marker technology. Once a research scientist identifies the gene within a soybean plant that makes it resistant to SCN, he or she can use gene marker technology to tell whether that gene made it into the result of a cross between 2 varieties.

“We’re able to pick out a plant in the lab and test it using marker technology to see if the trait is there before it goes in the field,” says Don McClure, soybean breeder for Syngenta. “It works extremely well for traits that are hard to test.”

As McClure says, it’s a rotten job to have to trudge out to a soybean plot and dig up roots to count cysts, especially when you’re not even sure the plant you’re evaluating has the resistant trait you’re trying to develop. Marker technology means researchers don’t have to waste time growing out the variety and exposing it to soybean cyst nematodes to determine whether the breeding effort was successful in conveying the SCN resistance.

Gene marker technology isn’t new. It’s roughly 10 years old but its effect — helped by new, faster methods of finding specific genes — is driving faster and more productive research.

“If the trait is based on a gene already in the genetics of that crop, commercialization can happen quicker if you use molecular markers,” says Istvan Rajcan, a public soybean breeder at the University of Guelph. “The big international players all have highly developed marker selection programs.”

Rajcan is using gene markers to help in his research on phytophthora, SCN and brown stem rot resistance and in his breeding program for high-oil soybeans suitable for biodiesel production.

On the SCN front, Rajcan found SCN resistance in a wild soybean variety from China that looks more like a climbing weed than a commercial soybean variety. He plans to breed the SCN resistance from the wild soybean into commercial lines for Ontario.

The first step is to determine which part of the wild plant’s genome enables the plant to be resistant to SCN. Once he has that identified, he starts crossing the original Chinese soybean plant with commercial varieties. The result of the first cross doesn’t look much more like a commercial variety than the Chinese progenitor. Many more crosses will be needed before the resulting plant would be commercially viable.

Just because the resistance gene is in one of the parent lines doesn’t mean it will make it through to the new cross. Through DNA marker technology, Rajcan can make sure the gene that causes SCN resistance made it to the new cross.

To use the marker technology, he takes a tiny leaf sample and puts it in a special tube with tiny steel beads. A machine then shakes the tube to break apart the DNA that makes up the leaf. Another machine takes this sample and heats it up to break apart the strands of DNA. Once they’re separated, the strands start to reproduce. The individual strands of DNA would be too hard to see but once they start to reproduce or copy they go into another machine where gel and special lights help show which genes are present.

If a leaf sample shows that none of the desired genes are present in the new cross, Rajcan can discard that plant and focus on crosses that are expressing the proper gene. Pioneer Hi-Bred has patented another technology that is helping them race new traits to market. They call it “gene shuffling”. Rachel Faust, communications co-ordinator with

Pioneer Hi-Bred, draws a sports analogy to explain the complicated process. She says gene shuffling doesn’t help discover or develop new genes; it just helps “train” genes for higher functionality.

Researchers start by heating the genes in a test tube where they separate. When the solution starts to cool the fragments come back together in new combinations. Proteins are expressed from each gene in subtly different ways, some of which could result in a trait that could improve performance. The researchers can test the new combinations and choose the best one to keep. Gene shuffling isn’t a way to discover or insert new genes. It’s just making existing genes work harder.