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Sequencing for shorter-day soybeans

Genotyping by sequencing (GBS) was initially developed at Cornell University and adapted by Dr. Francois Belzile, a molecular biologist and geneticist at Laval University, specifically for Quebec and Ontario’s public-sector soybean breeders. Using DNA extracted from a small segment of leaf material, the method yields a unique genetic fingerprint for each soybean line that is composed of thousands of DNA markers. The technique, already available to corn and rice breeders, has been applied to a representative collection of 300 soybean varieties chosen by a team of collaborating breeders, and has produced a vast database that is giving them new knowledge of parent materials and the lines used in their own trials.

“It’s like shining a flashlight on a very small portion of chromosomes and having a glimpse of different tidbits where, at each spot, we’re finding differences,” says Belzile. “By having a more intimate knowledge of what we have inside that plant, we’re able to better compare the performance of different mutations.”

One of the collaborative breeders who became involved is Dr. Louise O’Donoughue of le Centre de recherche sur le grains inc. (CÉROM), in Quebec. O’Donoughue’s work focuses on the development of improved short-season varieties. She is using the marker technology to characterize all eight known genetic regions that affect maturity in potential parental material and the Eastern Canadian germplasm. Before having access to the GBS database, O’Donoughue would have needed a full year to analyze one of these regions, but in the first year of access alone, she says, her team was able to study three regions and additionally identify two new early maturity mutations in one region.

“We have used the GBS approach to characterize both a collection that I put together of exotic lines from Japan, China, and eastern Europe that are potential parents for early maturity and the collection of lines that represent the Eastern Canadian germplasm,” says O’Donoughue. “For the first maturity region analyzed, we found that in the Eastern Canadian germplasm, around 40 per cent have the allele that does not confer photoperiod insensitivity or early maturity, but now that we know what allele is present in each of the lines, we can plan crosses to introduce the desired early maturity allele.”

As far as O’Donoughue is concerned, access to such detailed information will accelerate the breeding program and allow more efficient and economical selection of early maturity.

“If I have the markers for the maturity genes I want, I don’t even have to grow all the lines from a given cross, I can just test seedlings and keep only the ones that will be early,” she says.

This year, O’Donoughue says, she’ll even be able to report field results of some crosses made several years ago. It’s too early to report their yield potential, but O’Donoughue says she has at least 50 lines in her trials that have matured seven to 10 days earlier than Tundra, the Quebec standard for early maturity beans.  With the genotyping data, she can now understand why these lines are early. “By understanding better what’s in a particular plant, I can plan my crosses and look at the effects of different combinations of genes to see which ones are the best both in terms of maturity and yield,” she explains.  

Of course, all breeders know that without adequate yield performances farmers will not be pleased with short-season soybeans. Dr. Steve Molnar is a research scientist at Agriculture and Agri-food Canada (AAFC) who is also working on short-day breeding, though specifically on the genetic end of the AAFC program. He believes that in order to fully appreciate breeders’ recent accomplishments in improving short-day breeding stock, people need to remember that these scientists don’t have the luxury of being able to focus on just those eight regions of early maturity alone.

“Short season alone is not enough,” he says. “Even if you achieve short season, you still need to have lines that perform well for a lot of other characteristics such as protein, oil or sugar content.”

For example, Molnar’s recent work includes a study of early-season breeding stock for improved cold tolerance characteristics. Unfortunately, the GBS method was not available to be used in this eight-year study, but the team was able to identify varieties that expressed a greater tolerance for low temperatures during flowering, and, when crossed with similar parents, the progeny yield eight per cent more than the progeny of cold-sensitive parents. The challenge for researchers such as O’Donoughue is to match behaviour in the field to what Molnar analyzes in the genetic coding of a plant.
“You can make progress sometimes without knowing why you’re making progress and that’s good, because you can’t argue with success,” says Molnar, “but you may be limited in how far you can go if you don’t really understand why the progress is happening.”

As it turns out, this is exactly the problem Dr. Istvan Rajcan, a soybean breeder at the University of Guelph and part of the third collaborative team, is facing. After 20 years of success with OAC Bayfield, his team hasn’t ever known exactly how this variety and its progeny, such as OAC Wallace, became the high yielding varieties they are. While the researchers haven’t argued with the results, they also weren’t clear on how to repeat or improve on that performance. Rajcan is now on the hunt to see if there are variations within the chromosomes of this line that could be combined with variations in other parents to produce even higher-yielding offspring, and after addressing yield, he says it seems the sky is the limit.
“It’s become fairly important for soybeans that we export to Japan to have a higher sugar content,” Rajcan says, “so we can select for sucrose, or isoflavones, or vitamin E, and any number of compounds that are present in the seed could be either reduced or increased based on what we need while maintaining or even increasing seed yield.”

Rajcan says the work never goes as fast as anyone would like but the great thing about the emerging culture in this short day breeding world is greater emphasis on collaboration, regardless of geographic and political boundaries. By bringing some of the region’s top public breeders together and pooling their collective data, significant advancements of the short-season bean are nearly inevitable and the effects are bound to filter into private breeding programs faster than ever before.