Wheat, oats and barley are 3 of the most important cereal crops grown in Canada. In addition to our reliance on them as food crops, together, they represent billions of dollars in exports every year.
The long-term health and competitiveness of this critical part of our agri-food sector—and its contribution to global food security—depends on a number of factors, not least the ability of plant breeders to develop new and better varieties: plants that are resistant to an ever-evolving and growing number of pests and diseases; that offer higher yield and enhanced nutritional qualities; and that are able to thrive in different soil and climatic conditions.
Genomics technologies can help, but…
Dr. Nick Tinker studies the potential of genomics to enable breeders to better target their efforts to develop new varieties of oats and other important crops. (AAFC photo)
With funding support from the Government of Canada's Genomics Research and Development Initiative (GRDI), federal researchers like Dr. Nick Tinker at Agriculture and Agri-Food Canada (AAFC) are using advanced genomics technologies to better target and accelerate the breeding process.
"There's no question of the potential of genomics to advance breeding new varieties of these crops," says Dr. Tinker, a senior Research Scientist at AAFC in Ottawa. "The difficulty is dealing with the size and complexity of their genetic structure. The human genome has about 20,000 genes—wheat and oats have as many as 100,000."
And it's not just size. "Modern oats, for example, are descended from 3 wild ancestors, so you're dealing with 3 genomes all mixed together," says Dr. Tinker. "Trying to sequence that genome is like trying to put together 3 very big, very complicated jigsaw puzzles with the pieces for all 3 mixed together in one box."
Significant step forward
Still, progress is being made, and Dr. Tinker and his team at AAFC are playing an important part in that progress. Most recently, with support from the GRDI, Dr. Tinker led a research project that developed what might be considered a "work-around" to deal with the complexity of these cereal crops' genomes.
"With all 3 of these plants, about 90% of their genome is repetitive, and sequencing all of that would take a lot of time and money," says Dr. Tinker. "What we've done is use a fairly new technology known as gene capture or exome capture that literally pulls the genes of interest out of a DNA sample using a magnet, leaving all that repetitive DNA behind. This lets us assemble an almost-complete sequence of the parts of the genome that really matter, and then to do so for many crop varieties instead of just a few."
New database for breeders
Using a series of these DNA probes, Dr. Tinker and his colleagues completed sequences of the "gene space" of some 500 varieties of wheat, 200 varieties of oat and 200 varieties of barley, compiling 3 separate databases that can be accessed by breeders. "This gives us a way to identify better gene markers for use in genomic breeding," explains Dr. Tinker.
How it works
"For example, a breeder may have a genetic marker to identify rust resistance that has worked well in the past, but that doesn't work so well with current breeding lines. With this database, a breeder can look up some of the modern breeding lines that they are working with, look at the region where the rust-resistance marker they've been using is located in each of them and—for the first time—make a deliberate selection of new DNA markers that are customized to work in their breeding material.
"They can also use the database to look for correlations between the variations in those genetic sequences, and how those varieties have performed in different environments in the real world, identify new DNA markers associated with those correlations, and then develop new targets for genomic breeding."
Breeders see the potential
AAFC's oat and barley breeders in Ottawa, Ontario and Brandon, Manitoba are now working with Dr. Tinker on a full-scale study of genomic breeding. While the team continues to improve the database, and their approaches to single-gene prediction developed in their last project, they are now applying a novel approach called genomic selection—allowing selections to be made based on many genes at the same time. This, together with new high-resolution genome sequencing, is moving the team toward an era of "breeding by design".
"Getting our breeders on board is actually a big deal," says Dr. Tinker. "It can take 10 years or longer to go from the first cross to a new variety ready for market, so breeders are understandably very conservative when it comes to trying anything that might upset that process. The fact they are not just ready, but excited to use genomic selection in a significant part of their breeding program tells me we've got some good science here—something that can really accelerate the development of new and better varieties of these important crops."