Plant breeding is strictly a numbers game — but researchers have found a way to improve the odds with help from a new tool called a ‘breeder chip.’
“Breeding is like a lottery. The more tickets you buy, the greater the chance of success,” said Curtis Pozniak, a professor of plant sciences and wheat breeder at the University of Saskatchewan.
“But with a breeder chip, we now have the ability to improve our odds of identifying the very best genetics before they even hit the field.”
Developed as part of a 10-year-long project to sequence the wheat genome, the breeder chip uses more than 5,000 DNA markers from one end of the genome to the other to target specific genes. This information can then help plant breeders select for specific traits more accurately and predict the performance of individual breeding lines.
“We wanted to generate a blueprint of the wheat genome so that we have access to, and an understanding of, all the genes in wheat — the blueprint of what makes wheat wheat,” said Pozniak, who is also co-chair of the Wheat Initiative, an international body that helps co-ordinate wheat research (including the International Wheat Genome Sequencing Consortium).
“But really, the idea behind generating the wheat genome was always to use that to develop tools that we can use as breeders to improve selection efficiency.”
Traditionally, plant breeders have used a small number of DNA markers to help select for traits such as disease resistance and quality. But Pozniak’s team wanted to take that a step further, by using DNA markers for more complicated traits such as yield and fusarium head blight resistance.
“Those traits tend to be much more complex, so we needed a different strategy to apply DNA testing to support selection for those,” he said. “When we have some traits that are difficult to tackle, having access to these technologies gives us one more tool in the tool box to deal with managing those.”
But this breeder chip is only intended to supplement — not supplant — the work that plant breeders are already doing, he added.
“This isn’t going to replace all the other tools and technologies that we’ve been using as plant breeders,” he said. “It’s just one more tool in the tool box, and like any good carpenter, we’re going to be using the appropriate tool for the problem.”
Plant breeders will still need to evaluate the genetic materials and test new varieties in the field, a process that can take upwards of 10 years.
“Genetics are only one component that’s important to plant breeding. The other component is the environment that the plant is grown in, and that impacts how the plant will perform,” said Pozniak.
“So we still need to measure that and understand how a variety performs across a range of environments. That’s actually what takes the most time in breeding.”
A quicker route
While the breeder chip may not shorten the breeding process, it will make it more predictable. Right now, the plant-breeding process faces a key challenge — new genetics could go through the 10-year multi-generation field trial process and still not produce a viable variety.
The breeder chip will help reduce that risk.
“The chip is more useful in proving the reliability of our selections so that we’re testing material in the fields that has the best possible chance of becoming a variety,” said Pozniak.
Currently, plant breeders spend significant time evaluating the yield reliability of their materials in different nurseries and field plots across the Prairies, and then that process is repeated for a number of generations to ensure the variety is stable.
The breeder chip will complement that process “so that the material that we put out in the field has the best chance to become a variety,” said Pozniak. It will allow breeders to analyze their breeding materials, statistically predict their performance, make a selection based on that prediction, and then take the materials to the field for evaluation.
“The process is similar in the sense that breeders will still be taking materials to the field. But they’ll be increasing their odds of identifying good materials with the breeder chip.”
This type of genomic selection will also allow breeders to select for traits much earlier in the breeding process.
“It’s impossible, for instance, to measure grain yield of a potential variety early in the breeding program simply because you don’t have enough seed to plant across a whole bunch of different environments to evaluate yield,” said Pozniak. “But with a DNA test, you can actually start selecting for those traits well before you were able to in the past.”
While Pozniak’s team is still in the early stages of evaluating the breeder chip, the results have been promising so far.
“It will take time to evaluate our progress, but what we are seeing is that the material that we’re putting out in the field for some traits is better than it has been in the past.”
Pozniak is also leading the 10+ Wheat Genomes Project, an international effort to sequence the genomes of even more wheat varieties from breeding programs around the world.
“We’ve sequenced one wheat variety, but in order to really understand what makes one variety different from another at the DNA level, you need to be able to compare,” said Pozniak.
“Now we can start not just looking at the blueprints of one variety but the blueprints of many varieties so that we can understand what makes them different and what makes them better.
“It’s a very exciting time for wheat.”
That work is ongoing, he said. The team has completed the sequencing for 13 varieties from around the world (ensuring a high level of genetic diversity), and now it’s starting to compare those varieties.
“We’re seeing a tremendous amount of difference between varieties. Sometimes we’ll see one variety that has more disease resistance than another,” said Pozniak.
“If we knew the genetic basis for that difference, we might be able to select for it using DNA tests.”
It may seem like a complex process to find out how wheat ticks, but the ultimate goal of both the genome sequencing project and the breeder chip is a simple one — to produce new and improved varieties for wheat growers.
“The whole point of breeding is applying whatever tools we can to develop new varieties for producers,” said Pozniak. “In doing this, we’re improving the efficiency of plant breeding, and that ultimately will result in improved varieties for producers.”