Harnessing the power of 'informatics' to boost Canadian wheat breeding

from Western Grains Research Magazine
January 2004

New tools from informatics give Canada's wheat breeders new power to tackle Fusarium resistance and other complex traits, while boosting overall breeding precision and success. Dr. Daryl Somers leads an innovative new WGRF Endowment Fund project designed to tap this dramatic potential.

When it comes to breeding new varieties of wheat, success depends heavily on choosing the right plant parents.

To hedge their bets, breeders typically make a large number "parent crosses," of which only a select few eventually result in marketable varieties that payoff in both the field and the market. Following through on each cross is a long process, typically taking seven to 12 years, and there are no assurances of success.

Now, a new research project is underway that aims to boost the efficiency, power, speed and success of this process, bringing broad benefits to wheat growers and their industry.

Dr. Daryl Somers, a molecular genetics research scientist with Agriculture and Agri-Food Canada's Cereal Research Centre in Winnipeg, and colleagues are developing a new "informatics" system - a combination of a database and related software - designed to give wheat breeders access to better genetic information on which to base their breeding strategies. The system would help researchers pinpoint the best possible parents to cross for specific breeding goals, reducing the number of crosses needed while boosting the chances of breeding success. It would also allow them to pursue molecular breeding approaches that are more precise and effective than more traditional approaches.

Somers' project is the first supported under a new "innovation" category of the Western Grains Research Foundation Endowment Fund, in recognition of it's broad potential to benefit the western grain industry. (See background on the Endowment Fund.) For Western Grains Research Magazine, Somers discusses the project, what it means for wheat breeding in Western Canada and how wheat producers stand to benefit.

Q: What is molecular breeding and how does it relate to informatics?

A: Molecular breeding is simply a form of conventional breeding that allows breeders to have a better understanding of the parents that go into crosses. It's important that producers and others realize this is not an approach that involves genetic engineering or the development of genetically modified crops.

Molecular breeding is a specialized area of plant science that relies on collecting genetic information about plants. This information is essentially what is known as DNA fingerprinting information. When we have this sort of information, we can look at a particular wheat plant and understand it's genetic make up and history. By understanding it's genealogy and parentage, we can understand where particular genes are derived from. By better understanding our breeding material, we can also structure our breeding approaches accordingly for the best chances of success.

One aspect of our new Endowment Fund project is to work with approximately 400 'molecular markers' covering the wheat genome. Molecular markers are DNA-based indicators that will help breeders identify the presence of key wheat traits, such as specific disease resistance or quality characteristics. We're going to use those markers to genotype, or fingerprint, 200-300 different accessions of wheat, including all Canadian wheat varieties. This will create an unprecedented database of wheat genotypic information that can be used to determine which crosses may be more valuable than others.

An informatics-based database will organize all the genetic information and give breeders the opportunity to ask specific questions using the software to make selections and narrow down their search for the desired parents. Breeders will be able to look for particular traits they want to breed by going back through the history of the plant to see where traceable characteristics appear.

Q: Why hasn't this project been attempted before?

A: The area of informatics has been pretty productive in the last five years, but there has been a bit of a delay in getting the plant breeding community to take it up. Molecular breeding has been around for a number of years, but not at the level we're doing it now. In the past we could select for a particular resistance gene using a simple diagnostic DNA test. Now, there's more interest in looking at the entire wheat genome for a couple of parents you want to make a cross with. The sheer volume of information has dramatically increased, so it is now that we need to develop tools to basically manage this new data.

Q: How will this new system help the industry make progress toward Fusarium Head Blight resistance and other complex traits?

A: Fusarium Head Blight is probably the single most important reason we pursued the current research project. We currently have funding in place through the WGRF Wheat Check-off Fund and the Agriculture and Agri-Food Canada Matching Investment Initiative (MII) to accelerate the integration of Fusarium resistance genes, as well as leaf rust and midge resistant genes, into elite Canadian wheat.

For 20 months, we've been using almost exclusively molecular breeding to obtain this data. We have a lot of knowledge about where the genes are that control Fusarium resistance. But it has proven very difficult to detect the presence of these genes when examining lines in the field. By looking at DNA fingerprints, it is quite easy to see these genes. This information is available, but not in an easy format for all researchers to use. That's why we need to move forward with informatics, to store what we've learned about Fusarium and allow others to have access to the data for their own breeding use.

Q: What will the project mean for Canadian wheat breeding programs?

A: In wheat breeding, less than one percent of all the crosses made end up in a variety. To a layperson, that may seem incredibly inefficient, but that's the nature of the beast. What we want to do is provide new tools and new information so we can stop making crosses that won't result in anything, and start spending more time with fewer crosses that will result in superior material.

What is most important in plant breeding is picking your parents. For example, a plant breeder might make 50 crosses in one year. If we could provide them with much more precise information so they would only make 25 or 35 crosses, then they would have fewer crosses to deal with and would be able to spend more time and attention on their crosses understanding the results of their selection.

Breeders are already aware of what parents are available, but often this data comes in spreadsheets with numerous columns and reams of data. We're taking about developing software where we will have a full genome genotype of all possible parents. So when we ask, for example, which parents will provide high yield and Fusarium resistance, this informatics tool will indicate to the breeder which genes will be traceable in progeny and which are the best sets of molecular markers to do that tracking of those genes.

I honestly believe in the next three years, we're going to reach a tipping point in wheat breeding and molecular breeding. You have to imagine there is going to come a point where molecular breeding becomes routine and a very valuable part of the process. I firmly believe we are just a few years away from reaching this tipping point where it won't make sense to ignore large-scale molecular breeding.

Fusarium resistance, leaf rust resistance and yield all involve complex genetics. It makes sense to understand as much as you can about the plant parents, including genotype, before you make decisions about crossing one parent with another.

Q: What results can producers expect?

A: The bottom line is that we are expecting to develop better varieties faster. Overall, producers can expect greater annual gains in wheat trait improvement, for a variety of valuable traits.
With regard to Fusarium, there is no question we are going to have much more resistant material sooner because of the progress through molecular breeding. With more traditional approaches, we can continue plodding along and making progress, but Fusarium progress can be accomplished much faster with molecular breeding.

I suspect that within the next two years we will have some solid outdoor testing done of the products of our molecular breeding effort with Fusarium, and we'll have a much better idea of just how successful we're going to be.

Q: How does Canada compare with its wheat competitors in taking advantage of molecular breeding and informatics?

A: There is no doubt that other wheat exporting countries are currently making use of or will be making use of molecular breeding. From the Canadian perspective, it is very important we position ourselves as a leader in this area. The rate of innovation is increasing, and those countries that get to market first with the highest quality material are the ones that are going to be most successful in the international markets. We know the Europeans, Australians and to some extent, the U.S., are making headway in molecular breeding. Our current project is an important step for Canada to keep competitive with these countries and take advantage of a position at the forefront of innovation.

Western Grains Research Foundation is funded and directed by Western crop producers, and allocates approximately $5 million annually to research through the Wheat and Barley Check-off Funds and a separate $9 million Endowment Fund.