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Wheat breeding: Amazing changes

DePauw examines Carberry, a high-yielding, strong-strawed, semi-dwarf with resistance to Fusarium, leaf rust, stem rust, yellow rust, common bunt and loose smut. It is one of many varieties developed by his group using markers and doubled haploid techniques. Photo by Cam Barlow, AAFC.

Looking back at the past 40 years of wheat breeding in Canada, Ron DePauw says, “I’m absolutely amazed at all the changes.” Those changes include impressive advances in quality, disease and insect pest resistance, agronomic traits, and in the technologies used in breeding.

DePauw has seen those changes firsthand during his 48-year career in wheat breeding. He has just retired as senior principal wheat breeder with Agriculture and Agri-Food Canada (AAFC) at the Semiarid Prairie Agricultural Research Centre (SPARC) in Swift Current, Sask. Over the course of his career, he and his team of scientists and technicians have developed 61 varieties of wheat and triticale.

Canadian wheat breeding had its beginnings in the late 1800s. Wheat first came to Canada with settlers, missionaries and others. Many of the wheats they brought from their home countries were not suited to Canadian conditions. So in the late 1800s, William Saunders and his sons began efforts to breed varieties especially for the Prairies. They developed the famous Marquis variety by crossing Red Fife, thought to have come originally from Galicia (currently a province in western Ukraine), and Hard Red Calcutta, from a mountainous region in India. Marquis had Red Fife’s excellent bread wheat quality and Hard Red Calcutta’s early maturity. With that winning combination, Marquis provided a strong foundation for Western Canada agriculture and the economic growth of the nation. Today, about 95 per cent of all wheat produced in Canada is grown on the Prairies.

In the century since Marquis was released, Prairie wheat breeding has made continued progress, and the last 40 years are no exception.

Advances in traits
Over the past four decades, the quality attributes of Canadian wheat varieties have changed and diversified with updates to the wheat classes in the Canada Grain Act. “The changes in wheat classes are all in response to major market changes, such as shifting from a more European focus to an Asian focus, and to changes in what consumers are wanting,” DePauw explains.

For example, in 1993 the Canada Western Extra Strong class was established for varieties with very strong gluten (which previously had been included in the Canada Utility class); those varieties are suitable for making frozen dough products, and the new class helped spur the growth of that industry. In the 1980s, the Canada Prairie Spring Red and Canada Prairie Spring White classes were created for medium hard, medium protein quantity and medium gluten strength varieties targeted for markets in South America, the Middle East, and Southeast Asia. More recently, Canada Western Hard White Spring (2001) was established for the Asian-style noodle market, and General Purpose (2008) for the livestock and ethanol markets.

Along with targeting quality traits, wheat breeders develop varieties with resistance to emerging disease concerns. “Fusarium head blight was really not an issue on the Prairies until about the mid to late 1980s. It is now the number one disease issue. It impacts yield and quality, producing a mycotoxin that is harmful to humans and animals. And it is the most difficult disease in terms of incorporating good genetic resistance,” DePauw notes. “We’ve made progress, but we have not defeated the pathogen.”

Breeders are also working hard to stay ahead of changing rust pathogens. “Over the last 30 or 40 years, major shifts in the leaf rust pathogen have knocked out some very effective resistance genes. Yellow rust [also known as stripe rust] used to be mainly in the Pacific Northwest of North America, but now it is able to reproduce at warmer temperatures, so it can come up from northern Mexico through the Great Central Plains to Canada,” he says.

“Globally, the stem rust race Ug99 is very virulent on important resistance genes like Sr31 and Sr24. Ug99 and its variants could take out about 80 per cent of all the wheat varieties globally. Fortunately, researchers have been developing resistant materials, so if Ug99 gets to North America, we’ll have something for that.” (See sidebar.)

Breeders have also improved insect pest resistance, developing varieties like Lillian, which has stem solidness to combat the wheat stem sawfly, and varieties with a single gene called Sm1 that confers some resistance or tolerance to orange wheat blossom midge.

However, insects and pathogens are continually evolving, and eventually they will be able to defeat genetic resistance in a plant; if there is only a single resistance gene, then it is relatively easy for them to overcome that gene. In the case of Sm1, varieties with this single gene are sold with a refuge to minimize the selection of midges with the ability to overcome the gene. “The bag of seed that a farmer buys is a blend of 90 per cent of an Sm1 variety and 10 per cent of non-Sm1 variety. [Including a refuge in the bag] represents a huge change within the Canadian pedigreed seed system,” DePauw explains. “The Canadian Food Inspection Agency had to make changes in the regulations for that to occur, and the Canadian Seed Growers Association and many other players had to agree with the changes to facilitate pedigreeing a blend.”

Wheat breeders have also developed varieties suited to changes in farm equipment and agronomic practices over the past 40 years. For instance, they have added traits like shorter stature and stronger straw to make zero tillage and straight combining easier and more profitable.

Advances in breeding technologies
According to DePauw, advances in equipment, computerization and biotechnology have revolutionized the capacity of breeding programs over the past four decades.

Breeders, technicians and engineers have worked together to develop specialized small plot equipment to enable more plot work with the same amount of labour. Some examples include mini self-propelled planters that can seed multiple rows of variable row lengths, multi-row planters with the capacity to seed each row with its own specific seed lot, and mechanized plot trimmers to trim the plots so they are all exactly the same length for very accurate yield comparisons.

Computerization has revolutionized data collection and information management. “All of the information in our plant breeding program is integrated: to pedigree all of our genetic materials, to randomize the experiments, to generate electronic field books, to generate planting plans, to generate labels for the harvest bags,” DePauw notes.

As well, computers have transformed data analysis capacity. He says, “[In the late 1940s], it would take several months of work to do just one single analysis of variance of a lattice design. Now our technical people can do that in about half an hour.”

He adds, “Between computerization and equipment advances, I suspect that we are handling five to six times more breeding material with the same number of people [compared to 40 years ago].”

Dramatic changes have also occurred in breeding technologies. “When I was a graduate student, the words ‘biotechnology’ and ‘doubled haploidy’ did not exist,” DePauw says. “The first release of a doubled haploid wheat variety [in Western Canada] was in the late 1990s. Since about 2008, about one-third of the area planted to wheat in Canada is with cultivars that are doubled haploids.” In the doubled haploid technique, researchers first produce haploid cells, which have one of each of the chromosomes rather than a pair of each. Then they use a drug to induce those chromosomes to double, creating identical sets of chromosomes. So the doubled haploid technique is a faster way to create an inbred line that breeds true, compared to the conventional inbreeding process, which takes six to eight generations to develop a line that breeds true to itself.

Another key advance is molecular marker technology, which started to be used in Canada in about the mid-1990s. A molecular marker is a sequence of DNA that is associated with a particular trait. It can be used to quickly screen breeding material for that trait in the lab.

DePauw highlights two examples of the many Prairie wheat varieties developed using markers and doubled haploids. “The variety Lillian is a doubled haploid cultivar developed using marker-assisted selection. It has the Gpc-B1 gene [for high protein], and the Gpc-B1 gene is fortuitously linked to Yr36 [for yellow rust resistance], plus Lr34 [for leaf rust resistance], which is linked to Yr18 [for yellow rust resistance]. So Lillian has a solid stem for wheat sawfly resistance, plus yellow rust resistance and leaf rust resistance. Lillian was the most widely grown cultivar in Western Canada for three or four years. Another doubled haploid cultivar is Carberry, released for commercial production in 2012. It is a strong-strawed, semi-dwarf that has resistance to Fusarium head blight, leaf rust, stem rust, yellow rust, common bunt and loose smut. This combination of traits found favour with producers and it was the most widely grown CWRS [Canada Western Red Spring] variety in Canada in 2014.”

For many years, Canadian wheat breeding has been mainly a public sector endeavour, with AAFC playing a big role. However, AAFC is changing its priorities to focus more on the early steps in the breeding process, like germplasm development, with the idea that agri-business and producer groups would play a major part in the later steps, including variety testing and release. “My point of view is that competition contributes to a healthy environment. So wheat breeding shouldn’t be only public or only private; it has to be both,” says DePauw. He adds, “I think producer involvement is important so breeding programs are not subject only to government budget pressures, and so growers can get their seed from either public or private sector sources.”

Wide crosses for emerging disease threats
Sooner or later pathogens will evolve to overcome the existing resistance genes in wheat. And some of the new disease strains, like Ug99 stem rust, present very serious threats to wheat production. So George Fedak and his research team cross wheat with other grasses to bring in new resistance genes to enable our crops to withstand these emerging threats.

Back in 1990, Peter Lewington wrote a Top Crop Manager article about Fedak’s work with these “wide crosses.”  This research is just as crucial today as it was in 1990, but today’s technologies – like markers and doubled haploids – make this challenging work much more precise and faster.

“Finding these genes and then bringing them into wheat is a long process, but it’s doable and we’re getting more tools all the time,” Fedak, who is a wheat geneticist with AAFC in Ottawa, says.

Fedak and his team test a wide range of species for disease resistance, including the wild relatives of wheat and even other grasses, like quackgrass. For instance, they’ve found Ug99 resistance in species like rye, triticale, wheatgrasses and some of the wild wheats, and Fusarium head blight resistance in quackgrass.

When the researchers find a promising resistance gene, they use various techniques to make sure the gene is different from the previously discovered resistance genes for the same disease. “For example, in rye, there is a stem rust resistance gene called Sr31, which has been defeated by Ug99. So we’re checking all of our rye accessions with the marker for Sr31 to make sure the resistance we’re finding is not Sr31,”  Fedak says.

Once they have found a new resistance gene, the researchers begin the process of moving that gene into wheat. Fedak explains, “You start with a wheat variety that has crossability genes, and you cross your wild species onto that variety. Then for 24 to 48 hours after you make the cross, you apply growth hormones to the pollinated florets to stimulate embryo growth. Then, if you excise that young embryo at 14 days after pollination and put it on an artificial medium, it may grow.”

The result of such a cross is usually a sterile haploid. So the researchers either use a doubled haploid technique or they backcross it with the original wheat line to restore most of the wheat chromosomes while still retaining some of the material from the wild species. Then the progeny can be tested to see if they have the disease resistance trait.  

Wild species often have undesirable traits such as late maturity or poor seed set, so the researchers don’t want to bring in too many other genes along with the disease resistance gene. The extra, undesirable genetic material from the alien species is called linkage drag. Progress in breeding technologies over the last few decades, such as the development of more and more markers, has enabled the researchers to minimize linkage drag.

Using these types of techniques, Fedak’s team has achieved significant advances. For example, the researchers recently developed a wheat line with four resistance genes: one for leaf rust, two for Ug99 stem rust, and one for Fusarium head blight. In another project, a student has developed wheat lines that carry four different stem rust resistance genes, all resistant to Ug99, because pyramiding the four genes together results in much more durable resistance.

As he looks ahead, Fedak is concerned that few Canadian researchers are still doing this type of pre-breeding work to bring resistance genes from wild species into wheat and other crops. He recalls that, from about the late 1960s to early 1990s, AAFC scientists Eric Kerber and Peter Dyck crossed wheat with its wild cousins to produce a large supply of new disease resistance genes ready for use by breeders if and when the genes are needed. For instance, some of Kerber and Dyck’s stem rust resistance genes are resistant to Ug99, so Fedak’s team has been using those genes in the work to pyramid Ug99 resistance genes.

“I think we need a continued effort to bring new disease resistance genes into pretty well every crop,” Fedak says. “We need people to keep looking at wild species for new genes for leaf rust resistance, stem rust resistance, mildew resistance, Fusarium head blight, barley yellow dwarf virus – all kinds of diseases – and to put those in a background without too much linkage drag.”  That way, when the next devastating disease strain comes along, we’ll have genes on hand to fight back.

June 17, 2015  By Carolyn King