Features Cereals Plant Breeding
Preparing for a sustainable future

Back when he was a student, one of Raja Ragupathy’s teachers used to quote the proverb: don’t start digging a well only after the house catches fire. Nowadays, making preparations to deal with a risky future is a cornerstone of Ragupathy’s winter cereal breeding programs.

“[Based on climate change scenarios,] I and most other researchers envision a future in which the availability of water will be a prime limiting factor in crop production. Winter cereals allow Prairie crop growers to take advantage of the moisture available in late fall and early spring. That gives them an advantage over spring-seeded cereals,” explains Ragupathy, a research scientist with Agriculture and Agri-Food Canada (AAFC) at Lethbridge.

Along with his main program to breed perennial cereals, he is breeding winter durum, fall rye and winter triticale. “To prepare for a future where drought will be the new normal and water availability for irrigation will be very limited, we will need a very diverse array of crops. We can’t rely on spring wheat or canola alone.”

In addition to moisture use benefits, winter cereals have other advantages. For instance, they tend to out-yield spring-seeded cereals. Winter cereals usually grow quickly in the spring, helping the crop to out-compete weeds. They mature earlier than spring-seeded cereals, so they may have fewer problems with diseases promoted by warm weather. And winter cereals are valuable for preventing soil erosion in the fall and early spring.

Winter durum: a new crop for the Prairies
“Winter wheat has about a 15 to 20 per cent yield advantage over spring wheat, and durum wheat is a higher value crop. In my breeding program, I’m trying to combine the yield advantage of winter wheat with the price advantage of durum,” Ragupathy says.

He inherited his winter durum breeding program from Jamie Larsen, a research scientist now at AAFC Harrow, who started the program in 2015, and Jordan Harvie, a biologist who took care of the program in 2018. AAFC is an ongoing funder of this program. In addition, the Alberta Wheat Commission (AWC) and the Western Grains Research Foundation (WGRF) provided a three-year grant, starting in 2017, for the breeding work.

“Durum wheat can fetch a price premium over spring wheat and represents yet another crop option for farmers,” notes Lauren Comin, AWC’s director of research.

“A major issue with growing durum is its susceptibility to Fusarium head blight (FHB). Durum wheat lacks the available resistance genes that have been found in the bread wheat gene pool. While the incidence of FHB is still low in Alberta, it is certainly established in the southern regions – the durum growing area. A crop is susceptible to FHB at flowering, and one benefit of a fall-seeded cereal is that the flowering window may occur before the flowering window of spring wheat. Therefore, a winter durum crop may flower before the presence of conditions that favour FHB, and may avoid infection.

“And fall-seeded cereals offer other benefits,” Comin adds. “They are able to make use of more moisture than spring wheat – a benefit in dry areas. They also can help you manage your time better during seeding and harvest.”

Although winter durum is produced in other parts of the world, it is not being grown in Western Canada. “Winter durum is literally a new crop for the Prairies,” Ragupathy says. “Systematic spring wheat breeding for the Canadian Prairies is about 150 years old. Winter wheat breeding for Western Canada started in 1948. But our winter durum program is just five years old. We need to develop winter durum lines that have all the desired agronomic characteristics, disease resistance traits, and also the quality profile – Canadian wheats are known for quality across the world.”

Larsen started the breeding program by assembling a collection of winter durum breeding lines and cultivars from various European countries and the United States. Most of these lines were developed for milder overwintering conditions than in Western Canada.

So, the breeding program’s most crucial task is to develop lines that can survive harsh Prairie winters. To help with that, the program is tapping into the winter hardiness genes in western Canadian winter wheat varieties.

“Fortunately, we have a well-established, successful winter wheat breeding program led by Robert Graf here at Lethbridge,” Ragupathy says. So, Larsen, Harvie and now Ragupathy have collaborated with Graf to source winter hardiness from Graf’s lines, as well as lines from previous AAFC winter wheat breeders and the University of Saskatchewan’s breeding program.

A key challenge in crossing winter durum with winter wheat is that they are two different species. Durum wheat is Triticum turgidum subspecies durum, while winter wheat is Triticum aestivum, the same species as spring-seeded bread wheat.

“Durum wheat is a tetraploid, which means that its genome is composed of two sub-genomes, known as the A and B genomes. Bread wheat is a hexaploid wheat, with three sub-genomes: A, B and D,” Ragupathy explains.

“When you make a cross between durum and bread wheat, you get durum types, intermediate types and bread wheat types. So, essentially I’m looking for plants that are durum types but with the genes that regulate winter hardiness from bread wheat.”

The program’s winter durum lines are mainly evaluated for winter hardiness in the field in Lethbridge, Vauxhall and Saskatoon. Freezing tolerance tests in controlled-environment growth chambers are being optimized for use in the future.

Ragupathy is drawing on the power of genomics to speed up the breeding for winter hardiness. He explains that, in durum, a single locus (a location on the genome) controls 91 per cent of the variation for cold tolerance. This locus is known as Fr-A2. The same locus controls only 24 per cent of cold tolerance in winter wheat because of the impact of the genomic background. Ragupathy will be developing diagnostic DNA markers for this locus so he can screen lines for the trait.

He notes, “I want to genotype all the parental winter durum lines in our collection for the Fr-A2 locus. Then, I will correlate that genotype data with the results from the freezing tests and the field winter hardiness performance of the lines, and use that to identify the best parents for the crosses.”

As well, Ragupathy has a new three-year project that includes developing a genomic selection model for cold tolerance in winter durum. The idea is to be able to predict the cold tolerance behaviour of an individual winter durum plant based only on the plant’s genotypic profile. This approach allows a breeder to identify the most promising plants much earlier in the breeding process. WGRF and the Saskatchewan Wheat Development Commission are funding the project.

Once Ragupathy has a framework of winter-hardy lines, he will increase his emphasis on other traits. He is already on the lookout for lines with high yields, test weights and 1,000-kernel weights, shorter plant heights, and resistance to various diseases.

Since FHB resistance is a key trait, Ragupathy’s genomic prediction project also includes development of a model to predict FHB resistance in winter durum plants.

His research group is currently testing the winter durum lines for stripe rust resistance in Lethbridge. He plans to start testing for other priority wheat diseases – like leaf rust, stem rust, leaf spot and common bunt – in the coming years.

“For the quality traits, right now we are focusing on sprouting resistance, falling number, SDS-sedimentation per cent and grain protein content,” he says. Testing for other quality characteristics will be done on the program’s advanced lines as they come down the breeding pipeline.

Although the winter durum program is only five years old, some of the lines look promising in terms of characteristics like winter hardiness and yield. So when might the program start to release varieties?

“There is the possibility that some of these lines also have very good quality characteristics. If that turns out to be the case, then perhaps in eight to 10 years at a minimum, we might be releasing a winter durum variety,” Ragupathy says.

However, variety development will take longer if the quality traits need to be significantly improved. Even so, Ragupathy points out that recent advances in breeding tools can speed up the breeding cycle. For example, he is using a technique called microspore-based doubled haploid production in collaboration with John Laurie, a research scientist at AAFC Lethbridge. This technique is a way to create inbred breeding lines that is much faster than traditional methods.

Another possible factor influencing the timeline to variety release is that the constraints imposed to keep AAFC employees safe during the COVID-19 pandemic may slow the breeding work this year.

Some advanced breeding methods work exceptionally well with triticale, which speeds up progress in Ragupathy’s winter triticale program.

Fall rye: extra sustainability advantages
In addition to the benefits that all winter cereals offer, fall rye has some extra advantages. Ragupathy explains, “Fall rye has the best cold tolerance among all the winter cereals. It is also adapted to less intensive management than wheat, and to marginally productive lands and drought-prone areas. Its root system is deeper than wheat’s, allowing it to retrieve nutrients and water from deeper in the soil. And because of its large, vigorous root system, its carbon capture is better. Also, fall rye can be grown for grain or forage or as a cover crop.”

His fall rye breeding program’s priorities include grain yield, winter survival, heading date, plant height, standability, test weight, 1,000-kernel weight, falling number, grain protein and resistance to ergot, FHB and rust.

“We have a project with Anita Brûlé-Babel at the University of Manitoba. She is screening fall rye lines for FHB, stem rust and leaf rust. At Lethbridge, we are screening for stripe rust and ergot,” Ragupathy says. He is also optimizing practices like seeding rates and seeding dates to reduce ergot levels in rye.

AAFC is a key funder of the fall rye breeding program. The rye disease project is supported by Saskatchewan’s Agriculture Development Fund, WGRF, Western Winter Wheat Initiative, Saskatchewan Winter Cereal Development Commission, FP Genetics, Ducks Unlimited Canada, SeedNet and KWS.

Ragupathy’s research group works with open-pollinated ryes rather than hybrid ryes. He notes that private companies like KWS have produced some great, high-yielding hybrid varieties. But AAFC believes there is also a place for open-pollinated ryes, especially from a sustainable agriculture perspective.

“[Compared to hybrid ryes,] the lower cost seed, less intensive management and dual-purpose opportunity of open-pollinated ryes can mean that they are a good option for marginal lands,” Ragupathy says. He and his group are conducting various fall rye breeding activities related to sustainability considerations.

For example, he is part of a consortium of researchers working on a fall rye project under SusCrop, a European Union-funded research initiative on sustainable crop production. The project’s objective is to develop lodging-resistant and climate-smart rye as a contribution to sustainable cereal production in marginal environments. This project is currently in its first year.

“SusCrop sent us a hundred-plus lines, including lodging-resistant lines with a dwarfing gene,” Ragupathy notes. “Rye tends to be very tall; we need semi-dwarf lines in our open-pollinated ryes.” His group is now testing the SusCrop lines, and if these lines perform well, he will work on bringing the dwarfing gene into his Prairie lines.

Another of his sustainability-related projects looks at fall rye as a cover crop. This project is supported by the Canadian Agricultural Partnership-based Organic Science Cluster 3, co-ordinated by the Organic Federation of Canada in collaboration with the Organic Agriculture Centre of Canada at Dalhousie University, and funded by AAFC and organic sector partners. Duban Farms Ltd. in Coalhurst, Alta., is a partner in the cover crop project.

Fall rye cover crops can be used as an alternative to tillage for managing weeds in organic cropping systems. Organic growers are interested in no-till because frequent tillage can lead to problems such as soil erosion, nutrient loss and soil moisture loss.

In this project, fall rye is seeded in the fall and then terminated the following spring using a roller-crimper. Fall rye can quickly produce a lot of biomass in the spring, so this termination method results in a weed-suppressing mulch. A spring crop is seeded into the mulch.

“We are optimizing this method in collaboration with an organic farmer, Justin Duban,” Ragupathy says. “We are also identifying and developing fall rye lines that work well with this method, such as lines that have thin stems and a low regrowth capacity.”

Ragupathy is also making use of another sustainability advantage of rye. He explains, “With cross-pollinated crops like rye, you can use multiple parents, rather than just two parents. For instance, you might use five or six parents. Multi-parent breeding strategies result in varieties with more genetically mixed populations.” This genetic diversity means that the polycross variety’s plant stand tends to be more adaptable and better able to tolerate various stresses.

“For our polycross breeding strategy, we have identified some lines that are good for FHB resistance, stripe rust resistance, ergot resistance, leaf rust resistance, yield, short plant height, and so on. And we have crossed those lines to create some elite derivatives, which will be advanced in the breeding pipeline.”

He adds, “Developing and releasing these types of synthetic and composite lines takes less time than your standard line development in a self-pollinated crop like wheat.”

Improving winter triticale
“Triticale is a manmade cereal, a fertile cross between wheat and rye. From wheat, triticale has yield and quality characteristics. From rye, it has a very good root system, cold tolerance, drought tolerance and disease tolerance. Like rye, triticale is suited to marginal lands and low-input management,” Ragupathy says.

“The problem is the market is not there, so this is a small breeding program. We are developing two kinds of winter triticale lines: one is dual-purpose for biomass and grain, and the other is exclusively for biomass [for silage, grazing and cover crops].” The grain is mainly used for feed, although there is a niche market for food uses like specialty breads.

Ragupathy’s winter triticale program is targeting traits like heading date, maturity date, shorter plant height, lodging resistance, winter survival, yield, test weight, 1,000-kernel weight, falling number and ergot resistance. As well, the program is developing lines suited to roller-crimping as part of his organic agriculture project.

Interestingly, Ragupathy says the microspore-based method for developing inbred lines works exceptionally well with triticale. So even though his winter triticale program isn’t currently receiving much funding beyond AAFC’s support, it is making progress.

“In my breeding programs, the lines closest to release are in winter triticale. We have some winter triticale doubled haploid lines developed by Rob Graf and some from Poland that have good falling numbers, high test weights, and high grain protein contents of 12 to 13 per cent. Some lines have grain yields ranging from 4,700 to 5,080 kilograms per hectare under dryland conditions at Warner and as high as 8,000 kilograms per hectare under irrigation at Lethbridge. We also have some material in the pipeline with other interesting traits, such as awnless lines – a big plus for a forage cultivar.”

Ragupathy thinks it is important to keep working on this high-yielding, low-management crop because it has such potential. He emphasizes that diversifying crop rotations by adding minor winter cereals like winter triticale, fall rye and winter durum could help improve the health and resiliency of Prairie cropping systems in the face of changing climates, freak weather extremes, and shifting disease, weed and insect pest pressures.

“I am very passionate about translating advances from the lab to the land,” Ragupathy concludes. “My experience in both breeding and genomics is really helping me to increase the precision and efficiency of breeding to deliver winter cereal varieties with traits that farmers want and need now and in the future.”