‘Huge’ breakthrough made with wheat genetics atlas

Wheat breeding programs around the world have gained access to a powerful new genomic tool that will allow for the more rapid and accurate development of improved, high-yielding wheat varieties.

In a landmark research project led by the University of Saskatchewan, an international team of scientists has successfully sequenced the genomes for 15 individual wheat varieties originating from cereal breeding programs around the world.

The new genome maps will enable scientists and breeders to compare genetic resources within the varieties and much more quickly identify influential genes associated with wheat yield, pest resistance and other important crop traits.

The 10+ Genome Project involved nearly 100 international scientists from universities and plant breeding institutes in Canada, Switzerland, Germany, Japan, the United Kingdom, Saudi Arabia, Mexico, Israel, Australia, and the United States.

Research results, which were published recently in the academic journal Nature, provide the most comprehensive atlas of wheat genome sequences ever reported.

“This is huge,” said project co-leader Curtis Pozniak, a wheat breeder at the U of S’s Crop Development Centre.

“Just two years ago, we only had a single wheat genome available. And while that was useful because it was the first blueprint we had, we’ve now generated and compared multiple wheat genome sequences to help us understand the differences between them.”

Pozniak, who was recently appointed CDC director, said every wheat variety that’s been developed contains subtle genetic differences related to important traits such as yield, disease resistance, pest resistance and drought tolerance.

The new study will allow plant scientists to examine these differences in greater detail and select these genetic traits more quickly and accurately for incorporation into new, more productive and more resilient wheat varieties.

“This resource enables us to more precisely control breeding to increase the rate of wheat improvement for the benefit of farmers and consumers and meet future food demands,” Pozniak said.

The decision on which international wheat varieties would be included in the project was made based on a variety of factors with input from breeders and plant scientists around the world.

Canadian entries included two CDC wheat varieties — CDC Landmark and CDC Stanley, both developed by CDC wheat breeder Pierre Hucl.

Among other reasons, CDC Landmark was selected because it contains genes associated with stem solidness as well as a valuable gene known as Sm1 which confers tolerance to the orange blossom wheat midge, a potentially costly wheat pest.

The Sm1 gene has already been incorporated successfully into several midge-tolerant wheat varieties in Canada.

Characterizing the gene and mapping its location in the CDC Landmark genome will allow it to be accessed more easily by plant breeders in Canada and elsewhere.

Similarly, valuable genetic resources contained in other international wheat varieties have now been mapped and can be studied and accessed with much greater precision.

The second Canadian variety — CDC Stanley — was selected because it contains unique genetic material derived from a foreign plant species.

“We selected Stanley because it has an alien introgression in it, so it has foreign DNA from a species called A. ventricosa. We were interested in sequencing that variety because to my knowledge, it’s the only Canadian wheat variety that carries that introgression,” Pozniak said.

“It provides us with an opportunity to look at that DNA and how it was introgressed into modern spring wheat varieties here in Canada.”

The genetic introgression in CDC Stanley is known to express improved resistance to wheat diseases, including wheat rusts and other leaf diseases.

In certain environments, it has also been associated with yield bumps of four to 10 percent.

“There’s something about that particular introgression that has good disease resistance genes and, at least in some environments, is contributing to a yield benefit,” Pozniak said.

All told, the international research project was able to track the presence of unique genetic material derived from a number of foreign plant species described as “undomesticated relatives” of wheat.

DNA from the undomesticated species has been incorporated into domesticated wheat varieties over the past century, conferring improved disease and stress resistance in wheat.

Learning more about where these genetic resources are located in individual wheat genomes and how they were incorporated is a significant step forward in efforts to develop new varieties with desired traits.

More than 500,000 accessions of wild relatives of wheat have been collected from around the world.

If they can be stabilized and incorporated, wheat breeders believe they have significant potential to enhance the productive potential of cultivated wheat varieties.

“Genetic diversity is the lifeblood of any breeding program,” said Pozniak, when asked about the importance of using DNA from wild wheat relatives.

“We know there are interesting traits (in wild relatives) but it does take time to introgression these traits into cultivated material.”

Rapid advancements have been made in recent years in the ability of plant scientists and genomics experts to map the genomes of individual plant varieties.

In 2018, as part of another international consortium, U of S researchers played a key role in decoding the genome for a bread wheat variety known as Chinese Spring.

The Chinese Spring project resulted in the world’s first complete wheat genome reference and was hailed at the time as a significant technical milestone.

Shortly after that project was completed, the U of S began sequencing wheat varieties that were developed in Canada, and scientists elsewhere began similar work decoding the genomes of varieties that were being grown around the world.

The 10+ Genome project was an effort to co-ordinate those efforts and ensure a greater levels of collaboration and consistency.

The completed study represents the start of a larger effort to eventually generate unique genome sequences for a larger number of individual wheat varieties and add a new level of precision and efficiency to wheat breeding efforts around the world.

“Given the significant impact of the Chinese Spring reference genome on research and application, it is a major achievement that just two years later, we are providing additional sequence resources that are relevant to wheat improvement programs in many different parts of the world,” said project co-leader Nils Stein of the Leibniz Institute of Plant Genetics and Crop Plant Research in Germany.

As well, the Wheat Initiative, a co-ordinating body of international wheat researchers, has identified the 10+ Genome Project as a top research priority.

“This project is an excellent example of co-ordination across leading research groups around the globe,” said Peter Langridge, scientific co-ordinator for the Wheat Initiative.

“Essentially every group working in wheat gene discovery, gene analysis and deployment of molecular breeding technologies will use the resource.”

Pozniak equated the project’s results to finding a missing piece to a complex jigsaw puzzle that plant breeders have been working on for decades..

“Now we have increased the number of wheat genome sequences more than 10-fold, enabling us to identify genetic differences between wheat lines that are important for breeding,” he said.

“We can now compare and contrast the full complement of the genetic differences that make each variety unique.

“By having many complete gene assemblies available, we can now help solve the huge puzzle that is the massive wheat pan-genome and usher in a new era for wheat discovery and breeding.”

Wheat is widely considered one of the world’s most important and valuable cultivated cereal crops. The crop provides about 20 percent of total human caloric intake globally.

It’s estimated wheat production must increase by more than 50 percent by 2050 to meet increasing global demand.

The U of S team involved in the project also included the paper’s first author, Sean Walkowiak, with the Canadian Grain Commission, computer scientist Carl Gutwin, who developed

visualization software and a user-friendly database to compare the genome sequences, and Andrew Sharpe, director of genomics and bioinformatics at the university’s Global Institute for Food Security. Sharpe performed sequencing work through the Omics and Precision Agriculture Laboratory (OPAL), a state-of-the-art laboratory that provides genomics, phenomics and bioinformatics services.

Contact brian.cross@producer.com

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