Study Generates First Genomic Atlas For Global Wheat Improvement

USask-led study sequences genomes of 15 wheat varieties around the world

Saskatoon, SK (November 25, 2020) - In a landmark discovery for global wheat production, a University of Saskatchewan (USask)-led international team has sequenced the genomes for 15 wheat varieties representing breeding programs around the world, enabling scientists and breeders to much more quickly identify influential genes for improved yield, pest resistance and other important crop traits.

The research results, just published in Nature, provide the most comprehensive atlas of wheat genome sequences ever reported. The 10+ Genome Project collaboration involved more than 95 scientists from universities and institutes in Canada, Switzerland, Germany, Japan, the U.K., Saudi Arabia, Mexico, Israel, Australia, and the U.S.

“It’s like finding the missing pieces for your favourite puzzle that you have been working on for decades,” said project leader Curtis Pozniak, wheat breeder and director of the USask Crop Development Centre (CDC). “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.”

Scientific groups across the global wheat community are expected to use the new resource to identify genes linked to in-demand traits, which will accelerate breeding efficiency.

“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.

One of the world’s most cultivated cereal crops, wheat plays an important role in global food security, providing about 20 per cent of human caloric intake globally. It’s estimated wheat production must increase by more than 50 per cent by 2050 to meet increasing global demand.

In 2018 as part of another international consortium, USask researchers played a key role in decoding the genome for the bread wheat variety Chinese Spring, the first complete wheat genome reference and a significant technical milestone. The findings were published in the journal Science.

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

Nils Stein of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) and project co-leader from Germany said, “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.”

The 10+ Genome study represents the start of a larger effort to generate thousands of genome sequences of wheat, including genetic material brought in from wheat’s wild relatives.

The research team was able to track the unique DNA signatures of genetic material incorporated into modern cultivars from several of wheat’s undomesticated relatives by breeders over the century.

“These wheat relatives have been used by breeders to improve disease resistance and stress resistance of wheat,” said Pozniak. “One of these relatives contributed a DNA segment to modern wheat that contains disease-resistant genes and provides protection against a number of fungal diseases. Our collaborators from Kansas State University and CIMMYT (Mexico) showed that this segment can improve yields by as much as 10 per cent. Since breeding is a continual improvement process, we can continue to cross plants to select for this valuable trait.”

Pozniak’s team, in collaboration with scientists from Agriculture and Agri-Food Canada and National Research Council of Canada, also used the genome sequences to isolate an insect-resistant gene (called Sm1) that enables wheat plants to withstand the orange wheat blossom midge, a pest which can cause more than $60 million in annual losses to Western Canadian producers.

“Understanding a causal gene like this is a game-changer for breeding because you can select for pest resistance more efficiently by using a simple DNA test than by manual field testing,” Pozniak said.

The USask team also included the paper’s first author Sean Walkowiak (formerly with Pozniak’s team and now 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 USask Global Institute for Food Security, who did sequencing work through the Omics and Precision Agriculture Laboratory (OPAL), a state-of-the-art laboratory that provides genomics, phenomics and bioinformatics services.

The 10+ Genome Project was sanctioned as a top priority by the Wheat Initiative, a co-ordinating body of international wheat researchers.

“This project is an excellent example of co-ordination across leading research groups around the globe. Essentially every group working in wheat gene discovery, gene analysis and deployment of molecular breeding technologies will use the resource,” said Wheat Initiative Scientific Co-ordinator Peter Langridge.

Canadian funding came from the Canadian Triticum Applied Genomics (CTAG2) research project funded by Genome Canada, Genome Prairie, the Western Grains Research Foundation, Government of Saskatchewan, Saskatchewan Wheat Development Commission, Alberta Wheat Commission, Viterra, Manitoba Wheat and Barley Growers Association, and the Canada First Research Excellence Fund through USask’s Plant Phenotyping and Imaging Research Centre (P2IRC) initiative.

“This project is a prime example of how genomics can support increased resilience in food production and strengthen Canada’s export leadership,” said Genome Canada President and CEO Rob Annan.

“Deploying genomics to adapt agricultural production to climate change, address food and nutritional insecurity, and improve crop health is good for farmers and consumers, and our economy will see tangible returns from this research. Genome Canada is immensely proud of the exceptional work by the Canadian researchers and their international collaborators, which underscores the potential of genomics to make a positive impact on the lives of Canadians and others around the world.”

Israeli company NRGene, which has an office in Saskatoon, constructed the genomic assemblies. A complete list of international funding partners is available here: http://www.10wheatgenomes.com/funders/

About the University of Saskatchewan’s Crop Development Centre (CDC): The Crop Development Centre in the USask College of Agriculture and Bioresources is known for research excellence in developing high-performing crop varieties and developing genomic resources and tools to support breeding programs. Its program is unique in that basic research is fully integrated into applied breeding to improve existing crops, create new uses for traditional crops, and develop new crops. The CDC has developed more than 500 commercialized crop varieties. https://agbio.usask.ca/researc...

CIMMYT contributes to sequencing genomes of 15 wheat varieties around the world

(November 25, 2020) - In a landmark discovery for global wheat production, an international team led by the University of Saskatchewan and including scientists from the International Maize and Wheat Improvement Center (CIMMYT) has sequenced the genomes for 15 wheat varieties representing breeding programs around the world, enabling scientists and breeders to much more quickly identify influential genes for improved yield, pest resistance and other important crop traits.

The research results, just published in Nature, provide the most comprehensive atlas of wheat genome sequences ever reported. The 10+ Genome Project collaboration involved more than 95 scientists from universities and institutes in Australia, Canada, Germany, Israel, Japan, Mexico, Saudi Arabia, Switzerland, the UK and the US.

“It’s like finding the missing pieces for your favorite puzzle that you have been working on for decades,” said project leader Curtis Pozniak, wheat breeder and director of the USask Crop Development Centre (CDC). “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.”

“These discoveries pave the way to identifying genes responsible for traits wheat farmers in our partner countries are demanding, such as high yield, tolerance to heat and drought, and resistance to insect pests,” said Ravi Singh, head of global wheat improvement at CIMMYT and a study co-author.

One of the world’s most cultivated cereal crops, wheat plays an important role in global food security, providing about 20 per cent of human caloric intake globally. It’s estimated that wheat production must increase by more than 50% by 2050 to meet an increasing global demand.

The study findings build on the first complete wheat genome reference map published by the International Wheat Genome Sequencing Consortium in 2018, increasing the number of wheat genome sequences almost 10-fold, and allowing scientists to identify genetic differences between wheat varieties.

The research team was also able to track the unique DNA signatures of genetic material incorporated into modern cultivars from wild wheat relatives over years of breeding.

“With partners at Kansas State University, our CIMMYT team found that a DNA segment in modern wheat derived from a wild wheat relative can improve yields by as much as 10%,” said Philomin Juliana, CIMMYT wheat breeder and study co-author. “We can now work to ensure this gene is included in the next generation of modern wheat cultivars.”

The team also used the genome sequences to isolate an insect-resistant gene called Sm1, that enables wheat plants to withstand the orange wheat blossom midge, a pest which can cause more than $60 million in annual losses to Western Canadian producers.

“Understanding a causal gene like this is a game-changer for breeding because you can select for pest resistance more efficiently by using a simple DNA test than by manual field testing,” explained Pozniak.

The 10+ Genome Project was sanctioned as a top priority by the Wheat Initiative, a coordinating body of international wheat researchers.

“This project is an excellent example of coordination across leading research groups around the globe. Essentially every group working in wheat gene discovery, gene analysis and deployment of molecular breeding technologies will use the resource,” said Wheat Initiative Scientific Coordinator Peter Langridge.

The International Maize and What Improvement Center (CIMMYT) is the global leader in publicly-funded maize and wheat research and related farming systems. Headquartered near Mexico City, CIMMYT works with hundreds of partners throughout the developing world to sustainably increase the productivity of maize and wheat cropping systems, thus improving global food security and reducing poverty. CIMMYT is a member of the CGIAR System and leads the CGIAR programs on Maize and Wheat and the Excellence in Breeding Platform. The Center receives support from national governments, foundations, development banks and other public and private agencies. For more information visit www.cimmyt.org

Global collaboration is unlocking wheat's genetic potential

Manhattan, KS (November 25, 2020) - In a paper published Wednesday, Nov. 25, in Nature, Kansas State University researchers, in collaboration with the international 10+ Genome Project led by the University of Saskatchewan, have announced the complete genome sequencing of 15 wheat varieties representing breeding programs around the world -- an invaluable resource to improve global wheat production.

This effort gained momentum in 2018 when the Kansas State University team, in collaboration with the International Wheat Genome Sequencing Consortium, published the genome assembly of Chinese Spring, the first complete reference genome of bread wheat. With rapid advances in DNA sequencing technology, and with experience from assembling the first wheat genome, the 10+ Genome Project brought together the expertise and resources of more than 95 scientists from universities and institutes in Canada, Switzerland, Germany, Japan, the U.K., Saudi Arabia, Mexico, Israel, Australia and the U.S.

This study represents the start of a larger effort to generate thousands of genome sequences of wheat, including genetic material brought in from wheat's wild relatives.

"It's like finding the missing pieces for your favorite puzzle that you have been working on for decades," said project leader Curtis Pozniak, wheat breeder and director of the University of Saskatchewan Crop Development Centre. "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."

"Our team was uniquely suited to represent U.S. wheat in this effort here in America's breadbasket and as a land-grant institution with a strong history in wheat research," said Jesse Poland, associate professor at Kansas State University and director of the Feed the Future Innovation Lab for Applied Wheat Genomics and the Wheat Genetics Resource Center. "We are fortunate to have world leaders in breeding and genetics under one roof, and generous support from the National Science Foundation, Kansas Wheat and many others."

The Kansas team was responsible for sequencing and analyzing the hard red winter wheat variety Jagger, released in 1994 by the Kansas State University breeding program, now led by Allan Fritz. Jagger was a landmark wheat variety in the Great Plains and covered millions of acres for many years. It was selected for this project because of its relevance as a breeding parent as it is found in the pedigrees of current varieties across the U.S.

"Because of our collaboration in this project, we've had access to this phenomenal genomics resource as it's been built, which has already led to tremendous discovery," Poland said. "K-State plant genetics graduate student Emily Delorean is using data from the 10+ Genomes Project to develop a comprehensive analysis of important quality genes and develop better molecular breeding tools, which will have a huge impact on bread making."

In a companion publication published in Theoretical and Applied Genetics, Kansas State University scientists Liangliang Gao, Dal-Hoe Koo and team completed detailed characterization of the 2N introgression, a chromosome segment that was transferred from wild wheat relative Aegilops ventricosa, which is found in Jagger, but was not present in the original Chinese Spring reference genome. The 2N segment possesses resistance genes to multiple wheat diseases, including stem and leaf rust, nematodes and the emerging wheat blast disease. The team found that this chromosome segment is present in about 80% of Kansas wheat lines and also a large proportion of wheat around the world, marking its importance toward addressing global wheat improvement.

"Progress of this magnitude is only possible because of the strength of the international wheat breeding network and strong international collaborations in wheat research," said Justin Gilpin of Kansas Wheat. "It is exciting for the Kansas wheat growers to be part of this excellent work."

The work at Kansas State University was supported by the NSF, Kansas Wheat, the United States Agency for International Development, and the National Institute of Food and Agriculture. A complete list of international funding partners is available at http://www.10wheatgenomes.com/funders/.

Global wheat diversity mapped in huge international collaboration

(November 25, 2020) - Wheat is one of the crucial staple crops which underpins civilization, providing a vital source of protein for billions worldwide. However, the effects of climate change threaten future yields of the world’s most widely-cultivated cereal, production of which must increase by around 60% in the next 40 years if we are to meet global calorie demands.

Earlham Institute researchers along with colleagues at the John Innes Centre and the Natural History Museum have been at the heart of a global collaboration, published in Nature, working to give future wheat yields a much needed boost. Known as the 10+ Wheat Genomes project, the aim is to map all of the genetic diversity of wheat in what’s known as a ‘pan genome’.

“It’s like finding the missing pieces for your favorite puzzle that you have been working on for decades,” said project leader Curtis Pozniak, wheat breeder and director of the University of Saskatchewan Crop Development Centre (CDC). “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.”

Professor Anthony Hall, Head of Plant Genomics at EI - and a leader of the 10+ Wheat Genomes collaboration - said: “We have generated genomes for important wheat varieties from across the globe. Knowing the sequence of these genomes allows us to use wheat as a model crop species, in the same way we use rice and maize, and changes the way research and breeding can be done.

“It allows us to understand how breeding histories have shaped this complex genome, address fundamental questions about evolution and selection, and rapidly identify markers associated with genes controlling key agricultural traits.”

Earlham Institute researchers were the first to map the wheat genome in detail, and since then have contributed to each and every improvement with better assemblies and annotations. The aim of the latest research was to define the entire DNA sequence of multiple varieties of wheat sourced from breeding programmes across several continents, detailing where important genes can be found across these different varieties in the process.

Dr Bernardo Clavijo, Group Leader at EI - who led genome assembly for five cultivars - said: “The extraordinary plasticity and resilience of the hexaploid wheat genome, and a rich history of genetic recombination with related species, provide a great platform for genetic improvement. But the complexity of the genome, and the variation between different cultivars, makes it a challenge to fully exploit the breeding potential of this key crop.

“After our release of the first wheat reference to capture all the genic space of the Chinese Spring cultivar in 2015, we spent the next year polishing our methods to assemble four more UK varieties. This first glimpse at what multiple genome references could bring to the field showed the potential of more in-depth analysis of diverse wheat cultivars. Ever since we have advocated the need for the wheat community to move beyond a single reference.”

Once the genomes had been assembled, scientists across the world set to work comparing them. Amongst the findings were many large scale changes to DNA, including the introduction of genes from wild relatives of wheat, which could be traced to breeding programmes developed to improve the hardiness of the crop to prevent environmental damage.

Dr David Swarbreck, Group Leader at EI - who applied expertise in genome annotation - said: “Having a comprehensive set of genomes is just the beginning. To be useful to breeders, and eventually farmers, it’s important that we can map out the location of important genes, such as those involved in improving environmental tolerance. This is especially important in regions suffering from the extreme effects of climate change.

“Projected annotations based on the reference Chinese Spring gene set provide an initial insight into the genes that are shared between different varieties, providing a basis for further work that will enable us to examine more closely differences in gene content and expression.”

Many genes highlighted by the analysis, including those involved in pest and disease resistance, are already of great interest to breeders. The genomes will now be used as a platform to discover yet more genes, which will be crucial in breeding the next generation of crops.

“The identification of genes and networks controlling important traits links crop researchers back to the huge knowledge base of basic plant science research,” said Professor Hall. “Together, these substantial datasets are accelerating science discovery and giving us the tools to meet growing global demands for higher yielding, more sustainable, disease resistant and healthier wheat cultivars.”

The 10+ Wheat Genome Project collaboration involved more than 95 scientists from universities and institutes in Canada, Switzerland, Germany, Japan, the U.K., Saudi Arabia, Mexico, Israel, Australia, and the U.S. The study represents the start of a larger effort to generate thousands of genome sequences of wheat, including genetic material brought in from wheat’s wild relatives.