The Wheat Code is Finally Cracked

Wheat is the most widely cultivated crop on Earth. (Ruby O'Grady photo)

The wheat genome sequence will contribute to global food security

Bethesda, MD (August 16, 2018) - The International Wheat Genome Sequencing Consortium (IWGSC) published Aug. 16 in the international journal Science a detailed description of the genome of bread wheat, the world’s most widely cultivated crop. This work will pave the way for the production of wheat varieties better adapted to climate challenges, with higher yields, enhanced nutritional quality, and improved sustainability.

The research article – authored by more than 200 scientists from 73 research institutions in 20 countries – presents the reference genome of the bread wheat variety Chinese Spring. The DNA sequence ordered along the 21 wheat chromosomes is the highest quality genome sequence produced to date for wheat. It is the result of 13 years of collaborative international research.

A key crop for food security, wheat is the staple food of more than a third of the global human population and accounts for almost 20% of the total calories and protein consumed by humans worldwide, more than any other single food source. It also serves as an important source of vitamins and minerals.

To meet future demands of a projected world population of 9.6 billion by 2050, wheat productivity needs to increase by 1.6 per cent each year. In order to preserve biodiversity, water, and nutrient resources, the majority of this increase has to be achieved via crop and trait improvement on land currently cultivated rather than committing new land to cultivation.

With the reference genome sequence now completed, breeders have at their disposal new tools to address these challenges. They will be able to identify more rapidly genes and regulatory elements underlying complex agronomic traits such as yield, grain quality, resistance to fungal diseases, and tolerance to abiotic stress – and produce hardier wheat varieties.

“The wheat genome sequence lets us look inside the wheat engine,” says Rudi Appels, University of Melbourne and Murdoch University Professor, and AgriBio Research Fellow. “What we see is beautifully put-together to allow for variation and adaptation to different environments through selection, as well as sufficient stability to maintain basic structures for survival under various climatic conditions.”

It is expected that the availability of a high-quality reference genome sequence will boost wheat improvement over the next decades, with benefits similar to those observed with maize and rice after their reference sequences were produced.

“How do you thank a team of scientists who persevered and succeeded in sequencing the wheat genome and changed wheat breeding forever?” says Stephen Baenziger, University of Nebraska–Lincoln Professor and Nebraska Wheat Growers Presidential Chair. “Perhaps it is not with the words of a scientist, but with the smiles of well-nourished children and their families whose lives have been changed for the better.”

Sequencing the bread wheat genome was long considered an impossible task, due to its enormous size – five times larger than the human genome – and complexity – bread wheat has three sub-genomes and more than 85% of the genome is composed of repeated elements.

“The publication of the wheat reference genome is the culmination of the work of many individuals who came together under the banner of the IWGSC to do what was considered impossible,” explains Kellye Eversole, Executive Director of the IWGSC. “The method of producing the reference sequence and the principles and policies of the consortium provide a model for sequencing large, complex plant genomes and reaffirms the importance of international collaborations for advancing food security.”

The impact of the wheat reference sequence has already been significant in the scientific community, as exemplified by the publication on the same date of six additional publications describing and using the reference sequence resource, one appearing in the same issue of Science, one in Science Advances and four in Genome Biology. Moreover, more than 100 publications referencing the reference sequence have been published since the resource was made available to the scientific community in January 2017.

In addition to the sequence of the 21 chromosomes, the Science article also presents the precise location of 107,891 genes and of more than 4 million molecular markers, as well as sequence information between the genes and markers containing the regulatory elements influencing the expression of genes.

The IWGSC achieved this result by combining the resources it generated over the last 13 years using classic physical mapping methods and the most recent DNA sequencing technologies; the sequence data were assembled and ordered along the 21 chromosomes using highly efficient algorithms, and genes were identified with dedicated software programs.

All IWGSC reference sequence resources are publicly available at the IWGSC data repository at URGI-INRA Versailles and at other international scientific databases such as GrainGenes and Ensembl Plant.

The Science article is entitled "Shifting the limits in wheat research and breeding using a fully annotated reference genome" and can be read here.

The IWGSC, with 2,400 members in 68 countries, is an international, collaborative consortium, established in 2005 by a group of wheat growers, plant scientists, and public and private breeders. The goal of the IWGSC is to make a high-quality genome sequence of bread wheat publicly available, in order to lay a foundation for basic research that will enable breeders to develop improved varieties. The IWGSC is a U.S. 501(c)(3) non-profit organization. www.wheatgenome.org



Professor Cristobal Uauy - "Tackling the wheat genome has been a huge challenge." (Ruby O'Grady photo)

Scientists bring previously grainy wheat genome into focus

Norwich, UK (August 16, 2018) - The complete sequence of the huge wheat genome is published Thursday, and the enormous dataset will accelerate innovation in breeding resilient and disease resistant crops to feed a growing global population.

Wheat is the most widely-cultivated crop on Earth. It provides more protein than meat in the human diet, and contributes about a fifth of calories consumed by humans. It also has a large and complex genome with 16 billion base pairs – the building blocks of DNA – which is more than five times larger than the human genome.

But wheat is susceptible to drought and flood, and swathes of the crop are damaged each year by diseases such as wheat rust. The sequencing of its genome paves the way for much faster production of wheat varieties adapted to climate challenges, with higher yields, enhanced nutritional quality and improved sustainability.

Sequencing the genome has long been a huge challenge. As well as its enormity, it has three sub-genomes and a large part of it is composed of repetitive elements. This means that vast parts of the genome are very similar, if not identical, to each other. This has made it difficult, until now, to distinguish each sub-genome and to put together the genome into its correct order.

A paper published in Science by the International Wheat Genome Sequencing Consortium is authored by more than 200 scientists from 73 research institutions in 20 countries, including the John Innes Centre. It details the sequence of the 21 chromosomes, the precise location of 107,891 genes and more than 4 million molecular markers, as well as sequence information between the genes containing the regulatory elements influencing the expression of genes.

A second paper, led by a team at the John Innes Centre, provides annotation and resources to support researchers and breeders in understanding how wheat genes affect traits. This will help develop wheat varieties with greater yields, more resilient against environmental changes and improved resistance to diseases.

In previous work at the John Innes Centre, researchers have also fine-tuned a technique called ‘speed breeding’ whereby glasshouses are configured to shorten breeding cycles. Combined with the genome resources developed in the two new papers, this is significantly shortening the time to test whether genetic markers really do point to traits such as drought resistance and breeders can get new varieties to market more quickly.

Professor Cristobal Uauy

Professor Cristobal Uauy, Project Leader in crop genetics at the John Innes Centre, says, “Genomic knowledge of other crops has driven progress in selecting and breeding important traits. Tackling the colossal wheat genome has been a Herculean challenge, but completing this work means we can identify genes controlling traits of interest more rapidly. This will facilitate and make more effective the breeding for traits like drought or disease resistance. Where previously we had a broad view and could spot areas of interest, we can now zoom into the detail on the map.”

He adds, “It is anticipated that the world will need 60% more wheat by 2050 to meet global demand. We are in a better position than ever to increase yield, breed plants with higher nutritional quality and create varieties that are adapted to climate changes thanks to the research we and the international community are publishing.”

Dr Philippa Borrill

Dr Philippa Borrill, Research Fellow at the John Innes Centre, says, “The years of work that went into decoding the wheat genome are just the beginning. These results facilitate further collaboration between scientists, breeders and farmers to locate and identify genes to improve wheat yield in a sustainable and responsible way, to meet the needs of a growing population.”

Ricardo Ramirez-Gonzalez, a Scientific Programmer at the John Innes Centre, adds, “The genome is really a tool that allows us to address the challenges around food security and environmental change. We believe that we can boost wheat improvement in the next few years in the same way that rice and maize were refined after their sequences were completed.”

The full reports are available at:



Curtis Pozniak

University of Saskatchewan crop scientists help crack the wheat genome code

A University of Saskatchewan (U of S)-led research team has played a key role in an international discovery that will have an impact on the food security of millions of people around the world — the sequencing of the billion-piece jigsaw puzzle that is the bread wheat genome.

Saskatoon, SK (August 16, 2018) - The journal Science published on Aug. 16 the highest quality genome sequence produced to date for the bread wheat variety Chinese Spring. This was long considered an almost impossible task — the wheat genome is five times larger than the human genome and more complex — but also a critically important one in an era of climate change. Wheat is the world’s most widely cultivated crop, accounting for 20% of all calories consumed throughout the world.

For the past 13 years, more than 200 scientists from 73 research institutions in 20 countries have been endeavouring, through the International Wheat Genome Sequencing Consortium (IWGSC), to complete the genome sequence for bread wheat and make publicly available the new genomic assembly for breeders seeking to develop improved varieties.

“With funding from a range of partners and cutting-edge sequencing technology from our industrial partner NRGene, our research team at the U of S played a key role in the international consortium’s success, a discovery that has the potential for disruptive innovation in wheat improvement,” says Curtis Pozniak, researcher and wheat breeder at the Crop Development Centre in the U of S College of Agriculture and Bioresources.

“Essentially we have completed the wheat genome jigsaw puzzle with all the pieces put together in their correct positions and order, providing an enormous advantage for breeders when searching for genes that control important traits in the crop,” says Pozniak. “This breakthrough research will help produce better wheat varieties over the long term.”

Pozniak leads Canada’s contribution to the IWGSC-led wheat genome initiative through the Canadian Triticum Applied Genomics (CTAG2) project, which also includes scientists from the National Research Council, Agriculture and Agri-Food Canada (AAFC), the University of Guelph, and the University of Regina.

“The new genome assembly provides a chromosome-by-chromosome representation rather than the fractured picture available previously and will elevate wheat research and breeding to a level equal to, or even better than, other major crops,” says Andrew Sharpe, director of Genomics and Bioinformatics at the U of S Global Institute for Food Security (GIFS) and co-lead for the CTAG2 project.

AAFC wheat breeder Richard Cuthbert says, “Breeders will now have the information they need to identify economically important traits more rapidly, which will better enable development of wheat varieties with increases in yield, enhanced grain quality, improvements in disease resistance and more resilient to environmental stresses. The result will be more nutritious grain that can be grown more effectively and efficiently in harsher climates.”

In Canada, wheat accounts for more than $4.5 billion in annual sales and, when value-added processing is factored in, contributes more than $11 billion each year to the Canadian economy.

With the world’s population expected to reach 9.6 billion by 2050, Maurice Moloney, executive-director of GIFS at the U of S, said this discovery will have a major impact on global food security.

“In light of climate change, water shortages and limitations on the availability of arable land, we will need to rely on plant genetics to increase wheat productivity,” says Moloney. “Solving the massive puzzle of the wheat genome will go a long way towards accomplishing that, similar to the growth that was made in maize and rice crops after their reference sequences were assembled.”

U of S Vice-President Research Karen Chad says agriculture is a signature area of U of S research and the discovery highlights the importance of international research collaboration.

“No single researcher, university or country can solve global challenges like global food security,” she says. “Working together with our international partners, our scientists are now better able to understand the complex set of genetic instructions encoded in wheat DNA, and breeders around the world will soon have the tools they need for crop innovations that will advance global food security.”

The new sequence produced using NRGene’s technology was the backbone of the IWGSC genome assembly. This work was funded by Genome Canada, Genome Prairie, Western Grains Research Foundation, Saskatchewan Ministry of Agriculture via the CTAG2 project, the Saskatchewan Wheat Development Commission, the Alberta Wheat Commission, and the Canada First Research Excellence Fund through the Designing Crops for Global Food Security initiative at the U of S.

A number of international partners also contributed to the effort, including researchers at IPK Gatersleben in Germany, Kansas State University in the U.S., Tel Aviv University in Israel, and Illumina Inc.

“With the support of the University of Saskatchewan and its Global Institute for Food Security, NRGene delivered the assembly of the whole genome from start to finish in just three months, a remarkable computational feat given the complexity of the wheat genome,” says NRGene CEO Gil Ronen.

The Science article is entitled Shifting the limits in wheat research and breeding using a fully annotated reference genome and can be read here.

The U of S-led team also contributed to a second related Science article led by the U.K.-based John Innes Centre and published Aug. 16 entitled The transcriptional landscape of polyploid wheat that describes the repertoire of expressed genes in the new wheat genome sequence and can be read here. The next step for the U of S team will be to initiate a larger-scale international initiative to sequence the more than 10 cultivated wheat varieties from the main growing areas across the globe. The 10+ Wheat Genomes Project, started last year and led by Pozniak, is using the same NRGene technology to sequence the genomes. Sequencing for several varieties is already complete. More information can be found at: www.10wheatgenomes.com.



The sun rises on a Kansas State University wheat plot in Manhattan.

Wheat Code Finally Cracked; Wheat Genome Sequence Will Bring Stronger Wheat Varieties to Farmers

Manhattan, KS (August 16, 2018) — Kansas State University scientists, in collaboration with the International Wheat Genome Sequencing Consortium, published Aug. 16 in the international journal Science a detailed description of the complete genome of bread wheat, the world's most widely-cultivated crop.

This work will pave the way for the production of wheat varieties better adapted to climate challenges, with higher yields, enhanced nutritional quality and improved sustainability. The article is titled "Shifting the limits in wheat research and breeding using a fully annotated reference genome."

The research article — authored by more than 200 scientists from 73 research institutions in 20 countries — presents the reference genome of the bread wheat variety Chinese Spring. The DNA sequenceordered along the 21 wheat chromosomes is the highest-quality genome sequence produced to date for wheat. It is the result of 13 years of collaborative international research and the support of the National Science Foundation, Kansas farmers and many others.

"It is a dream come true for Kansas wheat farmers, who were the first to invest in the wheat genome sequencing project and were pivotal in rallying U.S. wheat farmers in support of the wheat genome sequencing project," said Bikram Gill, distinguished professor emeritus of plant pathology at Kansas State University who organized the first National Science Foundation and U.S. Department of Agriculture-sponsored workshop planning meeting on wheat genome sequencing in Washington, D.C., in 2003.

A key crop for food security, wheat is the staple food of more than a third of the global human population and accounts for almost 20 percent of the total calories and protein consumed by humans worldwide, more than any other single food source. It also serves as an important source of vitamins and minerals.

Kansas farmers grow an average of 340 million bushels of wheat each year, but acres planted to wheat have dropped dramatically over the past decade, from 10 million acres to fewer than 8 million. To meet future demands of a projected world population of 9.6 billion by 2050, wheat productivity needs to increase by 1.6 percent each year. To preserve biodiversity, water and nutrient resources, the majority of this increase has to be achieved via crop and trait improvement on land currently cultivated, rather than committing new land to cultivation. In order for farmers to dedicate these precious resources to wheat production rather than production of other crops, wheat farming must become profitable.

With the reference genome sequence now completed, breeders have at their fingertips new tools to address global challenges. They will be able to more rapidly identify genes and regulatory elements underlying complex agronomic traits such as yield, grain quality, resistance to fungal diseases and tolerance to physical stress — and produce hardier wheat varieties.

"Completion of the sequence is a landmark event that will serve as a critical foundation for future wheat improvement," said Allan Fritz, Kansas State University professor of agronomy and wheat breeder. "It is the key to allowing efficient, real-time integration of relevant genetics, making the selection process more efficient — it's a turbocharger for wheat breeding."

It is expected that the availability of a high-quality reference genome sequence will boost wheat improvement over the next decades, with benefits similar to those observed with maize and rice after their reference sequences were produced.

"Kansas wheat farmers have been supporting the wheat genome sequencing efforts through the Kansas Wheat Commission's wheat assessment since the establishment of the International Wheat Genome Sequencing Consortium in 2005, with a cumulative amount of nearly a quarter of a million dollars," said Justin Gilpin, chief executive officer for Kansas Wheat. "The sequence of the bread wheat genome has already had a positive effect on wheat improvement, which not only affects the science behind wheat breeding, but has a long-lasting positive outcome in regard to wheat producer productivity, profitability and, ultimately, livelihoods."

Sequencing the bread wheat genome was long considered an impossible task because of its enormous size — five times larger than the human genome — and complexity — bread wheat has three sub-genomes and more than 85 percent of the genome is composed of repeated elements.

"It is exciting to be a part of this landmark achievement," said Jesse Poland, associate professor at Kansas State University and director of the Wheat Genetics Resource Center and the U.S. Agency for International Development Innovation Lab for Applied Wheat Genomics. "This international effort, toward something that was once deemed impossible, will have tremendous impact on wheat in Kansas, and the world."

The impact of the wheat reference sequence has already been significant in the scientific community, as exemplified by the publication on the same date of six additional publications describing and using the reference sequence resource, one appearing in the same issue of Science, one in Science Advances and four in Genome Biology. In addition, more than 100 publications crediting the reference sequence have been published since the resource was made available to the scientific community in January 2017.

"We are extensively using the new reference sequence for more informed molecular breeding," Poland said. "It is really having a big impact."

In addition to the sequence of the 21 chromosomes, the Science article also presents the precise location of 107,891 genes and of more than 4 million molecular markers, as well as sequence information between the genes and markers containing the regulatory elements influencing the expression of genes.

The International Wheat Genome Sequencing Consortium achieved this result by combining the resources it generated over the last 13 years using classic physical mapping methods and the most recent DNA sequencing technologies; the sequence data were assembled and ordered along the 21 chromosomes using highly efficient algorithms, and genes were identified with dedicated software programs.

All consortium reference sequence resources are publicly available at its data repository at URGI-INRA Versailles and at other international scientific databases such as GrainGenes and Ensembl Plants.

The International Wheat Genome Sequencing Consortium, with 2,400 members in 68 countries, is an international, collaborative consortium, established in 2005 by a group of wheat growers, plant scientists, and public and private breeders. The goal of the consortium is to make a high-quality genome sequence of bread wheat publicly available, in order to lay a foundation for basic research that will enable breeders to develop improved varieties.