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Scientists Crack Wheat Genome Code

In 2005, farmer-directors of the Kansas Wheat Commission agreed to invest wheat farmer checkoff dollars into the newly formed International Wheat Genome Sequencing Consortium in an effort to sequence the wheat genome, long considered too large and too cumbersome to sequence. Now, 13 years later, that initial investment of $100,000 has led to the completion of the effort. An article in the August 16 issue of the journal, Science, details the collaborative effort. The article is titled "Shifting the limits in wheat research and breeding using a fully annotated reference genome."

More than 200 scientists from 73 research institutions in 20 countries worked to sequence the wheat genome for Chinese Spring, a bread wheat variety. The effort 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 coolest thing is that a group of farmers decided in 2005 to invest in this effort, when the rest of the world wheat community said it couldn’t be done,” says Justin Gilpin, CEO of the Kansas Wheat Commission. “Researchers said the wheat genome was too big, too complex, and too expensive. And now more than a decade later, to see it finally come to fruition, is exciting.”

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% 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," says 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."

Gilpin explains that wheat breeders have used a number of tools to speed development of new varieties to combat disease, pests, and environmental threats. However, wheat’s genetic complexity slows the process to create new varieties. “The one thing that’s held us back is to have that sequenced genome,” he says. “The ability to be precise is blurred. Now we can precisely identify a specific trait and get it incorporated with 100% certainty, to get the traits you need in a specific variety.”

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. “The impact will be in the next few years,” Gilpin says. “Not necessarily in getting new varieties in the hands of farmers, but in the way new varieties are developed.”

A tough task

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 subgenomes and more than 85% of the genome is composed of repeated elements.

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.

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.

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