A rich scientific harvest: The wheat genome is finally cracked

17 Aug 2018 --- The International Wheat Genome Sequencing Consortium (IWGSC) has published a detailed description of the genome of bread wheat, the world’s most widely cultivated crop in the international journal Science. 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 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.

According to the Food and Agriculture Organization, in order to meet future demands of a projected world population of 9.6 billion by 2050, wheat productivity must increase by 1.6 percent each year. In order to preserve biodiversity, water and nutrient resources, the majority of this increase must be achieved through crop and trait improvement on currently cultivated land.

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,” said 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?” said 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 percent 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,” explained 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.

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 for cultivation. In order for farmers to dedicate these precious resources to wheat production rather than the production of other crops, wheat farming must become profitable.

"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.

Cristobal Uauy, Project Leader in crop genetics at the John Innes Centre, which was also involved in the vast project 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 percent 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."

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."

Reference: "Shifting the limits in wheat research and breeding using a fully annotated reference genome."
International Wheat Genome Sequencing Consortium, Science, 17 August 2018, DOI: 10.1126/science.aar7191