Landmark study generates first genomic atlas for worldwide wheat

Researchers from the John Innes Centre and Earlham Institute have contributed to a major international collaboration that could catalyse a new era of wheat discovery.

The international team has sequenced the genomes of 15 wheat varieties from around the world enabling scientists and breeders to much more quickly find influential genes for improved yield, pest resistance and other important crop traits.

The research, led by the University of Saskatchewan (USask) and published in Nature, provides the most comprehensive atlas of wheat genome sequences ever reported, a resource described by the research team as a pan-genome.

The 10+ Genome Project collaboration involved more than 95 scientists from universities and institutes in Canada, Switzerland, Germany, Japan, the UK, Saudi Arabia, Mexico, Israel, Australia, and the USA.

The aim of the 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.

“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 find genes linked to in-demand traits, which will accelerate breeding efficiency.

At the John Innes Centre the group of Professor Cristobal Uauy collaborated on the study by using the novel wheat assemblies to define blocks across the genome called haplotypes. These blocks of genes are co-inherited together and rarely broken up by genetic recombination, and are selected by breeders in search of new crop lines with desirable traits.

Professor Cristobal Uauy said of this major bioinformatics and genomic collaboration: “Our haplotype-led approach using these novel wheat assemblies provides a powerful framework to increase the efficiency and precision of wheat breeding. This will help scientists implement strategies to introduce novel genetic diversity into modern germplasm, prioritise research targets, and assemble new gene combinations to optimise the agronomic performance of this key global crop.”

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

In 2018 as part of another international consortium, John Innes Centre and Earlham Institute 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.

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 is 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.

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.”

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 that can provide the 60% boost in calories we need over the next half century.

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 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 Peter Langridge, Scientific Coordinator for the Wheat Initiative.

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