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International Consortium Sequences, Annotates Bread Wheat Reference Genome

NEW YORK (GenomeWeb) – The International Wheat Genome Sequencing Consortium (IWGSC) has published an annotated bread wheat reference genome after 13 years of work.

The consortium sequenced the bread wheat variety Chinese Spring, which has been used to develop genetic resources used by wheat researchers though it is not itself an economically important crop. The IWGSC embarked on sequencing the Triticum aestivum cv Chinese Spring genome in 2005, beginning by developing physical maps of bacterial artificial chromosomes before incorporating newer sequencing approaches. Sequencing its genome was challenging due to its massive size, number of repeats, and its three highly similar subgenomes, the team noted.

As IWGSC researchers reported yesterday in the journal Science, they have now generated a reference sequence for the hexaploid bread wheat genome that they assembled into 21 chromosome-like pseudomolecules. This reference, they said, will help fuel additional studies as well inform breeding programs. Six other studies using the wheat genome resource have also now been published.

"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," IWGSC Executive Director Kellye Eversole said in a statement.

The consortium team generated short-read sequencing data for the Chinese Spring wheat variety using the Illumina platform, which they fed into a software package developed by NRGene called deNovoMagic2 for de novo genome assembly and scaffolding. By folding in additional genetic, physical, and sequence data, the researchers produced a 14.5 gigabase genome assembly with 21 pseudomolecules, with sequences that largely reflect wheat's 21 chromosomes. They estimated that these 21 pseudo-chromosomes encompass about 94 percent of the bread wheat genome.

They also uncovered 107,891 high-confidence protein-coding loci, which they noted are about equally distributed across the three wheat subgenomes. 

At the same time, the IWGSC team developed a transcriptome atlas of gene expression in 32 wheat tissues at different times of development or under various stress conditions. From this, they teased out tissue- and development-stage linked gene co-expression networks, such as one involving PHYB, FT, and FUL3 that is associated with flowering time, a key trait for crop adaptation to diverse environments.

"The wheat genome sequence lets us look inside the wheat engine," author Rudi Appels from the University of Melbourne said in a statement. "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."

In separate paper also appearing in Science, researchers led by the John Innes Center's Cristobal Uauy used the bread wheat genome resource to dive more deeply into the expression of homoeologs, or copies of the same gene from different ancestral sources.

As the wheat genome is thought to have been generated through interspecific hybridizations between three diploid species, it has numerous homoeologs — the IWGSC team found it to have more than 39,000 homoeologous groups. In this accompanying paper, the Innes Center-led team looked at RNA sequencing data from 850 wheat samples and found that about 30 percent of wheat homoeologs don't have a balanced expression.

The researchers suggested that these slight differences could be the first steps toward these homoeologs taking on new or sub-functions. They further traced these expression differences to epigenetic changes and transposable element variation. They also said targeting homoeologs could help breeders improve crops by affecting wheat traits.

Another team, meanwhile, has used the bread wheat genome as a jumping-off point to explore wheat allergens. Researchers led by the Norwegian University of Life Sciences' Odd-Arne Olsen reported in Science Advances that it relied on the new reference sequence in combination with public databases of wheat proteins and peptides to uncover proteins associated with wheat allergy and conditions such as celiac disease in humans. The team uncovered 828 genes that encode such allergens, and noted that the levels of these proteins varied with temperature stress. They also mapped these proteins, which they said could aid in the development of low-allergy foods.

Four other papers appearing in Genome Biology presented tools to better understand and analyze the wheat genome to home in on important agronomical traits. The Université Clermont Auvergne's Frédéric Choulet and his colleagues examined the effects of transposable elements on wheat genomic structure, while a Melbourne-led team combined optical and physical mapping to improve the wheat assembly. When applied it to chromosome 7A, the assembly uncovered seven fructosyl transferase genes, which are important for grain quality.

A University of Zurich-led team, meanwhile, compared chromosome 2D from the Chinese Spring cultivar to the Swiss spring wheat line and found a high level of sequence conservation between the two. However, they also found large indels that could affect plant immunity.

Lastly, Université Paris-Saclay-led researchers described a web portal they've dubbed Wheat@URGI that provides scientists and breeders access to the bread wheat genome and related tools.

"The genome is really a tool that allows us to address the challenges around food security and environmental change," the Innes Center's Ricardo Ramirez-Gonzalez said in a statement. "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."