Scientists Finally Crack Wheat’s Absurdly Complex Genome

Scientists decoded the genome of rice in 2002. They completed the soybean genome in 2008. They mapped the maize genome in 2009. But only now has the long-awaited wheat genome been fully sequenced. That delay says nothing about wheat’s importance. It is arguably the most critical crop in the world. It’s grown on more land than anything else. It provides humanity with a fifth of our calories. But it also has one of the most complex genomes known to science.

For a start, wheat’s genome is monstrously big. While the genome of Arabidopsis—the first plant to be sequenced—contains 135 million DNA letters, and the human genome contains 3 billion, bread wheat has 16 billion. Just one of wheat’s chromosomes—3B—is bigger than the entire soybean genome.

To make things worse, the bread-wheat genome is really three genomes in one. About 500,000 years ago, before humans even existed, two species of wild grass hybridized with each other to create what we now know as emmer wheat. After humans domesticated this plant and planted it in their fields, a third grass species inadvertently joined the mix. This convoluted history has left modern bread wheat with three pairs of every chromosome, one pair from each of the three ancestral kinds of grass. In technical lingo, that’s a hexaploid genome. In simpler terms, it’s a gigantic pain in the ass.

Typically, geneticists sequence genomes by breaking DNA into small segments, reading them separately, and assembling the pieces back together. But if each chromosome occurs six times, how do you know where to put any given piece?

Worse still, 85 percent of wheat’s DNA consists of repetitive sequences, so even if you narrow a piece down to the right chromosome, it’s still a chore to work out where exactly it should sit. It’s like solving a giant jigsaw puzzle that depicts the same patch of blue sky three times over.

Traditionally, it has taken a lot of trial and error to create new varieties of wheat that, say, tolerate cold or resist fungal diseases. “You throw things together and go through this long process of annual breeding in the hope that your variety has the right package of genes—and that takes years

This is already happening. Using the completed genome, the team identified a long-elusive gene (with the super-catchy name of TraesCS3B01G608800) that affects the inner structure of wheat stems. If plants have more copies of the gene, their stems are solid instead of hollow, which makes them resistant to drought and insect pests. By using a diagnostic test that counts the gene, breeders can now efficiently select for solid stems.

The IWGSC has also started to work out when different genes are turned on as wheat germinates and grows, and how these patterns of activity vary across the three subgenomes. If scientists can figure out how to switch on specific genes at particular points in the plant’s life cycle, people could potentially breed wheat in real time, “in response to the growing season and environment,” Bentley says. “That would be incredibly cool.”

Researchers might also be able to more easily temper the dark side of wheat. Many people are allergic to gluten and other wheat proteins, leading to disorders like celiac disease, baker’s asthma, and non-celiac wheat sensitivity. Scientists have managed to identify many of the specific proteins responsible, “but until now, we couldn’t determine the genes that encoded those proteins,” says Odd-Arne Olsen from the Norwegian University of Life Sciences. His team has now identified 356 such genes. Of these, 127 are new to science, and 222 were known but had been incorrectly sequenced.

The team also found that wheat produces more of the allergens behind celiac disease when grown at high temperatures, which suggests that baked goods might become more allergenic as the world continues to warm. But perhaps, by understanding the genes behind such allergens, breeders will be able to counteract that trend and create less-allergenic varieties.

Using the genome, breeders could also use gene-editing techniques like crispr to rapidly alter the traits of their crops. The IWGSC showed how easy this could be by identifying wheat genes that influence flowering time and altering them with crispr to create varieties that bloom a few days earlier than usual. These techniques could also be used to move beneficial traits from wild wheat species into domestic strains.

The main hurdles to such changes are public approval and regulatory restrictions. Last month, the European Union’s highest court ruled that crispr-edited crops count as genetically modified organisms, even if they don’t involve introducing genes from other organisms. Such crops will now face a long and expensive approval process that will likely discourage many companies from investing in them. “Now we have the knowledge and the tools, but it won’t be straightforward to implement either,” Olsen says.

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