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 grasses. 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.

“You have no idea where things go,” says Kellye Eversole, who leads the International Wheat Genome Sequencing Consortium, or IWGSC—a group of researchers from 19 countries who have been trying to crack the genome since 2005. After 14 years, around $75 million, and a few incomplete drafts, the team has now published the nearly complete genome of a wheat variety called Chinese Spring, mapping more than 107,000 of its genes. “It’s really a miracle that we finished,” Eversole says.

Unexpectedly, a much smaller six-person team, led by Steven Salzberg from Johns Hopkins University, released its own version of a near-complete wheat genome last year, by using new technologies that read out very long stretches of DNA. But while Eversole applauds the small team’s accomplishment, she notes that its version “doesn’t have the level of detail that we have in ours, and it’s that detail that makes a difference for breeders.”

“The genome sequence of maize had a big impact on creating better varieties,” Eversole notes. By contrast, wheat production has lagged behind, and the crop’s profitability has recently dropped. That’s problematic because researchers estimate that the world will need to grow 60 percent more wheat by 2050 to feed its booming population.

“Whatever your views on a wheat-based diet, there is no escaping its importance in global food security,” says Alison Bentley, who was not part of the consortium. Bentley is the director of genetics and breeding at the United Kingdom’s National Institute of Agricultural Botany, and although she says that people have made huge progress in breeding wheat in the absence of a genome, having one will speed everything up.

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,” says Eversole, who grew up in Oklahoma as part of a farming family. But with a full genome at hand, breeders can identify the genes behind particular traits, and ensure that these are present in their crops. “The goal is to build a better breeder’s toolbox and increase profitability for growers,” she says.

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.

“It will take some time before the benefit to the breeding community is realized,” says Ravi Singh from the International Maize and Wheat Improvement Center in Mexico. “But in our own program, we are already using this resource to identify important genomic regions behind traits like grain yield, disease resistance, tolerance to heat and drought, and nutritional quality.”

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.”

Her only word of caution is that the new genome comes from an unusual variety, Chinese Spring, which “not many farmers would recognize as wheat.” Still, Chinese Spring is historically important as the foundation of a lot of early wheat research. And now that its genome is out, it’ll be much easier for scientists to sequence a wider range of cultivars, and understand the genetic underpinnings of different traits.

Researchers might also be able to more easily temper the dark side of wheat. Many people are allergic to glutens 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.

Of course, it’s unlikely to be that simple. Olsen notes that the same proteins behind wheat allergies also determine the baking quality of flour. Similarly, Eversole notes that wheat varieties that contain more protein also tend to grow at lower yields. There are always trade-offs, but the team hopes that a full genome will make it easier to navigate them.

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.