CRISPR: A new toolbox for better crops

Sometime around 2020, a new corn variety will mark a huge leap in how humans design agricultural crops. It will be the first commercialized, gene-edited plant altered using CRISPR/Cas9 technology. But don’t be surprised if the corn debuts without much hype. It is a starchy or “waxy” corn that is not much different from varieties already on the market. When the seed firm DuPont Pioneer first announced the new corn in early 2016, few people paid attention. Pharmaceutical companies using CRISPR for new drugs got the headlines instead.

But people should notice DuPont’s waxy corn because using CRISPR—an acronym for clustered regularly interspaced short palindromic repeats—to delete or alter traits in plants is changing the world of plant breeding, scientists say. Moreover, the technique’s application in agriculture is likely to reach the public years before CRISPR-aided drugs hit the market.

Until CRISPR tools were developed, the process of finding useful traits and getting them into reliable, productive plants took many years. It involved a lot of steps and was plagued by randomness.

“Now, because of basic research in the lab and in the field, we can go straight after the traits we want,” says Zachary Lippman, professor of biological sciences at Cold Spring Harbor Laboratory. CRISPR has been transformative, Lippman says. “It’s basically a freight train that’s not going to stop.”

Using CRISPR to add—or remove—a plant trait is faster, more precise, easier, and in most cases cheaper than either traditional breeding techniques or older genetic engineering methods. Although scientists can use CRISPR to add genes from other species to a plant, many labs are working to exploit the vast diversity of genes that exists within a plant species. In fact, enhancing many of the most valued traits in agriculture doesn’t require adding DNA from other species.

Gene-edited crops have the potential to revive some of the early promise that genetic engineering has not fulfilled, such as making plants that are higher yielding, drought tolerant, disease resistant, more nutritious, or just better tasting. In addition, CRISPR can efficiently improve not just row crops such as corn but also fruits and vegetables, ornamentals, and staple crops such as cassava.

Proponents hope consumers will embrace gene-edited crops in a way that they did not accept genetically engineered ones, especially because they needn’t involve the introduction of genes from other species—a process that gave rise to the specter of Frankenfood.

But it’s not clear how consumers will react or if gene editing will result in traits that consumers value. And the potential commercial uses of CRISPR may narrow if agriculture agencies in the U.S. and Europe decide to regulate gene-edited crops in the same way they do genetically engineered crops.

DuPont Pioneer expects the U.S. to treat its gene-edited waxy corn like a conventional crop because it does not contain any foreign genes, according to Neal Gutterson, the company’s vice president of R&D. In fact, the waxy trait already exists in some corn varieties. It gives the kernels a starch content of more than 97% amylopectin, compared with 75% amylopectin in regular feed corn. The rest of the kernel is amylose. Amylopectin is more soluble than amylose, making starch from waxy corn a better choice for paper adhesives and food thickeners.

Like most of today’s crops, DuPont’s current waxy corn varieties are the result of decades of effort by plant breeders using conventional breeding techniques.

Breeders identify new traits by examining unusual, or mutant, plants. Over many generations of breeding, they work to get a desired trait into high-performing (elite) varieties that lack the trait. They begin with a first-generation cross, or hybrid, of a mutant and an elite plant and then breed several generations of hybrids with the elite parent in a process called backcrossing. They aim to achieve a plant that best approximates the elite version with the new trait.

But it’s tough to grab only the desired trait from a mutant and make a clean getaway. DuPont’s plant scientists found that the waxy trait came with some genetic baggage; even after backcrossing, the waxy corn plant did not offer the same yield as elite versions without the trait. The disappointing outcome is common enough that it has its own term: yield drag.

Because the waxy trait is native to certain corn plants, DuPont did not have to rely on the genetic engineering techniques that breeders have used to make herbicide-tolerant and insect-resistant corn plants. Those commonly planted crops contain DNA from other species.

In addition to giving some consumers pause, that process does not precisely place the DNA into the host plant. So researchers must raise hundreds or thousands of modified plants to find the best ones with the desired trait and work to get that trait into each elite variety. Finally, plants modified with traditional genetic engineering need regulatory approval in the U.S. and other countries before they can be marketed.

Instead, DuPont plant scientists used CRISPR to zero in on, and partially knock out, a gene for an enzyme that produces amylose. By editing the gene directly, they created a waxy version of the elite corn without yield drag or foreign DNA.

Plant scientists who adopt gene editing may still need to breed, measure, and observe because traits might not work well together or bring a meaningful benefit. “It’s not a panacea,” Lippman says, “but it is one of the most powerful tools to come around, ever.”

DuPont was an early adopter of CRISPR technologies, before Monsanto and other seed industry rivals. In 2015, the company signed technology license deals with Vilnius University and Caribou Biosciences. Caribou was founded by CRISPR research pioneer Jennifer Doudna of the University of California, Berkeley.

Gutterson says his team started work on the new waxy corn in early 2015. “One observation or lesson we have with our first product is that the reduced time to market is significant,” he says. It will take less than five years, compared with about eight for a hybrid, to get the new corn to farmers.

Waxy corn was an ideal variety on which to try CRISPR for a first commercial product, Gutterson says. It has a trait that has been long marketed and is familiar to farmers.

Another reason was that plant scientists understand the corn genome and the waxy trait in particular. “You really have to understand the gene for the trait, the genome, and the effect of the edit,” Gutterson says. “Many versions of this gene exist in nature. It made it easy for us to get exactly the property we want.”

According to plant scientists, better understanding of a species’ genome, including the identity of genes that code for desired traits, is the main hurdle to widespread use of gene editing. Researchers have had access to the full corn genome only since 2010, and they are still sequencing a number of important corn varieties.

“Plants—like animals—have lots of genes, most of which we don’t understand,” notes Heike Sederoff, professor of systems and synthetic biology at North Carolina State University. “We don’t know what they do or why they are there or how they got there.”

But here, too, CRISPR easily beats out competing techniques. To figure out the function of one of the 20,000 to 30,000 genes in a plant, scientists either knock out the gene or dial up its impact by adding copies. “We used to use viruses or bacteria that insert DNA, but the targeting part is really difficult,” Sederoff says.

“That’s where CRISPR helps us. It allows us to very specifically target a gene and either take it out or modify it. We can study any gene, and we can do more than one at a time. And it’s not hard to do.”

Sederoff’s lab is studying ways to increase the amount of oil produced by oilseeds such as canola and the industrial crop camelina. Her team is looking for genes that control how a plant transports sugar or regulates the amount of sugar that goes out of its stem and into the seed, where it is converted into fatty acids. “Can we make more seeds? Can we change the composition or size of the seeds?” she asks.

In one set of experiments, Sederoff used CRISPR to place a gene that makes tomatoes sweet into an oilseed plant. Seed yield doubled. She reports it took less than two years, compared with the 10 years that older techniques would require. In the long run, researchers might find and use native oilseed genes that work like the one taken from the tomato to create a higher-yielding crop that isn’t transgenic.

Cold Spring Harbor’s Lippman is also working with tomatoes. His team is looking for the genes that control how many, when, and where flowers—and thus tomatoes—are produced on plants. That means understanding what happens in the stem cells that produce flower branches, called inflorescences.

In the past, breeders had trouble fine-tuning the amount and pattern of inflorescences. The problem, Lippman discovered, is that two traits that arose during decades of domestication and crop improvement combined to thwart the altering of flower production via additional breeding. One of the traits helped the plant support heavier fruit; the other eliminated a joint on the fruit stem to prevent tomatoes from falling off before harvesting.

With CRISPR, Lippman notes, what was done can be undone. “We have ways now to use gene editing to separately modify fruit size and weight, the branches that make flowers, and the amount of flowers, as well as the architecture of a plant from a compact bush to one that keeps growing.”

A different breeding mistake may be to blame for modern tomato varieties’ lack of flavor and aroma. Research shows that as breeders sought traits for productivity, uniformity, and harvest-ability, the tastier traits were inadvertently lost. Wild tomatoes and heirloom varieties still carry those genes.

“Now let’s breed them in or edit them to bring back a better-flavored tomato, which is what everybody asks for all of the time,” Lippman says.

Cotton growers are also excited about the quality improvement that CRISPR gene editing could bring. “Cotton is a small-acreage crop compared with corn and soy,” explains Kater D. Hake, vice president of agricultural and environmental research at Cotton Inc., a promotion organization supported by cotton farmers. “With the regulatory cost associated with traditional biotechnology, cotton has been off the radar except for extremely high-value traits such as insect and weed control.”

Researchers are probing the cotton genome, which was first sequenced in 2015, to find genes that control the shape, structure, length, and strength of cotton fibers. “It’s a sustainability story,” Hake says. “When you push cotton quality up, you can make stronger, finer yarns so garments require less total mass of cotton and are more durable.”

Indeed, researchers have no shortage of ideas for how to use CRISPR to make higher-quality, more sustainable crops that consumers may desire. But to date, most of the work has been to prove the concept. It’s not yet clear which innovations will actually reach the market.

One concern is that smaller seed firms and research organizations aren’t geared up to develop and commercialize crops with new traits; they ceded most of that ground to agriculture giants such as DuPont decades ago.

Benson Hill Biosystems, a St. Louis-based start-up, is working with small seed companies and academic researchers to help them pursue crop improvement projects using its data-driven genomics platform. For example, the firm is working with the family-owned seed firm Beck’s Hybrids and potato experts at J.R. Simplot Company to bring more R&D power in-house.

“We believe DuPont and Monsanto will play a decreasing role relative to innovation across the industry,” Benson Hill Chief Executive Officer Matthew Crisp asserts. “It will be like the shift in big pharma 10–15 years ago when early-stage discovery went to smaller players.” Crisp says CRISPR gene editing and genomic data tools will level the playing field for new trait introductions.

Another constraint is that a few organizations control important patents for CRISPR, some of which have been the subject of lawsuits. So scientists at Benson Hill are working on a way to replace Cas9, the enzyme that cuts the DNA. Crisp calls the work “CRISPR 2.0” and says he expects the tools to be even more efficient—and easier to access—than current ones. Researchers at the University of California, Berkeley, are also developing Cas9 alternatives.

But as CRISPR technology advances, questions persist about government regulation and consumer acceptance.

Today, companies that wish to market a gene-edited plant can ask the U.S. Department of Agriculture whether their product will require regulatory review. So far, for plants that do not contain foreign genes, USDA has responded that it does not have the authority to regulate. Transgenic plants, in contrast, are regulated because they contain genes from other species or from a vector organism that may introduce a plant pest into the environment.

That regulatory framework, which was set up in 1987, is undergoing a comprehensive review; USDA is accepting comments through June 19 about how it should assess risk in modified crops. In addition, other countries may write different, more onerous rules.

Many researchers share the view that regulators should focus on whether added or altered traits pose a foreseeable risk and not on the process used to get the trait into the plant.

“I propose doing regulation based on the phenotype—the specific characteristics you put in,” says Gregory Jaffe, director of the biotechnology project at the consumer advocacy group Center for Science in the Public Interest. “Clearly, one aspect of doing risk assessment is that how you put the trait in could inform risk assessment.” Using a Brazil nut gene to improve disease resistance, for example, could introduce a nonnative protein that may be allergenic, Jaffe points out.

Jaffe and others say regulatory changes and the new editing technologies could blur the line between what is and is not a genetically modified organism (GMO). Currently, food containing genetically modified ingredients must carry a label. It’s not clear if CRISPR-edited products will also require a label.

That’s one reason why Jaffe has proposed a registry for both the public and the food industry to track what crops come from gene editing. “It’s important not to make the kinds of mistakes that were made with GMO crops,” Jaffe says. “We should start with more transparency in the food chain.”

Benson Hill’s Crisp agrees that the industry must be more transparent and do a better job at outreach. “We need to ensure that consumers are informed about the benefits and not inundated with misinformation or a lack of information.”

Food shoppers will likely be won over with gene-edited products that directly benefit them, Jaffe predicts. And he’s already got something in mind: “I would like a better-tasting tomato.”