How a breakthrough gene-editing tool will help the world cope with climate change

Jennifer Doudna, one of the inventors of the breakthrough gene-editing tool CRISPR, says the technology will help the world grapple with the growing risks of climate change by delivering crops and animals better suited to hotter, drier, wetter, or weirder conditions.

“The potential is huge,” says Doudna, who shared the 2020 Nobel Prize in chemistry for her role in the discovery. “There is a coming revolution right now with CRISPR.”

Last month, the Innovation Genomics Institute (IGI), which Doudna founded, hosted the Climate & Agriculture Summit at the University of California, Berkeley, where speakers highlighted the role that genome editing can play in addressing the rising dangers of climate change. Doudna sat down for a brief interview with MIT Technology Review on the sidelines of the closed-door event.

She and her coauthors published their landmark paper on the technique in Science 12 years ago, demonstrating that a bacterial immune system could be programmed to locate and snip out specific sections of DNA. The earliest patients have begun receiving the first approved medical treatment created with the genomic scissors, a gene therapy for sickle-cell disease—and a growing list of foods created with CRISPR are slowly reaching grocery store shelves. 

Many more CRISPR-edited plants and animals are on the way, and a number of them were altered to promote traits that could help them survive or thrive in conditions fueled by climate change, beginning to fulfill one long-standing promise of genetic engineering. That includes the offspring of two cattle that Acceligen, a Minnesota-based precision breeding business, edited to have shorter coats better suited to hotter temperatures. In 2022, the US Food and Drug Administration determined that meat and other products from those cattle “pose low risk to people, animals, the food supply, and the environment” and can be marketed for sale to American consumers.

Other companies are harnessing CRISPR to develop corn with shorter, stronger stalks that could reduce the loss of crops to increasingly powerful storms; novel cover crops that can help sequester more carbon dioxide and produce biofuels; and animals that could resist zoonotic diseases that climate change may be helping to spread, including avian influenza.

For its part, IGI is working to develop rice that can withstand drier conditions, as well as crops that may suck up and store away more carbon dioxide, the principal greenhouse gas driving climate change.

Older genetic modification techniques, which involve moving genes from one organism into another, have already delivered agricultural blockbusters, including crops that are resistant to herbicides and corn, potatoes, and soybeans with enhanced protections against pests. The use of such tools to alter crops sparked fears that so-called Frankenfoods would worsen allergies and cause diseases in humans, though these health worries were widely overblown. 

The grand hope is that CRISPR’s ability to precisely remove specific parts of the DNA within the existing genomes of plants and animals will make it faster and easier to create climate-resilient crops and livestock, avoiding many of the pitfalls of earlier breeding and editing techniques. The added promise is that the resulting products may prove more appealing to the public, since they often won’t carry DNA from other organisms—and won’t be labeled as bioengineered. (CRISPR can, however, be used to create such transgenic plants and animals as well.)

“It’s very exciting to see these products coming out, because they have real-world impacts that are incredibly important, especially as we’re dealing with the changing climate and with our expanding population,” says Doudna, a biochemistry professor at the University of California, Berkeley.

But there are still considerable obstacles to developing and commercializing transformative new crops and animals, as well as limits to how much the tool may help farmers and communities in regions that become excessively hot, dry, or wet in the coming decades. 

The coming CRISPRed foods

In recent years, the US Department of Agriculture has loosened its rules on governing and labeling genetically modified foods in ways that clear the path for many CRISPR alterations. 

The department still often oversees and requires disclosures for transgenic plants and animals. But it determined that it will not regulate foods when genome-editing tools like CRISPR are used to make “a single modification that could have otherwise been produced through conventional breeding” over longer time periods. 

“We’re simply providing a trait that could have occurred naturally,” Doudna says of the regulatory distinction. “It’s just that we accelerated that process with CRISPR.”

The USDA has confirmed to companies or research groups that several dozen crops developed through the use of CRISPR would be exempt from regulation, according to a review of public documents by MIT Technology Review. 

Harnessing CRISPR and similar technologies will be crucial to feed a growing global population without dramatically expanding the land, fertilizer, and other resources dedicated to farming, says Chavonda Jacobs-Young, the USDA’s chief scientist. Jacobs-Young appeared on stage at the UC Berkeley conference and also spoke with MIT Technology Review.

“We need high-tech tools,” she says. “That’s going to be an important key to us helping make sure that we have a safe, abundant, delicious … and affordable food supply.”

GLENN RAMIT/INNOVATIVE GENOMICS INSTITUTE

Conventional breeding methods—which include cross-breeding varieties of plants and animals or using radiation or chemicals to create mutations—is a messy process. It can create numerous changes throughout the genome that aren’t necessarily beneficial, requiring significant trial and error to tease out improvements. 

“The exciting thing with CRISPR for gene editing is you can make changes exactly where you want them,” says Emma Kovak, senior food and agriculture analyst at the Breakthrough Institute. “It’s absolutely huge in terms of saving time and money.”

As powerful and precise as CRISPR is, however, it still takes considerable work to target the right part of the genome, to evaluate whether any changes provide the hoped-for benefits—and, crucially, to ensure that any edits don’t come at the cost of overall plant health or food safety.

But improved gene-editing tools have also helped to revive and accelerate research to better understand the complex genomes of plants, which are often several times longer than the human genome. This work is helping scientists identify the genes responsible for relevant traits and the changes that could deliver improvements.

Doudna says we’ll see many more crops altered to bolster resilience to climate change as the research in this field progresses.

“In the future, as we uncover more and more of those fundamental genetics of traits, then CRISPR can come in as a very practical application for creating the kinds of plants that will deal with these oncoming challenges,” she says.

Practical plants and polite cows

IGI’s efforts to develop a type of rice that could be more drought tolerant than standard varieties highlight both the promise and challenges ahead.

Several research groups have used CRISPR to disable a gene that influences the number of tiny pores in the plant’s leaves. These pores, known as stomata, allow rice to take in carbon dioxide, emit oxygen, and release water as a means of controlling temperature. The hope is that with fewer stomata, the plants could preserve more water in order to survive and grow in drier conditions. 

But it’s proved to be a tricky balancing act. Earlier research efforts knocked out the so-called STOMAGEN gene. That eliminated as much as 80% of pores, which certainly reduced water loss. But it also undermined the plants’ ability to absorb carbon dioxide and release oxygen, both of which are critical to photosynthesis. 

IGI researchers zeroed in on a different gene, EPFL10, which had a less dramatic effect, reducing the number of pores by about 20%. According to research that the group published, this tweak helped the plants preserve water but didn’t affect its ability to regulate temperatures or exchange gases.

“It takes plant breeding to the next level,” Doudna says of CRISPR. “We can adjust the numbers of those pores by dialing up or down certain genes … to the levels that actually support plant growth [and] allow farmers to produce rice of the quality and with the yields that they need, but without the loss of water.” 

The organization is also exploring ways that CRISPR could address climate change more directly. That includesa research program aimed at reducing the methane that cattle belch out, which is the primary source of greenhouse-gas emissions related to livestock.

IGI is working with researchers at the University of California, Davis, and elsewhere to explore whether CRISPR and other emerging tools could be used to alter microbes in the stomachs of cattle in ways that would reduce their production of the powerful greenhouse gas. 

A number of research groups and startups are working to reduce those emissions through feed additives, often derived from a type of seaweed. But the hope is that changes to the microbiome of cows could be permanent and inheritable, says Brad Ringeisen, executive director of the IGI.

“If we succeed, it could potentially be something that could be applicable to nearly every cow in the world,” he says.

Labeling and safety

Kovak says there are still plenty of challenges that could hold up the development of CRISPR-edited animals and plants, including the continuing regulatory obstacles facing products where foreign DNA is introduced or more complicated edits are made. So could the ongoing battles over the intellectual rights to the tool and the variants of it that are emerging, and the costs or burdens that companies must bear to make use of the technology.

Doudna herself has been at the center of a messy, bitter, and twisting dispute with the Broad Institute over ownership of the key CRISPR patents. (The Broad is affiliated with MIT, which owns MIT Technology Review.) Each group has secured numerous patents in various countries for certain aspects and varieties of the tool. 

The continuing legal battles have created complexity and uncertainty for companies hoping to harness CRISPR to develop commercial products. 

Doudna has founded or cofounded several startups, including Caribou Biosciences, which has sublicensed access to certain CRISPR patents for uses including agriculture. She didn’t respond to a follow-up question on this issue before press time.

“While we have seen a lot of progress in a relatively short time, having the various CRISPR patents controlled by a few entities has at times slowed or stopped some agricultural products from hitting the market,” the IGI’s Ringeisen said in an email response. 

But he adds that there’s been ongoing progress on discovering and using related gene-editing tools that aren’t already tied up in patents.

Meanwhile, natural-food retailers, skeptics of genetically modified organisms, and others have harshly criticized the USDA’s stance on governing and labeling genetically altered foods. They assert that altered crops have had harmful environmental consequences and that the rules don’t provide consumers with the transparency they need to make informed choices about the foods they buy and consume. 

Doudna stresses that it is crucial to use CRISPR and similar tools cautiously. But she says the US has struck the right balance in its approach to regulation and labeling.

“It’s really informed. It really is based on science,” she says. “Rather than looking at how that plant or crop was created, the question is, What is the final product?”

She says the IGI has strived to act as a “voice of reason” on these issues, helping to counter fears and misunderstandings by providing scientific information about how CRISPR can be used to treat human diseases, help farmers adapt to climate change, or address other threats in people’s lives.

“From the very beginning, of course, it was clear that this was going to be a powerful tool that could be misunderstood and could be misused,” she says. “But it also has tremendous potential to help us tackle a lot of these challenges.”