By crossing that tough roadside carrot with today’s grocery-store variety, Simon may be able to breed a new type that is orange and sweet but also more tolerant of high temperatures. Across the world, other scientists are working on similar climate-adapted crops: a drought-tolerant bean, salt-tolerant rice, a tomato relative that can grow in swampy soil. “It’s a lot of work,” Simon says. But there’s also a lot at stake, from the micro to the macro. The selection at your store depends on thriving crops. Far more consequentially, so does food security around the globe. Of the tens of thousands of edible plants on the planet, we count on fewer than 20 types—including corn, wheat, beans, rice—to feed the world, and many of them are at risk.
Breeding Climate-Hardy Crops
Kate Dehler
To understand climate-adapted crops, it helps to understand the origins of the produce we eat today. Not one of the plump, pretty fruits and vegetables at the market was born that way, so to speak. Thousands of years ago, farmers began domesticating wild plants, choosing the ones they considered best—the biggest, the fastest-growing, the most delicious—and crossing them to get new generations that combined these desirable traits. An ear of corn, for example, gradually morphed from a scraggly specimen with maybe two rows of kernels to a hefty cob with 20.
But for every wild crop selected for desirable traits that made it good to eat and easy to farm, many others were ignored. Wild plants, despite being hardy, often grow slowly, bruise easily or don’t taste very good, among other flaws. “You need to remember that a pretty small gene pool actually went into each domesticated crop,” says Stephanie Greene, Ph.D., a plant physiologist with the USDA who researches and conserves wild crop cousins. On the other hand, plants left in the wild got more resilient over time. “They adapted to grow in crazy environments,” says Greene. “And so we’re reaching out into the wild gene pool to look for those useful genes that might not have been captured when we domesticated the species.”
Of the tens of thousands of edible plants on the planet, we count on fewer than 20 types of crops to feed the world, and many of them are at risk.
Breeders call this introgression; put another way, the wild trait of interest is bred into the elite line. When a devastating fungal disease (late blight of tomato) threatened tomatoes around a decade ago, breeders discovered that a tomato wild relative from Peru wasn’t susceptible and introgressed that resistance into tomatoes. Over the years, many crops have borrowed genes from wild ancestors to fight diseases. Climatic events—temperature swings, rain, drought—are a newer focus. An early victory happened in 2006, when Pamela Ronald, Ph.D., a plant pathologist and geneticist at the University of California, Davis, and her colleagues isolated a gene in an ancient rice species that allowed the crop to survive underwater for 14 days, leading to the development of a flood-resistant rice.
Breeding for climate tolerance is harder than breeding for color, flavor, size or yield. Simon can see if his cross-pollinated carrots are orange or taste if they’re sweet. “I eat a lot of carrots over the course of a year,” he says. But to know if a carrot offspring has inherited the ability to survive scorching temperatures isn’t obvious. Currently, he has 3,000 plots of carrots growing in the California desert, about 8 miles from the Mexican border. The plants that can take the heat will make the cut for the next round of backcrossing with the elite pool. “It’s a good 10 to 15 years to move the genes from a wild carrot,” Simon says. “If we push hard.”
A High-Tech Solution
Introgression is slow because it opens the door to many genetic changes, some that may be less desirable. “To take a step forward, you also need to kind of take steps back,” explains Nicholas Karavolias, a plant biology Ph.D. candidate at the University of California, Berkeley. “Let’s say this wild crop ancestor has really good disease tolerance. But it also has terrible yields. You’re inviting both traits in, only to have to breed one out again.”
As an undergrad, Karavolias worked in a conventional breeding program, but at Berkeley he now focuses on a potentially faster route to climate-adapted crops: CRISPR-Cas9, the gene-editing technology that made headlines last year for restoring vision in patients with a rare genetic eye disorder. (Using this molecular tool, sometimes called genetic scissors, doctors sent an enzyme into the eye’s nerve tissue to “snip” and correct the mutated gene.) Jennifer Doudna, Ph.D. , the co-developer of CRISPR who co-won the 2020 Nobel Prize in chemistry, is excited about what the tool can do with plants, “especially as we deal with the challenges of climate change,” she said at a lecture in September.
Karavolias is more focused on the potential of using CRISPR to perform knockouts. Similar to what doctors did with the vision-impaired patients, this involves identifying genes that, if deleted, could improve a plant’s climate tolerance, and then using the Cas9 tool to cleave those genes. This can be less difficult than inserting genetic code, and in some countries, subject to fewer regulations. “It’s kind of sociopolitical, why we’re pursuing knockouts,” he says.
In September, Karavolias and colleagues published a review of work researchers around the world have done in the field of climate-adapted agriculture. “More or less, every example is based on a knockout,” he says. For example, knocking out a gene in rice plants known as OsRR22, which was associated with salt susceptibility, helped the plants grow in sodium-rich conditions, potentially of use in areas where rising sea levels have led to saltwater-contaminated fields.
Karavolias has worried about climate change since 2005, the day that his third-grade teacher warned his Long Island class about global warming, as it was then commonly called. “It just really clicked for me,” he says. “I decided that it was terrifying.” Often, in the car with his family on hot days, he would scream the words “global warming” over and over until a sibling talked him down. As he got older, he began to think about how he could be part of the solution. It was personal too. His parents, who emigrated from Cyprus, both came from farm families. “I’ve seen the ways that my uncle, raising olive or citrus crops in Cyprus, could benefit from technology, varieties, developments that occur,” he says.
Karavolias recently shipped off his latest project, a drought-tolerant rice variety, for field testing. It took him three years to get this far. There are no guarantees, but he hopes that the seed will be ready for distribution in another few years. It has the potential to help rice farmers all over the world, from Colombia to Arkansas.
Plant geneticist Zachary Lippman, Ph.D.“Can we elevate an entire family of orphan crops? This is where I think genome editing gets really exciting.”
Plant geneticist Zachary Lippman, Ph.D.
“Can we elevate an entire family of orphan crops? This is where I think genome editing gets really exciting.”
Rediscovering “Lost” Crops
Lippman’s lab works with orphan crops, such as the African eggplant, a distant relative of the tomato. One edible and attractive cultivar, grown in sub-Saharan Africa, is small and red and looks like a cross between a tomato and a miniature pumpkin. Other varieties are white or orange. Some can grow in swampy, inhospitable soil or in upward of 110°F heat. Many are prickly and impractically large. Lippman is using CRISPR to try to eliminate the prickles, shorten stems and kick up the yield. “Farmers facing crop loss should have the ability to say, ‘OK, I want to try the African eggplant. It’s going to be able to grow in soils that are more challenging,'” he says.
In 2018, Lippman achieved a similar transformation in the groundcherry, a South American orphan crop with sweet berries. He got a lot of attention for it, but notes that working with orphan crops is not a slam dunk—it’s more complicated than that. “The reality is that a lot of this is still a black box,” he says. Yet: “The other side of the coin is that it’s working.”
Ultimately, he sees potential in a combination of gene editing and conventional breeding. With CRISPR he can make a few leaps, called step changes—using what he knows about, say, the tomato’s DNA to target the gene that might increase yield or accelerate growth in the African eggplant, its orphan-crop relative. From there, conventional breeding could step in to try for adaptations where it’s not so obvious which genes to target, ones that might take a few generations of selection to achieve.
There are many orphan crops to explore, Lippman notes, adding that “teff is a great example.” The grain is nutritious and drought-tolerant. On the flip side, rain can wipe it out pretty easily, and the plant’s tiny seeds—the smallest of all grains in the world—often blow away in the wind. “It’s a horrible plant,” Lippman says. “Is it worthwhile to make it into a genome-edited less-horrible plant or not-at-all horrible plant? I don’t know. But those questions can and should be asked across the board.”
Crops That Might Be Coming to a Grocery Near You
Back on Long Island, Lippman let his thoughts move from what’s possible now to what might happen in 10 or 15 years. Eventually, he says, breeders might be able to use CRISPR to rewrite a plant’s entire genome, editing dozens of traits in one sweep. “We can be realistic now, but we should also be optimistic, open-minded and embracing technology and all that’s coming with it,” he says. “Let’s roll, let’s run—you know, let’s just do this.”
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