When I was a young kid, our neighborhood didn’t have any grocery stores. The only place to buy fruits and vegetables was at our local farmer’s market. My mom would pick out the freshest tomatoes and sauté them with eggs into a simple dish that became my comfort food.
The tomatoes were hideous to look at—small, gnarled, miscolored, and nothing like the perfectly plump and bright beefsteak or Roma tomatoes that eventually flooded supermarkets. But they were oh-so-tasty, with a perfect ratio of tart and sweet flavors that burst in my mouth.
These days, when I ask for the same dish, my mom will always say, “Tomatoes just don’t taste the same anymore.”
She’s not alone. Many people have noticed that today’s produce is watery, waxy, and lacking in flavor—despite looking ripe and inviting. One reason is it was bred that way. Today’s crops are often genetically selected to prioritize appearance, size, shelf life, and transportability. But these perks can sacrifice taste—most often, in the form of sugar. Even broccoli, known for its bitterness, has variants that accumulate sugar inside their stems for a slightly sweeter taste.
The problem is that larger fruit sizes are often less sweet, explains Sanwen Huang and colleagues in Shenzhen, China. The key is to break that correlation. His team may have found a way using a globally popular crop—the tomato—as an example.
By comparing wild and domesticated tomatoes, the team hunted down a set of genes that put the brakes on sugar production. Inhibiting those genes using CRISPR-Cas9, the popular gene-editing tool, bumped up the fruit’s sugar content by 30 percent—enough for a consumer panel to find a noticeable increase in sweetness—without sacrificing size or yields.
Seeds from the edited plants germinated as usual, allowing the edits to pass on to the next generations.
The study isn’t just about satisfying our sweet tooth. Crops, not just tomatoes, with higher sugar content also contain more calories, which are necessary if we’re to meet the needs of a growing global population. The analysis pipeline established in the study is set to identify other genetic trade-offs between size and nutrition, with the goal of rapidly engineering better crops.
The work “represents an exciting step forward…for crop improvement worldwide,” wrote Amy Lanctot and Patrick Shih at the University of California, Berkeley, who were not involved in the study.
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For eons, humanity has cultivated crops to enhance desirable aspects—for example, better yields, higher nutrition, or looks.
Tomatoes are a perfect example. The fruit “is the most valuable vegetable crop, worldwide, and makes substantial overall health and nutritional contributions to the human diet,” wrote the team. Its wild versions range in size from cherries to peas—far smaller than most current variants found in grocery stores. Flavor comes from two types of sugars packed in their solid bits.
After thousands of years of domestication, sugars remain the key ingredient to better-tasting tomatoes. But in recent decades, breeders mostly prioritized increasing fruit size. The result are tomatoes that are easily sliced for sandwiches, crushed for canning, or further processed into sauces or pastes. Compared to their wild ancestors, today’s cultivated tomatoes are roughly between 10 to 100 times larger in size, making them far more economical.
But these improvements come a cost. Multiple studies have found that as size goes up, sugar levels and flavor tank. A similar trend has also been found in other large farming fruits.
Ever since, scientists have tried teasing out the tomato’s inner workings—especially genes that produces sugar—to restore its taste and nutritious value. One study in 2017 combined genomic analysis of nearly 400 varieties of tomatoes with results from a human taste panel to home in on a slew of metabolic chemicals that made the fruit taste better. A year later, Huang’s team, who led the new study, analyzed the genetic makeup and cell function of hundreds of tomato types. Domestication was associated with several large changes in the plant’s genome—but the team didn’t know how each genetic mutation altered the fruit’s metabolism.
It’s tough to link a gene to a trait. Our genes, as DNA strands, are tightly wound into mostly X-shaped chromosomes. Like braided balls of yarn, these 3D structures bring genes normally separated on a linear strand into close proximity. This means nearby, or “linked,” genes often turn on or off together.
“Genetic linkage makes it difficult to alter one gene without affecting the other,” wrote Lanctot and Shih.
Fast Track Evolution
The new study used two technologies to overcome the problem.
The first was cheaper genetic sequencing. By scanning through genetic variations between domesticated and wild tomatoes, the team pinpointed six tomato genes likely responsible for the fruit’s sweetness.
One gene especially caught their eye. It was turned off in sweeter tomato species, putting the brakes on the plants’ ability to accumulate sugar. Using the gene-editing tool CRISPR-Cas9, the team mutated the gene so it could no longer function and grew the edited species—along with normal ones—under the same conditions in a garden.
The Sweet Spot
Roughly 100 volunteers tried the edited and normal tomatoes in a blind trial. The CRISPRed tomatoes won in a landslide for their perceived sweetness.
The study isn’t just about a better tomato. “This research demonstrates the value hidden in the genomes of crop species varieties and their wild relatives,” wrote Lanctot and Shih.
Domestication, while boosting yield or size of a fruit, often decreases genetic diversity for a species because selected crops eventually contain mostly the same genetic blueprint. Some crops, such as bananas, can’t reproduce on their own and are extremely vulnerable to fungi. Analyzing genes related to these traits could help form a defense strategy.
Conservation and taste aside, scientists have also tried to endow crops with more exotic traits. In 2021, Sanatech Seed, a company based in Japan, engineered tomatoes using CRISPR-Cas9 to increase the amount of a chemical that dampens neural transmission. According to the company, the tomatoes can lower blood pressure and help people relax. The fruit is already on the market following regulatory approval in Japan.
Studies that directly link a gene to a trait in plants are still extremely rare. Thanks to cheaper and faster DNA sequencing technologies, and increasingly precise CRISPR tools, it’s becoming easier to test these connections.
“The more researchers understand about the genetic pathways underlying these trade-offs, the more they can take advantage of modern genome-editing tools to attempt to disentangle them to boost crucial agricultural traits,” wrote Lanctot and Shih.
Image Credit: Thomas Martinsen on Unsplash
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