When I was a little boy, there were no grocery stores in our neighborhood. The only place to buy fruits and vegetables was at our local farmer’s market. My mom would pick the freshest tomatoes and saute them with eggs into a simple meal that became my comfort food.
The tomatoes were ugly to look at – small, twisted, different in color and nothing like the perfectly plump and light beefsteak or Roma tomatoes that eventually flooded the supermarkets. But they were oh-so-delicious, with a perfect balance of sour and sweet that burst in my mouth.
These days, when I ask for the same dish, my mom always says, “Tomatoes just don’t taste the same anymore.”
She is not alone. Many people have noticed that today’s produce is watery, waxy and lacks flavor – despite looking ripe and appealing. One reason is that he was bred that way. Today’s crops are often genetically selected to favor appearance, size, storage and transportability. But these benefits can come at the expense of taste – most often in the form of sugar. Even broccoli, known for its bitterness, has varieties that store sugar inside their stems for a slightly sweeter taste.
The problem is that larger fruit sizes are often less sweet, explain Sanwen Huang and colleagues in Shenzhen, China. The key is to break this correlation. His team may have found a way to use a globally popular crop, the tomato, as an example.
By comparing wild and domesticated tomatoes, the team tracked down a set of genes that inhibit sugar production. Inhibiting these genes using CRISPR-Cas9, a popular gene-editing tool, increased the fruit’s sugar content by 30 percent — enough for a consumer panel to detect a noticeable increase in sweetness — without sacrificing size or yield.
Seeds from the modified plants germinated as usual, allowing the modifications to be passed on to subsequent generations.
Study isn’t just about satisfying our sweet tooth. Crops, not just tomatoes, with higher sugar content also contain more calories, which are essential if we are to meet the needs of a growing global population. The analytical pipeline created in the study is set to identify additional genetic trade-offs between size and nutrition, with the aim of rapidly preparing better crops.
The work “represents an exciting step forward … for crop improvement worldwide,” wrote Amy Lanctot and Patrick Shih of the University of California, Berkeley, who were not involved in the study.
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Throughout the ages, humans have cultivated crops to improve desirable aspects—for example, better yields, higher nutrition, or appearance.
Tomatoes are a perfect example. Fruit “is the most valuable vegetable worldwide and contributes significantly to the overall health and nutrition of the human diet,” the team wrote. Its wild versions range in size from cherries to peas—much smaller than most of the current varieties found in grocery stores. The taste comes from two types of sugar packed into solid pieces.
After thousands of years of domestication, sugars remain a key ingredient for the better taste of tomatoes. But in recent decades, breeders have mostly favored increasing fruit size. The result is tomatoes that can be easily cut into sandwiches, crushed for canning or further processed into sauces or pastes. Compared to their wild ancestors, cultivated tomatoes today are roughly 10 to 100 times larger, making them much more economical.
However, these improvements come at a cost. Several studies have found that as size increases, sugar levels and taste tank. A similar trend was also found for other large agricultural crops.
Since then, scientists have been trying to tease out the inner workings of the tomato—especially the genes that produce the sugar—to restore its flavor and nutritional value. One 2017 study combined genomic analysis of nearly 400 tomato varieties with results from a human taste panel to look at a host of metabolic chemicals that make the fruit taste better. A year later, Huang’s team, who led the new study, analyzed the genetic makeup and cellular function of hundreds of tomato varieties. Domestication was associated with several large changes in the plant’s genome – but the team did not know how each genetic mutation changed the fruit’s metabolism.
It is difficult to associate a gene with a trait. Our genes, like strands of DNA, are tightly coiled into chromosomes, mostly in the shape of an X. Like a knitted ball of yarn, these 3D structures bring genes normally separated on a linear strand into close proximity. This means that nearby or “linked” genes are often turned on or off together.
“Genetic linkage makes it difficult to change one gene without affecting the other,” Lanctot and Shih wrote.
Fast Track Evolution
The new study used two technologies to overcome the problem.
The first was cheaper genetic sequencing. By scanning the genetic variation between domesticated and wild tomatoes, the team pinpointed six tomato genes that are likely responsible for the fruit’s sweetness.
One gene in particular caught their attention. In the sweeter varieties of tomatoes, it was turned off, inhibiting the plants’ ability to accumulate sugar. Using the CRISPR-Cas9 gene-editing tool, the team mutated the gene so that it could no longer function, and grew the modified species—along with the normal ones—under the same conditions in the garden.
Sweet spot
Roughly 100 volunteers tried modified and normal tomatoes in a blind experiment. CRISPRed tomatoes won by a wide margin for their perceived sweetness.
The study is not just about a better tomato. “This research demonstrates the value hidden in the genomes of crop varieties and their wild relatives,” Lanctot and Shih wrote.
Domestication, while increasing yield or fruit size, often reduces the genetic diversity of a species because the selected crops end up containing mostly the same genetic blueprint. Some crops, such as bananas, cannot reproduce on their own and are extremely susceptible to fungi. Analysis of the genes associated with these traits could help develop a defense strategy.
Aside from preservation and taste, scientists have also tried to equip crops with more exotic features. In 2021, Sanatech Seed, a company based in Japan, produced tomatoes using CRISPR-Cas9 to increase the amount of a chemical that suppresses nerve transmission. According to the company, tomatoes can lower blood pressure and help people relax. The fruit is already on the market after being approved by regulatory authorities in Japan.
Studies that directly link a gene to a trait in plants are still extremely rare. Cheaper and faster DNA sequencing technologies and increasingly accurate CRISPR tools are making testing these connections easier.
“The more scientists understand the genetic pathways underlying these trade-offs, the more they can use modern genome-editing tools to try to tilt them to enhance key agricultural traits,” Lanctot and Shih wrote.
Image credit: Thomas Martinsen on Unsplash