An 80,000-year history of the tomato
Creating the perfect vegetable
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Walk into a supermarket anywhere in the world and chances are you’ll be able to find a tomato in mere minutes. While technically a fruit, the tomato is more often grouped with vegetables because, due to its low sugar content, it is used more like a vegetable in cuisine. In fact, tomatoes have long been by far the most frequently consumed canned vegetable, as well as one of the most commonly eaten overall. In 2019, the average American ate more than 30 pounds of tomatoes, making it second to only the potato in total consumption. Tomatoes come by this popularity honestly too: their low calorie count and high vitamin content make them quite healthy.
None of this would be possible, however, without thousands of years of plant breeding and genetic engineering. The wild ancestors of today’s tomatoes were much smaller than their modern-day counterparts and grew in sprawling patterns, making them ill-suited to large-scale agriculture. Extensive breeding programs created the first domesticated tomatoes, and subsequently shaped them into a food with largely uniform qualities that could be mass produced. In doing this, agronomists collectively made a series of choices that vastly improved tomatoes’ ability to feed humanity, though sometimes at the expense of secondary qualities like taste. In recent decades, breeders have also adopted new genetic tools to more precisely choose the traits they want, allowing them to reclaim these lost characteristics.
Nearly 80,000 years ago, Central and South America were home to a blueberry-sized plant called Solanum pimpinellifolium – the ancestor of modern tomatoes. Wild descendants of this plant, called currant tomatoes, can still be eaten today but are more labor-intensive to pick and less versatile in the kitchen than their domesticated cousins. Some varieties are also toxic to humans. Native Americans recognized the utility of having a larger, safer plant and began breeding accordingly. By roughly 7,000 years ago they had created precisely this: Solanum lycopersicum, the common tomato.
This domestication process also produced an intermediate type of fruit, which today is known as the cherry tomato. This semi-domesticated variety ultimately gave rise to the common tomato as well as the cherry tomatoes available commercially today. Tomato domestication was not strictly linear and ancestral cherry tomatoes spread throughout Latin America over time, losing and regaining traits along the way. This continuous intermingling helped ensure that by the time the tomato reached its domesticated form, S. lycopersicum, it still came in a variety of colors, shapes, and sizes. However, the overall genetic diversity of the tomato had already decreased precipitously by this point due to heavy selection for agriculturally beneficial traits. By favoring tomatoes with certain desirable qualities, breeders had drastically increased the percentage of plants with the gene variants that caused these traits, excluding other versions found in the wild. It was this more streamlined version of the tomato that then spread around the world.
In the mid-sixteenth century, Spanish conquistadors brought the first tomatoes to Europe, from where they quickly spread around the world. The fruits that reached Europe were visually diverse; many were yellow, earning the tomato its famous golden apple nickname. By the early seventeenth century, tomatoes had spread through the Spanish-occupied Philippines to reach China. Via Europe, they also reached the Middle East and North Africa in the early nineteenth century.
While Spanish and Italian cuisine quickly incorporated tomatoes, an influential British history of plants characterized them as poisonous and the reputation stuck. Tomatoes were primarily grown ornamentally in Britain and North America at first, and it wasn’t until the mid-nineteenth century that they were widely considered safe to eat in these areas. This allowed tomatoes to benefit from the plant breeding revolution that took place in the ensuing decades. During this period, agronomy gained more scientific thrust as breeders gained awareness of Charles Darwin’s theory of natural selection and Gregor Mendel’s selective breeding experiments. With these insights in hand, they were able to more systematically cross plants to combine their beneficial traits.
Ohio’s Alexander Livingston created the first tomato suitable for widespread commercialization in 1870, cementing himself as one of the most important traditional tomato breeders. Called the Paragon, Livingston’s new variety was bigger and meatier than older tomatoes and also looked more uniform, with an increasingly standardized color and texture. So great were Livingston’s contributions that by 1910, his company was responsible for half of the major American tomato varieties. While individual gardeners would continue to grow the older ‘heirloom’ varieties, Livingston’s success ensured that most new tomatoes would look and taste a certain way.
The next generation of tomato breeders built on Livingston’s contributions, establishing bright red tomatoes as the industry standard but unintentionally sacrificing other qualities in the process. By the mid-1940s, tomato breeders worldwide had all selected for a trait called uniform ripening. This ensured that all fruit started out green and became bright red upon maturation, eliminating the blotches found in heirloom varieties. Beyond producing eye-catching tomatoes, uniform ripening allowed growers to quickly determine which fruit were ripe, increasing the efficiency of their farming.
A 2012 study uncovered the genetic underpinning of this trait, revealing that uniform ripening came at the cost of sugar production and therefore sweetness. Tomatoes wouldn’t be as widely or cheaply available as they are today without uniform ripening but this choice is not without costs.
In the 1970s, biologists developed the first methods to splice foreign genes into the DNA of living cells, creating the first genetically modified organisms (GMOs). Plant breeders quickly adopted these techniques, and the Flavr Savr tomato became the first FDA-approved GMO food to hit store shelves in 1994. While the Flavr Savr lasted longer and resisted fungal growth, its sales were impeded by public distrust of GMO foods so the product was pulled from stores’ shelves after just three years. But this was the iteration of a technology that would soon allow horticulturalists to create new tomatoes with greater precision than before.
Shortly after the the Human Genome Project and Celera Genomics published their sequences of the entire human genome in 2001, tomato researchers formed a new consortium to sequence their crop. This initial tomato genome was published in 2012 and researchers quickly began sequencing various ancestral varieties to reconstruct the fruit’s evolutionary history. By comparing the genomes of numerous tomato varieties with different physical traits, researchers could identify the genes responsible for those traits – a technique known as quantitative trait locus mapping. This allowed them to discover lost versions of genes related to traits including size and flavor that had inadvertently been selected out over time.
During the same period, biologists developed new genome editing systems – such as CRISPR – that allowed them to edit specific genes without introducing external DNA. Breeders had abandoned sweet tomatoes because they necessarily had a different version of the gene responsible for uniform ripening – the two traits were incompatible. With CRISPR, it became possible to edit other genes related to sugar production in order to create tomatoes with the best of both worlds. Late last year, one group did just this, creating fruit containing up to 30 percent more sugar without a size or yield penalty. Using CRISPR, scientists have also created tomatoes that grow larger, contain more antioxidants, resist herbicides, and last longer on shelves.
Editing techniques that insert foreign DNA have also been developed further, notably leading to the creation of a purple tomato containing snapdragon flower DNA, which was approved by the FDA in 2023. While its eye-catching skin was a nice bonus, the purple tomato was primarily created to be nutrient dense. The fruit contains three times as many antioxidants as the typical tomato, which helps protect cells from damage caused by unstable molecules called free radicals.
Tomato breeding’s history stretches back tens of thousands of years, making genome sequencing and editing incredibly recent advances. As it becomes cheaper to sequence more varieties and improved editing tools emerge however, breeding seems poised to speed up even further.
Tomato evolution also provides an interesting example of the effects of genetic diversity. While modern tomatoes are much less genetically diverse than their wild counterparts, the size range of our current varieties far outstrips their ancestors. Genome editing and other modern breeding methods could be used to introduce alternative versions of key genes responsible for important tomato traits. By increasing genetic diversity at the spots where it counts the most, researchers can mitigate the worst consequences of modern tomatoes’ loss in overall genetic diversity.
New genome editing methods that alter DNA without introducing foreign genetic material aren’t subject to GMO regulations in the US and EU, meaning that modified tomatoes are likely to be approved at an increasingly fast rate. One day, supermarkets might even stock tomatoes with shapes, colors, and flavor profiles not found in even the rarest heirloom varieties.
Evan DeTurk is a science writer and molecular biologist at UC Berkeley.
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