The modern potato evolved from a wild tomato fling 9 million years ago, scientists say

The humble modern-day potato, first domesticated about 10,000 years ago, got its start in the Andes mountains before becoming a key crop the world depends on. But because plants don’t preserve well in the fossil record, its lineage has remained largely a mystery.

Now, a team of evolutionary biologists and genomic scientists has traced the origins of this starchy staple to a chance encounter millions of years ago involving an unlikely plant relative: the tomato.

The researchers analyzed 450 genomes from cultivated and wild potato species, and the genes revealed that an ancient wild tomato plant ancestor naturally bred with a potato-like plant called Etuberosum 9 million years ago — or interbred, as both plants had originally split off from a common ancestor plant about 14 million years ago, according to a study published Thursday in the journal Cell.

While neither tomatoes or Etuberosums had the ability to grow tubers — the enlarged, edible part of domesticated plants such as potatoes, yams and taros that grow underground — the resulting hybrid plant did. Tubers evolved as an innovative way for the potato plant to store nutrients underground as the climate and environment in the Andes became colder — and once cultivated, resulted in a dietary mainstay for humans. There are now more than 100 wild potato species that also grow tubers, although not all are edible because some contain toxins.

“Evolving a tuber gave potatoes a huge advantage in harsh environments, fueling an explosion of new species and contributing to the rich diversity of potatoes we see and rely on today,” study coauthor Sanwen Huang, president of the Chinese Academy of Tropical Agricultural Sciences and a professor at the Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, said in a statement. “We’ve finally solved the mystery of where potatoes came from.”

The scientists have also decoded which genes were supplied by each plant to create tubers in the first place. Understanding how potatoes originated and evolved could ultimately help scientists breed more resilient potatoes that are resistant to disease and shifting climate conditions.

Digging into the spud’s enduring mystery

Potatoes, tomatoes and Etuberosums all belong to the genus Solanum, which includes about 1,500 species and is the largest genus in the nightshade family of flowering plants. At first glance, potato plants look nearly identical to Etuberosum, which initially led scientists to think that the two were sisters that came from a common ancestor, said study coauthor JianQuan Liu, a professor in the college of ecology at Lanzhou University in Gansu, China.

Etuberosums include just three species, and while the plants have flowers and leaves similar to those of potato plants, they don’t produce tubers.

“Etuberosums are a special thing,” Dr. Sandy Knapp, study coauthor and research botanist at the Natural History Museum in London, told CNN. “They’re things that you probably would never see unless you went to the Juan Fernandes islands, the Robinson Crusoe islands in the middle of the Pacific, or if you were in the temple rainforest of Chile.”

But charting out the lineage of potatoes, tomatoes and Etuberosums revealed an unexpected wrinkle that seemed to indicate that potatoes were more closely related to tomatoes on a genetic level, Knapp said.

The team used phylogenetic analyses —a process similar to determining in humans a parent-daughter or sister-sister relationship on a genetic level — to determine the relationships among the different plants, Liu said.

The analysis showed a contradiction: Potatoes could be a sister to Etuberosums or tomatoes, depending on different genetic markers, Liu said.

The 14 million-year-old common ancestor of tomatoes and Etuberosums, and the plants that diverged from it, don’t exist anymore and “are lost in the mists of geological time,” Knapp said. Instead, the researchers looked for genetic markers within the plants to determine their origins.

“What we use is a signal that’s come through from the past, which is still there in the plants that we have today, to try to reconstruct the past,” Knapp said.

To track that signal through time, the researchers compiled a genetic database for potatoes, including looking at museum specimens and even retrieving data from rare wild potatoes that are hard to find, some of them occurring in just a single valley in the Andes, Knapp said.

“Wild potatoes are very difficult to sample, so this dataset represents the most comprehensive collection of wild potato genomic data ever analyzed,” study coauthor Zhiyang Zhang, a researcher for the Agricultural Genomics Institute at Shenzhen at the Chinese Academy of Agricultural Sciences, said in a statement.

A genetic road map written by chance

The research revealed that the first potato, and every subsequent potato species, included a combination of genetic material that derived from Etuberosums and tomatoes.

Climatic or geological changes likely caused an ancient Etuberosum and a tomato ancestor to coexist in the same place, Liu said.

Given that both species are bee-pollinated, the likely scenario is that a bee moved pollen between the two plants and led to the creation of the potato, said Amy Charkowski, research associate dean of Colorado State University’s College of Agricultural Sciences. Charkowski was not involved in the new research.

The tomato side supplied a “master switch” SP6A gene, which told the potato plant to start making tubers, while a IT1 gene from the Etuberosum side controlled the growth of the underground stems that formed the starchy tubers, Liu said. If either gene were missing or didn’t work in concert, potatoes never would have formed tubers, according to the researchers.

“One of the things that happens in hybridization is that genes get mixed up,” Knapp said. “It’s like shuffling a deck of cards again, and different cards come up in different combinations. And fortunately for this particular hybridization event, two sorts of genes came together, which created the ability to tuberize, and that’s a chance event.”

The evolution of tuberous potatoes coincided with a time when the Andes mountains were rapidly rising due to interactions among tectonic plates, which created a huge spine down the western side of South America, Knapp said. The Andes are a complex mountain range with numerous valleys and a range of ecosystems.

Modern tomatoes like dry, hot environments, while Etuberosums prefer a temperate space. But the ancestor of the potato plant evolved to thrive in the dry, cold, high-altitude habitats that sprang up across the Andes, with the tuber enabling its ultimate survival, Knapp said. Potatoes could reproduce without the need for seeds or pollination. The growth of new tubers led to new plants, and they could flourish across diverse environments.

Creating a hardy potato for an uncertain future

The cultivated potato we consume today is currently the world’s third most important staple crop, and with wheat, rice and maize, is responsible for 80% of human caloric intake, according to the study.

Understanding the potato’s origin story could be the key to breeding more innovation into future potatoes; reintroducing key tomato genes could lead to fast-breeding potatoes reproduced by seeds, something with which Huang and his team at the Chinese Academy of Agricultural Sciences are experimenting.

Modern crops face pressures from environmental change, the climate crisis and new pests and diseases, Knapp said.

Seed potatoes are of interest because they may be more genetically diverse and resistant to disease and other agricultural risks, Knapp said. Vegetatively reproducing potatoes — cutting a potato into pieces and planting them to create a crop — results in genetically identical potatoes that can be wiped out if a new disease comes along.

Studying wild species that have come up against and evolved in response to such challenges could also be crucial, she added.

Charkowski’s lab is interested in how wild potatoes resist disease, and why some plant pests and diseases only affect potatoes or tomatoes.

“In addition to helping us understand potato evolution and potato tuber development, the methods used (in this study) can also help researchers learn about other traits, such as disease and insect resistance, nutrition, drought tolerance, and many other important plant traits in potato and tomato,” Charkowski said.

Potatoes remain an important crop in arid regions or areas with short summers and high altitudes — places where other major crops don’t grow, she said.

The findings also show potatoes in a different light: the result of a chance encounter of two very different individuals, said study coauthor Dr. Tiina Särkinen, a nightshade expert at the Royal Botanic Garden Edinburgh.

“That’s actually quite romantic,” she said. “The origin of many of our species isn’t a simple story, and it’s very exciting that we can now discover these tangled, complex origins thanks to the wealth of genomic data.”

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