Evolutionary origins of the potato revealed – and a tomato was involved

The potato is one of the world’s food staples, first cultivated thousands of years ago in the Andes region of South America before spreading globally from the 16th century. But despite its importance to humankind, the evolutionary origins of the potato have remained puzzling – until now.

A new analysis of 450 genomes from cultivated potatoes and 56 genomes of wild potato species has revealed that the potato lineage originated through natural interbreeding between a wild tomato plant and a potato-like species in South America about 9 million years ago.

This hybridization event led to the appearance of the nascent potato plant’s tuber, an enlarged structure housing nutrients underground, according to the researchers, who also identified two crucial genes involved in tuber formation. Whereas in a tomato plant the edible part is the fruit, in the potato plant it is the tuber.

“Potatoes are truly one of humanity’s most remarkable food staples, combining extraordinary versatility, nutritional value and cultural ubiquity in ways few crops can match,” said Sanwen Huang, a genome biologist and plant breeder at the Chinese Academy of Agricultural Sciences and senior author of the study published on Friday in the journal Cell.

“People eat potatoes using virtually every cooking method – baking, roasting, boiling, steaming and frying. Despite being stereotyped as carbohydrates, potatoes offer vitamin C, potassium, fiber and resistant starch, and are naturally gluten-free, low-fat and satiating – a nutrient-dense calorie source,” Huang added.

Resistant starch is a type of carbohydrate that resists digestion in the small intestine and ferments in the large intestine, feeding beneficial bacteria in the gut.

The modern-day potato plant’s scientific name is Solanum tuberosum. Its two parents identified in the study were plants that were the ancestors of a potato-like species now found in Peru named Etuberosum, which closely resembles the potato plant but lacks a tuber, and the tomato plant.

These two plants themselves shared a common ancestor that lived about 14 million years ago, and were able to naturally interbreed when the fortuitous hybridization event occurred five million years after they had diverged from each other.

“This event led to a reshuffling of genes such that the new lineage produced tubers, allowing these plants to expand into the newly created cold, dry habitats in the rising Andes mountain chain,” said botanist Sandra Knapp of the Natural History Museum in London, a co-author of the study.

This hybridization event coincided with the rapid uplift of the Andes. With a tuber, the potato plant was able to adapt to the changing regional environment and thrive in the harsh conditions of the mountains.

“Tubers can store nutrients for cold adaptation, and enable asexual reproduction to meet the challenge of the reduced fertility in cold conditions. These allowed the plant to survive and rapidly expand,” Huang said.

The study’s findings, according to the researchers, may help guide improved cultivated potato breeding to address environmental challenges that crops presently face due to factors such as climate change.

There currently are roughly 5,000 potato varieties. The potato is the world’s third most important food crop, after rice and wheat, for human consumption, according to the Peru-based International Potato Center research organization. China is the world’s leading potato producer.

“It always is hard to remove all the deleterious mutations in potato genomes in breeding, and this study opens a new door to make a potato free of deleterious mutations using the tomato as the chassis of synthetic biology,” Huang said.

The study also may open the door to generate a new crop species that could produce tomato fruit above ground and potato tubers below ground, according to Zhiyang Zhang, a postdoctoral researcher at the Chinese Academy of Agricultural Sciences.

The potato and tomato are members of the nightshade family of flowering plants that also includes tobacco and peppers, among others. The study did not investigate the evolutionary origins of other tuberous root crops that originated in South America such as the sweet potato and yuca, which are members of different families of flowering plants.

While the parts of the tomato and potato plants that people eat are quite different, the plants themselves are very similar.

“We use different parts of these two species, fruits in tomatoes and tubers in potatoes,” Knapp said. “If you look at the flowers or leaves, these are very similar. And if you are lucky enough to let your potato plant produce fruits, they look just like little green tomatoes. But don’t eat them. They are not very nice.”