Potato origins mystery solved after 9 million years

An ancient encounter between distant plant relatives forever changed agriculture. About nine million years ago, natural interbreeding between a tomato ancestor and a South American Etuberosum species led to the first true potato.

This unexpected hybridization created a plant with one powerful trait: the ability to grow tubers underground.

Published in the journal Cell, the study reveals how this hybrid event transformed evolution. Tubers enabled plants to store nutrients below the surface, helping them survive climate shifts and colonize new terrains.

“Our findings show how a hybridization event between species can spark the evolution of new traits, allowing even more species to emerge,” said co-author Sanwen Huang of the Chinese Academy of Agricultural Sciences. “We’ve finally solved the mystery of where potatoes came from.”

Potatoes are more tomato than expected

While the potato resembles some tuberless Chilean species, it shares more genetic ties with tomatoes. To investigate, the researchers sequenced 450 cultivated potato genomes and 56 wild relatives.

They discovered that all potatoes carry a stable genetic blend from both Etuberosum and tomato-like ancestors.

The two lineages diverged around 14 million years ago, yet still interbred after 5 million years of separation. This compatibility led to the birth of the modern potato lineage with tuber-forming capabilities.

“Wild potatoes are very difficult to sample, so this dataset represents the most comprehensive collection of wild potato genomic data ever analyzed,” said study first author Zhiyang Zhang.

Origins of modern potatoes

By tracing the source of tuber-related genes, the study showed how specific gene combinations enabled tuber development. One gene, SP6A, came from the tomato ancestor. It acts like a timer, signaling when to begin tuber formation.

Another gene, IT1, came from Etuberosum and drives the actual growth of the underground stem structures.

Without these two genes, tubers would not exist. Their presence in the hybrid offspring gave the new lineage a nutritional edge.

This combination also solved a long-standing contradiction. While tuberless Etuberosum plants resemble modern potatoes, they lacked these hybrid genes. Potatoes, on the other hand, inherited the best of both parents.

Tubers helped potatoes survive

The potato’s evolutionary breakthrough matched a dramatic environmental shift. The Andes mountains were rising rapidly during this period. These changes brought colder, harsher conditions.

Underground tubers allowed the hybrids to store energy and survive drought, frost, and low oxygen.

Tubers gave potatoes another advantage: asexual reproduction. A single tuber can sprout new plants without seeds or flowers. This helped the species spread across diverse ecosystems, from mountain slopes to temperate grasslands.

Rewiring of plant hormone systems

The research uncovered even deeper changes. Potato hybridization did not just merge genes. It altered hormonal pathways. Tuber formation involves a shift from flowering-focused reproduction to underground storage growth.

The researchers found reduced expression of flowering genes and increased activation of genes that promote storage organ formation. These changes involved key hormones like gibberellins, which control plant development.

The hybrid lineage adjusted hormone balances to support tuber growth while limiting flower formation when necessary.

The SP6A and IT1 genes did not act alone. They interacted with regulators of sugar transport and underground stem expansion. This suggests that tuber evolution affected entire physiological networks.

How hybridization fuels plant diversity

Hybridization between distant plant lineages is rare, but powerful. It can bypass reproductive barriers, create new species, and introduce useful traits. In the potato’s case, hybridization created an entirely new reproductive strategy using vegetative propagation through tubers.

This ability allowed potatoes to diversify rapidly. The Andes became a hotspot for wild potato speciation. Each species adapted to different altitudes and climates.

“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,” Huang said.

Tomatoes helped create potatoes

The potato is now one of the world’s most essential crops, feeding billions. But its success began with one wild encounter between tomato-like and Etuberosum ancestors.

Through ancient hybridization, potatoes gained the ability to thrive underground, reproduce without seeds, and adapt to varied environments. Their tubers became both survival tools and culinary staples.

Scientists have finally traced that origin story, showing how a distant botanical union shaped the potato and our diets.

The study is published in the journal Cell.

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