Modern cultivated potatoes (right) closely resemble wild Solanum etuberosum plants from Chile (left), even though those wild relatives cannot form tubers. This paradox – potatoes looking like a plant with no tubers, yet genetically tied to tomatoes – long puzzled scientists. Now, a comprehensive genome study reveals the answer: about 9 million years ago, a wild tomato ancestor naturally crossed with a tuberless Etuberosum plant. This hybridization endowed the offspring with the tuber trait, setting the stage for the potato lineage we know today.

The Evolutionary Puzzle of Potatoes

• Shared genus, different traits: Potatoes and tomatoes both belong to the nightshade genus Solanum, but potatoes’ closest wild look-alikes (Etuberosum species) lack underground tubers.
• Genetic clues: Detailed genetic analyses showed that cultivated potatoes carry more DNA in common with tomatoes than with those tuberless relatives.
• Lingering mystery: This conflicting evidence – striking physical similarity to a tuberless plant but a closer genetic tie to tomatoes – left the potato’s origin a long-standing mystery.

The Ancient Hybridization Event

Researchers sequenced over 450 genomes of cultivated potatoes and their wild relatives to untangle this mystery. They found that every potato species today carries a balanced mix of genetic material from both tomato-like and Etuberosum ancestors. This pointed to a single ancient hybrid origin. The evidence suggests that tomatoes and Etuberosum shared a common ancestor roughly 14 million years ago, and then diverged. About 9 million years ago in the Andes, a wild tomato relative and a tuberless Etuberosum naturally interbred. The hybrid offspring combined genes from each parent and became the first tuber-bearing plant – the ancestor of all modern potatoes. Key findings include:

• Timeframe: Solanum ancestors split ~14 million years ago, then hybridized ~9 million years ago.
• Genomic evidence: Every potato genome is a “mosaic” of tomato and Etuberosum DNA, indicating a one-time hybrid speciation event, not multiple smaller gene transfers.
• Birth of potatoes: This ancient cross created the Petota lineage (all tuber-bearing potatoes). In effect, the hybrid plant gained the ability to form tubers – a trait absent in both parent species.

Genetic Origins of Tuber Formation

The emergence of tubers depended on two critical genes inherited from the different parents:

• SP6A (tomato-derived): This gene acts as a “master switch” that triggers the potato plant’s developmental program to start forming tubers.
• IT1 (Etuberosum-derived): This gene regulates the growth of the underground stems that swell into tubers.

Neither parent plant alone had the full tuber-forming system: tomatoes carried SP6A but lacked compatible stem-growth genes, while Etuberosum contributed IT1 but no SP6A equivalent. Only their hybrid offspring inherited both parts. Together, SP6A and IT1 acted in concert to produce the first potato tubers. As one author notes, this is “the first to show that hybridization generated a new type of organ, the tuber”. In other words, the hybridization event effectively unlocked a novel genetic switch for tuber development, a powerful “jackpot” that neither lineage could achieve alone.

Ecological Impact and Species Radiation

The hybrid potato’s new tuber trait provided a huge ecological advantage as the Andes Mountains were rising. The timing coincided: between about 6 and 10 million years ago the Andes uplifted, creating cold, dry high-altitude habitats. The tubers — rich storage organs of water and nutrients — allowed early potatoes to survive these harsh conditions. With a tuber, a plant could endure drought and cold by tapping reserves underground. Moreover, tubers enable asexual reproduction: potatoes sprout new plants from buds on the tuber itself, without needing seeds or flowers. This meant the hybrid potatoes could quickly colonize new niches. The result was rapid diversification: the tuber-bearing lineage expanded into grasslands, alpine meadows and other Andean ecosystems. Over time, this led to a “explosion of new species” in the potato lineage. Today, the Petota group includes the cultivated potato and roughly 107 wild potato species adapted to diverse South American habitats.

Implications for Modern Agriculture

Uncovering this ancient hybrid origin has practical lessons for today’s crop science. For example:

• Breeding resilient varieties: Knowing that SP6A and IT1 together create tubers gives breeders clear genetic targets. By editing or selecting these pathways, scientists may boost tuber yield, improve stress tolerance (drought, cold), and even engineer potatoes to grow faster or resist disease.
• Conserving wild relatives: The study highlights the value of wild Solanum species. The genetic diversity in those wild tomatoes and Etuberosum plants is a reservoir of traits (like SP6A/IT1) that could be used to improve cultivated potatoes. Preserving this diversity ensures we don’t lose the evolutionary “tools” nature has crafted.
• Harnessing hybridization: More broadly, the finding shows hybridization can produce brand-new organs or features. This may inspire researchers to explore interspecies crosses (or synthetic biology “chimeras”) to generate novel crop traits. Just as a tomato-tuber cross created the potato, other controlled crosses might yield crops with new combinations of useful traits, a strategy for adapting agriculture to changing climates.

By piecing together genomes of dozens of species, scientists have now filled the gap in the potato’s family tree. The discovery that potatoes “sprouted” from a tomato-like ancestor nearly 9 million years ago not only solves a long-standing botanical riddle, but also guides future efforts to cultivate hardier, higher-yield potatoes for a growing world.