The potato is one of the most important and delicious crops on the planet. But without a fortunate encounter 9 million years ago, it may have never existed.

The potato, it turns out, is not a “purebreed.” It’s the result of an ancient and accidental hybridization that occurred between an ancestor of the modern tomato and a now-extinct member of a wildflower group known as Etuberosum.

Thanks for the tubers, nature

The potato (Solanum tuberosum) has 107 relatives. All of them have tubers, underground stems or roots that act as storage organs for nutrients like starch and water. These tubers are what we call “potatoes,” the flowers and fruits of the potato plant are actually poisonous.

For decades, researchers have been trying to figure out how potatoes evolved and how they developed this innovation. The potato lineage, known to botanists as Petota, clearly had two very close relatives. These were the Tomato lineage and the Etuberosum lineage, a small group of three wild, non-tuber-bearing species from South America. But which one was its true sibling?

The evidence was maddeningly inconsistent. Some genetic analyses suggested the tomato was the potato’s closest relative. Others pointed squarely to Etuberosum. It was like the same person took a genetic test and got different results all the time. So, to solve the puzzle, a massive research effort led by scientist Sanwen Huang brought cutting-edge technology to the problem.

Potato genetics

They didn’t just look at a few genes here and there. They analyzed the entire the genome of 128 different plants: 101 genomes from the potato lineage (covering 44 different wild species), 15 from the tomato lineage, and 9 from the Etuberosum. Many of these were sequenced for the first time, providing an unprecedented, high-definition view into the potato’s deep genetic past.

“Wild potatoes are very difficult to sample, so this dataset represents the most comprehensive collection of wild potato genomic data ever analyzed,” says the paper’s first author Zhiyang Zhang of the Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences. 

They then reconstructed the evolutionary relationships between the three lineages using various methods. First, they confirmed that some parts of the potato genome are more similar to the tomato genome, while other parts are more similar to the Etuberosum genome, a hallmark of hybridization. This mosaic was smoking gun for a single, ancient hybridization event that formed a brand-new, stable lineage.

They also used specialized statistical tools to confirm that hybridization is by far the most likely event that created the potato, but they didn’t stop there. The team conducted experiments to show that proteins from the parental lineages interact in a way that could promote the production of tubers. They also used the “genetic scissors” CRISPR to knock out specific genes in potato plants, confirming their role in tuber development.

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

How to build a potato

Here’s the interesting part, however: neither tomatoes nor Etuberosum have tubers. The very name E-tuberosum is Latin for “without tubers.”

The tuber is a key innovation, a specialized organ distinctive of potatoes, but neither of the parental lineages had this ability. The tomato ancestor produced fruits above ground, and the Etuberosum ancestor produced thin, non-swollen underground stems called rhizomes. The tuber was something entirely new, born from the fusion of two different genetic worlds.

The research team found that the genetic pathways controlling tuber formation were a patchwork of genes inherited from both parents. This is a concept scientists call the alternate inheritance of highly divergent parental genes.

To prove this beyond a doubt, the researchers used modern gene-editing technology (CRISPR) to knock out some of these hybrid-origin genes in a wild potato species. The results were dramatic and unambiguous. When they knocked out a key gene inherited from the tomato side, the mutant plants got confused; they started growing small tubers on their aerial branches instead of underground. When they knocked out a gene from theEtuberosum side, CLF, the result was even more stark: the plants became dwarfs and completely lost the ability to form underground stolons and, consequently, any tubers at all.

Seeing that one mutant caused ectopic organs and another caused the loss of them provided powerful, direct proof that this precise combination of genes from two distinct ancestors was essential for the tuber to exist.

A happy accident for plants and humans

Armed with tuber superpower, the ancestral potato was ready to take on the world. The timing of its hybrid origin, around 8-9 million years ago, was no coincidence. It happened just as the Andes mountains were undergoing a period of rapid and dramatic uplift. This geological upheaval created a vast array of new, challenging environments: high-elevation plateaus, cold and dry grasslands, and seasonal forests.

For the new hybrid lineage, the tuber was a passport to these forbidding landscapes. It acted as a survival pack, providing the energy and water needed to endure cold winters and dry seasons. Perhaps most importantly, it offered a reliable method of asexual reproduction. The early hybrids were likely less fertile, a common issue when two distant species cross. The ability to simply sprout a new plant from a tuber meant the lineage could survive and stabilize even if sexual reproduction was initially difficult.

Nowadays, the world produces approximately 375 million tonnes of potatoes every year, but potatoes are vulnerable to a variety of pests, diseases, and environmental stresses that can significantly impact yield and quality. This finding could help researhers hybridize new variants of potato that are more resilient or more nutritious.

This new understanding of the potato’s hybrid origins has profound implications. It is a stunning, real-world demonstration that hybridization is not always an evolutionary dead end. Instead, it can be a powerful and creative force, an “evolutionary catalyst” that can merge ancient genetic lineages to produce novel traits and jump-start the colonization of new worlds.

Journal Reference: Cell, Zhang et al. “Ancient hybridization underlies tuberization and radiation of the potato lineage” https://www.cell.com/cell/fulltext/S0092-8674(25)00736-6