The Potato’s Mysterious Family Tree Revealed—And It Includes Tomatoes
Nine million years ago, in the shadow of the rising Andes Mountains, a key ancestor of the beloved modern-day potato was born. And now new research shows this pivotal event—and the mashed, baked, and fried bounty it routinely delivers today—only happened with crucial help from another treasured kitchen staple: the tomato.
According to a study published on Thursday in Cell, the prehistoric potato precursor was a hybrid of nearby-growing plants in the lineages of the tomato and Etuberosum, a section of species in the genus Solanum. The latter visually resembles the modern-day cultivated potato plant, which is part of the lineage of the Solanum section Petota. But it lacks the ability to produce the distinctive tubers that store all that useful nutrition in a convenient, fist-sized underground package.
“We have always thought that these three lineages were closely related,” says study co-author Sandra Knapp, a research botanist at the Natural History Museum in London. “But what the relationships between those three lineages were [was] not clear; different genes told us different stories. Our group came together to look into the why!”
The potato is one of the world’s most widely used staple crops (along with corn, wheat, and rice). But until now, its genetic backstory had been elusive to scientists. Though potatoes resemble Etuberosum and were known to share some genes with tomatoes, scientists hadn’t managed to pin down the evolutionary story that somehow tied these plants together.
Knapp and her international team of researchers began by analyzing more than 100 genomes from modern-day potatoes and tomatoes, as well as the largest collection of Etuberosum genomes ever analyzed. The scientists found that each potato genome carried a balanced mosaic of genes from the tomato and Etuberosum lineages. Team members pieced together all the possible phylogenetic trees that could have related the three lineages—and they found strong evidence that the potato was likely not a sister of either the tomato or Etuberosum. The team could then conclude that the potato was a result of a hybridization between the two.
But another mystery remained: neither the tomato nor Etuberosum have tubers, thick parts of the stem that burrow underground and store nutrients for plants such as potatoes, yams, and taros. So how did tubers develop in potato plants?
The researchers found that each ancestral parent contained one key gene that—when combined—allowed tubers to grow. Tomatoes contributed the SP6A gene, which acts like a master switch to begin tuber formation. And from the Etuberosum side, another gene called IT1 controls the growth of stems that become tubers.
“We are aware that hybridization generates new traits and new species,” says the study’s senior researcher Sanwen Huang, an agriculturist at the Chinese Academy of Agricultural Sciences. “However, this study is the first to show that hybridization generated a new type of organ, the tuber, which later became [a key part of] one of the staple foods of humanity.”
Tomatoes and Etuberosum likely hybridized during a period of rapid uplift in the Andes range. The resulting tubers enabled the potato’s ancestors to reproduce asexually and thus survive in new, higher-elevation habitats. Today tubers allow potatoes to grow resiliently in a range of environments and climates, supporting our ever-growing assortment of potato-based foods.
“Now we have a story to tell about potato origins,” says Walter De Jong, a plant geneticist at Cornell University, who was not involved in the study, “another addition to our growing understanding of what makes a potato a potato.”
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