Unveiling the evolution of tomatoes

From wild, blueberry-like fruit to the large domesticated tomatoes that people enjoy today, the evolution of one of the world’s most popular crops has been somewhat of an enigma until now.

Piecing together gaps in its history, a new genetic study suggests the modern tomato is more likely related to weed-like fruit in Mexico than to semi-domesticated versions in South America as commonly thought.

This discovery challenges the simplified notion that tomato domestication comprised two key transitions: from the wild Solanum pimpinellifolium L. to the cherry-sized S. lycopersicum L. var. cerasiforme (SLC) and then to the fully domesticated S. lycopersicum L. var. lycopersicum.

“We found that the SLC, this ‘intermediate’ group, has had a much more varied evolutionary history than simply being a stepping stone between wild and modern cultivated tomatoes,” explains senior author Ana Caicedo from the University of Massachusetts Amherst, US.

Shedding light on the “historically contentious” debate about SLC, the researchers’ analyses indicate this plant originated first as a wild species more than 70,000 years ago, which predates any domestication by humans.

This finding was unexpected, says Caicedo, “and shows how complex the evolutionary trajectory of crop domestication can be”.

Typically, plant domestication involves cultivating wild specimens with desirable traits then later improving those qualities through selective breeding – but the process is protracted and can encounter several environmental disruptions including weather changes, water availability or pathogens.

The authors argue, therefore, that limited focus on the original wild species and final domesticated product could miss some favourable genes and traits along the plant’s evolutionary trajectory and therefore opportunities to improve current crops.

This could include strains that are disease or drought resistant, says first author Hamid Razifard, or have higher antioxidant and sugar content to enhance the fruit’s health benefits and taste, such as the researchers discovered in intermediate populations.

Their analyses derived from 394 published tomato genome sequences and whole genome sequences they generated for 166 samples, with special attention to the intermediate variants largely overlooked by research until now.

They believe the SLC, originating as a wild species in Ecuador, was later cultivated by indigenous people to create medium-sized fruits, says Razifard. Two subgroups may have travelled north to Central America, possibly unintentionally as weedy companions.

“Remarkably, these northward extensions of SLC seem to have lost some of the domestication-related phenotypes present in South America”, Razifard says. People still use them as food but don’t intentionally cultivate them.

“It’s still a mystery how tomatoes have moved northward,” he adds. “All we have is genetic evidence and no archaeological evidence because tomato seeds don’t preserve well in the archaeological records.”

But by showing the evolutionary complexities of the tomato’s domestication, the authors “advocate for a broader sampling and higher care in defining the populations considered intermediate in the domestication history of any crop”.

The study was published in the journal Molecular Biology and Evolution.