Plant Scientists Shed Light on 125-Million-Year-Old Genetic Mystery

Researchers at Cold Spring Harbor Laboratory have discovered that two distantly related model plants, Arabidopsis thaliana and the tomato (Solanum lycopersicum), can use very different regulatory systems to control the same exact gene. Incredibly, the scientists linked this behavior to extreme genetic makeovers that occurred over 125 million years of evolution.

Cold Spring Harbor Laboratory scientist Danielle Ciren and colleagues used genome editing to create over 70 mutant strains of tomato and Arabidopsis thaliana plants.

Each mutation deleted a piece of regulatory DNA around a gene known as CLV3.

The researchers then analyzed the effect each mutation had on plant growth and development.

When the DNA keeping CLV3 in check was mutated too much, fruit growth exploded.

“CLV3 helps plants develop normally,” Dr. Ciren said.

“If it wasn’t turned on at the exact time that it is, then plants would look very different.”

“All the fruits would be ginormous and not ideal. You have to balance growth and yield.”

“If a plant has giant tomatoes but only two, is that as beneficial as a lower yield?”

“There’s no simple solution. You’re always sacrificing something when you’re trying to get something improved.”

For tomatoes, engineering mutations near the beginning but not the end of the CLV3 gene dramatically affected fruit size.

For Arabidopsis thaliana, areas around both parts of the gene needed to be disrupted.

This indicates something happened over the last 125 million years that made the plants evolve differently. Exactly what occurred remains a mystery.

“You can’t go back to the common ancestor because they don’t exist anymore,” Dr. Ciren said.

“So it’s hard to say what was the original state and how have things been mixed up.”

“The most simple explanation is that there’s a regulatory element that’s conserved in some capacity, and it’s been altered in subtle ways. It is a bit unexpected.”

“What is certain is that genetic regulation is not uniform between plant species.”

“Unearthing these genetic differences could help make crop genome engineering more predictable.”

“And that would be a big win not just for science but for farmers and plant breeders across the globe.”

The study is published in the journal PLoS Genetics.

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D. Ciren et al. 2024. Extreme restructuring of cis-regulatory regions controlling a deeply conserved plant stem cell regulator. PLoS Genet 20 (3): e1011174; doi: 10.1371/journal.pgen.1011174