Davis, California, USA
April 23, 2026
- Somatic mutations can be helpful in nature, but they're a headache when propagating clonal plants in the lab.
- Researchers at UC Davis found tissue culture in the lab leads to more somatic mutations; in one type, 35 times more than in-field propagation.
- In this paper, the scientists suggest not leaving clones in tissue culture for extended periods, and DNA review of propagated clones early in the research process.
Researchers studied two forms of clonal propagation commonly used in scientific labs. One of those is clonal embryos, like the one pictured here; embryos are the precursors to seeds. They found clonal embryos can have up to 35 times the number of somatic mutations found in a plant that was propagated using a cutting and grown in the field. (Hannah McCurry/UC Davis)
People are cloning their favorite houseplants at home: In the wake of the pandemic-era return to gardening, do-it-yourself kits for cloning your own roses or pothos are a thing. Tik-Tok influencers promote #propagation using ordinary ingredients such as honey and aloe vera juice.
Plant scientists use clones for their research, but they’re different from the kind grown from cuttings. “There are more advanced forms of cloning, a type of ‘tissue culture,’ where you put clusters of plant cells in Petri dishes and then regenerate whole plants from these,” explained Grey Monroe, an assistant professor in the UC Davis Department of Plant Sciences. Scientists grow these clones by the thousands, along with a potential headache: The resulting little plants can carry loads of mutations, and so must be culled out for research to continue.
They’re called somatic mutations, and Monroe and team have taken a major step toward understanding the genetics behind them. Their breakthrough is expected to save other scientists time and money in the research process. Eventually, it should also give a boost to plant breeders creating improved varieties of food crops for farmers and shoppers.
A paper explaining somatic mutations in detail – and importantly, how to avoid them – was published April 22 in the prestigious journal, Proceedings of the National Academy of Sciences. Ph.D. candidate Matthew Davis, who works in Monroe’s lab, is the lead author, and Patrick J. Brown, a tree breeding expert also with the department, is a co-corresponding author along with Monroe. Another department contributor is Charles Leslie, who has explored walnut breeding for more than three decades.
Their breakthrough harks to five decades of puzzling. In 1983, the famous plant geneticist Barbara McClintock talked about mutations happening in plant tissue culture when she accepted the Nobel Prize for physiology (she was the first woman to win the prize by herself). She had discovered what she called “jumping genes” – bits of DNA that can move from one location in the genome to another. Her research had explained the role of jumping genes in mutations, but she acknowledged the mystery that lay beyond: Exactly how mutations happen at the level of the plant genome and why, McClintock said, was the next frontier.
To make and grow plant clones they can use in their research, scientists commonly use tissue culture. Here, graduate student Steven Lee takes a tiny snippet of plant tissue and places it in a small plastic dish that contains nutrients the snippet needs to grow into a plant; he’s in the lab of Patrick J. Brown, a principal investigator on the project. A downside of this process is, tissue culture can prompt genetic mutations in the new plant. (Matthew Davis/UC Davis)
Helpful in nature, a headache in the lab
A benefit of clonal propagation, in general, is it produces plants that are replicas of the parent – like that rare orchid blooming under your grow-light – but without the pollen-and-pistil sexual reproduction that makes seeds you can plant, and which introduces variables you might not want.
Scientists use the tissue culture kind of clonal propagation for all kinds of lab work, such as developing new varieties of tomatoes and strawberries that can resist disease with less pesticides or thrive with less water.
But in the process, Monroe said, “People often see all this weird stuff…albino plants or new, sometimes undesired, traits.”
Ph.D. candidate Matthew Davis, left, holds a tiny bit of walnut plant tissue that has been clonally propagated through tissue culture. Other leaders in the research team look on: Second from left is Charles Leslie, a long-time walnut breeder; Grey Monroe, an assistant professor and co-lead investigator; and Patrick J. Brown, a nut tree breeder and co-lead investigator; all in the UC Davis Department of Plant Sciences. (Kehan Zhao/UC Davis)
Those weird variations are the somatic mutations, and there can be lots of them. Eliminating goofy plants from the experiment pool slows researchers down and absorbs precious resources.
Somatic mutations are changes in the underlying DNA of cells. They happen naturally in various locations throughout the plant, such as the stem and the branch.
Good news: In nature, somatic mutations can lead to new genetic variations, which makes them useful for long-lived plants like trees and bushes. Natural somatic mutations can also be tasty, even beautiful: Navel oranges, nectarines, seedless grapes, pinot gris grapes and variegated corn are examples.
It’s another matter in the lab. Scientists have suspected for decades that tissue culture itself may lead to the mutations that pop up in their lab plants, Davis said. Now, the team’s research proves it.
The fix: Less time in culture + early detection
Davis, Monroe and others on the team took tissue from walnut plants that had been cloned between 1985 and 2022. As a control, they also took tissue from a walnut tree that had been grown in the field from a cutting.
Researchers use many types of clonal propagation, depending on the plant and what they’re testing. So, the team looked at two forms: clonal embryos, which are the precursors to seeds; and micropropagated shoots, a technique often used in the nursery industry.
The team then used recently developed DNA sequencing technology to analyze all the plants’ genome sequences. They found that plants grown in tissue culture had more genetic mutations than those grown out in the field, and more time spent in tissue culture meant more mutations.
Several clonal embryos growing in tissue culture. The arc in the lower right is an air bubble. (Hannah McCurry/UC Davis)
The big surprise: Clonal embryos showed 35 times more mutations than the tree grown in the field from a cutting. Among those were some large-scale genetic mutations, with entire chromosomes duplicated and jumping genes activated hundreds of times, Davis reported.
“These mutations are not affecting walnuts people are growing, not trees growing in commercial orchards,” Monroe emphasized. “The dramatic mutations we saw were specifically in experimental collections.
“This basically confirms Barbara McClintock’s intuition,” Monroe said.
The scientists then leveraged this discovery to develop new techniques for studying the anatomy and development of plants. By using new methods, scientists can now learn how specific plant structures form from the original cells, Davis explained.
This discovery impacts scientific research broadly, because researchers have focused on making plant breeding faster and more efficient. Taking a different tack, Davis’ results provide a starting point to develop methods that reduce the number of mutations early in the research process, because mutations can build up over time. Some propagation material has been maintained in tissue culture for decades, he noted.
Davis recommended two steps to minimize that problem: reduce the time propagation material is kept in tissue culture, and check the DNA of regenerated material to spot mutations early on.
Monroe compared these steps to a car company that beefs up quality control early in the manufacturing process, avoiding defects that trigger a mass recall of autos costing millions of dollars.
“This technique will help plant scientists do better what they’re already doing,” Monroe said.
Other researchers on the project from the UC Davis Department of Plant Sciences are Chaehee Lee, Li Meinhold, Megan Lorenc and Franklin Lewis.
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