Plant scientists use clones for their research, but they’re different from the kind people grow from cuttings. Scientists grow these clones in Petri dishes by the thousands, along with a potential headache: The resulting little plants can carry loads of mutations that must be culled out for research to continue.

They’re called somatic mutations and a team at UC Davis has 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 Proceedings of the National Academy of Sciences. Ph.D. candidate Matthew Davis is the lead author. Grey Monroe, an assistant professor and Patrick J. Brown, a tree breeding expert – both in the UC Davis Department of Plant Sciences – are co-corresponding authors.

Their breakthrough follows 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. McClintock 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 how mutations happen at the level of the plant genome and why, McClintock said, was the next frontier.

More time in tissue culture, more mutations

A benefit of clonal propagation, in general, is it produces plants that are replicas of the parent.

But in the process of culturing clonal tissue, Monroe said, "People often see all this weird stuff…albino plants or new, sometimes undesired, traits."

Those are the somatic mutations – changes in the underlying DNA of cells. They happen naturally in various locations throughout the plant, such as the stem and the branch. 

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. 

The team then looked at two common forms of clonal tissue used in research: clonal embryos (embryos are the precursors to seed); and micropropagated shoots, a technique often used in the nursery industry.

Next, they used recently developed DNA sequencing technology to analyze all the plants’ genomes. 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.

The big surprise: Clonal embryos showed 35 times more mutations than the control 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 … 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.

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.

"This technique will help plant scientists do better what they’re already doing," Monroe said.