Thale cress (Arabidopsis thaliana) has one of the smallest genomes in the plant kingdom and is a laboratory darling around the world owing to its relatively short code. First sequenced in 2000, the humble weed has only 120 million base pairs in its genome (humans, by contrast have about 2.9 billion), but it still packs plenty of genetic mystique.
A new study has uncovered the rate of the plant’s spontaneous mutations as they happen across generations—a finding that could help illuminate the evolutionary history of plants and selective breeding efforts in the future.
“While the long-term effects of genome mutations are quite well understood, we did not know how often new mutations arise in the first place,” Detlef Weigel, director at the Max Planck Institute in Germany, and coauthor of the study which appeared online Thursday in Science, said in a prepared statement.
The group studied genetic changes of five different plant lines across 30 generations. After carefully comparing each full genome, they found that only about 20 base pairs had mutated in each line.
“The probability that any letter of the genome changes in a single generation is thus about one in 140 million,” Michael Lynch of the Department of Biology at Indiana University in Bloomington and study collaborator, said in a statement.
Locating these small numbers required some high-powered sequencing. “To ferret out where the genome had changed was only possible because of new methods that allowed us to screen the entire genome with high precision and in very short time,” Weigel said. Despite the new sequencing capabilities, the team still rechecked each letter’s position 30 times to make sure suspected mutations were being accurately assessed. As high-throughput sequencing becomes more widely available, researchers should be able to conduct more mutation-rate studies. One ongoing study at Michigan State University that is tracking evolutionary change in E. coli, for example, has analyzed hundreds of mutations across 40,000 generations of the bacteria.
The new findings might prove to be more than a simple gee-whiz figure. This study revealed that mutations were occurring at about the same rate across the full genome—not just in specific parts. This might help explain why efforts to keep some plants at bay with single-gene-targeting herbicides are often only briefly successful. It should also hearten researchers who are searching for ways to improve crops—making them more drought-tolerant or better producers—to know that these mutations are likely already occurring. But to truly expedite strategic breeding for many crops, full genome sequencing, as was recently accomplished for corn, will be crucial to giving horticulturalists a genetic map to different traits.
The group has also been able to use the findings to peer back into Arabidopsis thaliana ‘s genetic past. Previously, researchers had speculated that it and its closest relative, Arabidopsis lyrata, had split about five million years ago. The new genetic data suggests a divergence at least 20 million years ago.
Although these results are from a lowly mustard relative, the data might also have implications for understanding human genetic change.
“If you apply our findings to humans, then each of us will have on the order of 60 new mutations that were not present in our parents,” Weigel said. A study published in Current Biology in August estimated that each individual had something more along the lines of 100 to 200 new mutations. Whatever the exact number, the modest mutation rate can have a big impact when spread across some six billion individuals. And even though natural selection usually appears to work on a relatively slow timescale, with so many mutations, nature can be assaying new combinations all the time. “Everything that is genetically possible is being tested in a very short period,” Lynch said.
Image courtesy of Wikimedia Commons/Suisetz