Findings could lead to advances in plant breeding, human genetics.
A simple roadside weed may hold the key to understanding and predicting DNA mutation, according to new research from the University of California, Davis, and the Max Planck Institute for Developmental Biology in Germany.
The findings, published on January 12 in the journal Nature, radically change our understanding of evolution and could one day help researchers breed better crops or even help humans fight cancer.
Mutations occur when DNA is damaged and left unrepaired, creating a new variation. The scientists wanted to know if mutation was purely random or something deeper. What they found was unexpected.
“We always thought of mutation as basically random across the genome,” said Grey Monroe, an assistant professor in the UC Davis Department of Plant Sciences who is lead author on the paper. “It turns out that mutation is very non-random and it’s non-random in a way that benefits the plant. It’s a totally new way of thinking about mutation.”
Researchers spent three years sequencing the DNA of hundreds of Arabidopsis thaliana, or thale cress, a small, flowering weed considered the “lab rat among plants” because of its relatively small genome comprising around 120 million base pairs. Humans, by comparison, have roughly 3 billion base pairs.
“It’s a model organism for genetics,” Monroe said.
Lab-grown plants yield many variations
Work began at Max Planck Institute where researchers grew specimens in a protected lab environment, which allowed plants with defects that may not have survived in nature be able to survive in a controlled space.
Sequencing of those hundreds of Arabidopsis thaliana plants revealed more than 1 million mutations. Within those mutations a nonrandom pattern was revealed, counter to what was expected.
“At first glance, what we found seemed to contradict established theory that initial mutations are entirely random and that only natural selection determines which mutations are observed in organisms,” said Detlef Weigel, scientific director at Max Planck Institute and senior author on the study.
Instead of randomness they found patches of the genome with low mutation rates. In those patches, they were surprised to discover an over-representation of essential genes, such as those involved in cell growth and gene expression.
“These are the really important regions of the genome,” Monroe said. “The areas that are the most biologically important are the ones being protected from mutation.”
The areas are also sensitive to the harmful effects of new mutations. “DNA damage repair seems therefore to be particularly effective in these regions,” Weigel added.
Plant evolved to protect itself
The scientists found that the way DNA was wrapped around different types of proteins was a good predictor of whether a gene would mutate or not. “It means we can predict which genes are more likely to mutate than others and it gives us a good idea of what’s going on,” Weigel said.
The findings add a surprising twist to Charles Darwin’s theory of evolution by natural selection because it reveals that the plant has evolved to protect its genes from mutation to ensure survival.
“The plant has evolved a way to protect its most important places from mutation,” Weigel said. “This is exciting because we could even use these discoveries to think about how to protect human genes from mutation.”
Knowing why some regions of the genome mutate more than others could help breeders who rely on genetic variation to develop better crops. Scientists could also use the information to better predict or develop new treatments for diseases like cancer that are caused by mutation.
“Our discoveries yield a more complete account of the forces driving patterns of natural variation; they should inspire new avenues of theoretical and practical research on the role of mutation in evolution,” the paper concludes.
For more on this discovery, see DNA Mutations Do Not Occur Randomly.
Reference: “Mutation bias reflects natural selection in Arabidopsis thaliana” by J. Grey Monroe, Thanvi Srikant, Pablo Carbonell-Bejerano, Claude Becker, Mariele Lensink, Moises Exposito-Alonso, Marie Klein, Julia Hildebrandt, Manuela Neumann, Daniel Kliebenstein, Mao-Lun Weng, Eric Imbert, Jon Ågren, Matthew T. Rutter, Charles B. Fenster and Detlef Weigel, 12 January 2022, Nature.
Co-authors from UC Davis include Daniel Kliebenstein, Mariele Lensink, Marie Klein, from the Department of Plant Sciences. Researchers from the Carnegie Institution for Science, Stanford University, Westfield State University, University of Montpellier, Uppsala University, College of Charleston, and South Dakota State University contributed to the research.
Funding came from the Max Planck Society, the National Science Foundation and the German Research Foundation.
That variation neither need to be or are always equiprobable random or even random at all has long been a theme in hypotheses such as evolution of mutation rates, which this may be seen as a subclass of.
The broader claim, deriving from that evolution as a natural process is causal and selection cannot “time travel” information to the earlier variation event it acts on, is that “variation is indifferent to selection”. [In physics terms you may say that variation is orthogonal to selection.]
This seems to be an exception to the norm, rather than the norm, which the title suggests.
It is very intriguing though.
Clickbait title. The Nature article just confirms some exceptions. Shame!
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There isn’t enough INFINITY in your insane rant.
In lake county Florida the little flowers are actually called bushy astors and many,many bees get nectar from these little flowers low to the ground used as pollinators.
This is so obvious. They are only looking at the dna of seeds that successfully germinated. Far more likely any mutation in those core genes failed to produce viable offspring.
It’s one thing to talk about mutation in DNA but has anyone ever explored where DNA came from? How did it begin? We’re only discovering it & its amazing properties. I give credit to our mighty, loving God who created the universe & all the marvelous life forms on the earth in 6 24-hour days (He rested on the 7th as an example for us). Granted Adam & Eve’s sin in Eden began the downward spiral of decay & mutation that we experience today but, as noted in the article, God built in many healing & protective properties in our DNA. Praise the Lord for His mighty acts!
The origin of DNA is pretty clear. Most complex bio molecules are self-assembled from less complex compounds, which fit together like Lego bricks, due to perfectly clear chemical reactions. DNA is made up of commonly available ribose sugars and nucleic acid, which have also been observed on comets. Just add water – no god required.
… you tend to erase my comments… this is just so wrong…
“The origin of DNA is pretty clear.” This is pretty false in a naturalistic perspective (it’s just darwinian/evolutionary propaganda, as misleading as many others in evolutionary gender).
Separating the parts of something is not the same as knowing it’s origin and how exactly it was created. DNA is about information. Where did it (the information) come from?
Btw, if that is the case (if the mistery of DNA origin is solved in a naturalistic view,
“Why don’t you educate origin of life researchers on how it’s done?” / “Go ahead! Make a cell!” – link below, to confront unsubstantiated evolunary/naturalistic propaganda with reality):
There is a paper by Barbara Wright (2004) on stress-directed mutagenesis (SDM), the opposite concept of random mutations. In addition, the hypothesis about the existence of ad-hoc mutations has already been summarized in my book “Evolución de las especies por mutaciones ad-hoc” (2022 in press). Finally, if any scientific institution is interested in this project, I have an invention patent drawn up in which it is shown that a genetic algorithm based on ad-hoc mutations is capable of abstractly mimicking many cases of evolution, and even proving that, by switching to random mode said algorithm, it collapses and loses all simulation capacity. The document is called:
“System to construct evolutionary models of living organisms” (eduardoraadantonAgmaildotcom