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Good mutations: Stalking evolution through genetic mutation in plants

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plant mutation genetic evolutionThale 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

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  1. 1. robert schmidt 12:41 pm 01/1/2010

    My question is; how reliable is a mutation count across multiple generations in determining the mutation rate? Would not only base pair mutations that are advantageous or benign be represented? Would an organism with a smaller genome be less resilient to base pair mutations? Would the probability of a base pair mutation being passed on to future generations be the same in a fern (with a large genome) as it is with Thale cress? It might be interesting to create an experiment in which a number of random mutations are inserted into the genome and then tracked over a number of generations to determine how well they are conserved.

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  2. 2. tharriss 2:19 pm 01/2/2010

    Hard to tell from the article if they compared each generation for changes, or on the 1st and 30th generation. If it was the 1st and 30th only, I agree some mutations might have occurred, then gotten replaced by later mutations so only the later one showed up, but even that seems unlikely to change the final number by very much.

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  3. 3. Michael Hanlon 12:31 am 01/3/2010

    So, which is the driver of Evolution: Natural Selection or Mutation?

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  4. 4. robert schmidt 10:03 am 01/3/2010

    @Michael Hanlon, I don’t think it is either/or. You need both for it to happen. Mutation provides a field of candidates and natural selection choices the winners. I guess ultimately, the reason organisms need to adapt is because resources are scarce, the world is dangerous and the environment changes.

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  5. 5. happy 11:19 am 01/3/2010

    Can we distinguish between true mutations,and parameterized changes to DNA (like the microbial memory below) adaptation at the point of pollinization?

    Microbial memory
    In microbes, genetic memory is present in the form of inversion of specific DNA sequences serving as a switch between alternative patterns of gene expression.[11]

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  6. 6. mo98 8:22 am 01/4/2010

    What is the role of background radioactivity in the case for logging mutations? Have any experiments been made in a hyporadioactive environment?

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  7. 7. johnk 11:25 am 01/6/2010

    happy. With regard to microbes, I go along with Margulis from observations of lichens, and from the area of taxonomic flux which may be likened to ‘evolutionary soup’ ie the lichens, moulds, fungi, visrii, bacteria, mosses, seaweeds, etc. It seems that this area is the ‘engine’ of evolution rather than looking for it mainly in the higher species. Johnk

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