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Climate-Shaped Arabidopsis Genome

Two genome-wide studies, backed up by field experiments, identify SNPs that correlate with Arabidopsis fitness in various climates.

By | October 6, 2011

Arabidopsis thalianaFLICKR, SEDEER

Taking different approaches to ask the same question—how does a plant genetically adapt to climate—two research groups found that Arabidopsis thaliana, a model organism in plant studies, has numerous climate-related single nucleotide polymorphisms (SNPs) that help it thrive in the changing environment.

“There are a lot of people who thought there wouldn't be any signature of climate in Arabidopsis—that it is more adapted to local disturbance or local selective pressures,” said Johanna Schmitt, a study author on one of the papers and a professor at Brown University. “But these papers tell us that we can find evidence at the genetic level that climate has played a role in shaping plant fitness.”

The papers, published today (October 6) in Science, agree that the plant has adapted to changing conditions, but there's no consensus yet on the primary mechanism. Schmitt's study found that standing variation—the polymorphisms already in the population—played a major role, while the other paper found greater evidence of selective sweeps by newly introduced mutations.

The latter study, led by Joy Bergelson of the University of Chicago, started with genome-wide scans of 948 Arabidopsis lines from different areas around Europe. The researchers then looked for those SNPs that were over-represented in the various climates, and used them to predict which plants would fare best in a particular climate. In the field, the group tested those predictions by examining various strains of Arabidopsis that had been planted in France, and found that, indeed, those plants that had the largest number of SNPs favorable to that climate had the best success in the field.

Laura J. Martin, a Brown graduate now a Ph.D candidate at Cornell, takes a census of surviving Arabidopsis plants at the field site in Norwich, England.
Laura J. Martin, a Brown graduate now a Ph.D candidate at Cornell, takes a census of surviving Arabidopsis plants at the field site in Norwich, England.
COURTESY JUDITH ROE

“The key observation we made is that selective sweeps”—in which a favorable mutation quickly spreads throughout a population—“seem to have played an important role in adaptation to climate, and may be necessary in the future,” Bergelson told The Scientist. If plants need to rely on new mutations to respond to a changing climate, that “puts limits on how rapidly plants can adapt,” she added.

Bergelson's approach “demonstrates the strength of broad scale associations for identifying SNPs that might be important for adaptation to climate,” said Sally Aitken at the University of British Columbia.

Schmitt's group used a different strategy by starting in the field. The researchers examined the fitness of different lines of plants that had been taken from sites around Europe, then each planted in gardens in England, Finland, Germany, and Spain, chosen to represent a range of climates. The group then measured the survival and fruit production of the different lines in these various climates, and conducted genome-wide scans to hunt for SNPs correlated with that success.

Surprisingly to Schmitt, “the genetic basis of fitness is almost entirely different in different climates.” She and her colleagues found that SNPs that helped a plant in one climate were not necessarily deleterious in another climate. “So it's not a particular gene, but entirely different genes that seem to be responsible for high performance at different sites,” she said.

Aitkin, who was not involved in the research, is doing a genome-wide study of SNPs and climate in trees. “This kind of work helps us to generate knowledge on candidate genes that are involved in responses to temperature and moisture” in particular climates, which is valuable for understanding plants' response to current and future climate change, she said.

“Clearly they're showing that Arabidopsis can adapt to climate,” Ivan Baxter, a researcher at the USDA's Agricultural Research Service, said of the two studies. “But the capacity [to adapt] is going to be very species-specific.”

Baxter, who also did not participate in the research, told The Scientist that it will be interesting to see what adaptations are generalizable to other types of plants, and he expects that this is just the beginning of genome-wide studies on plants' adaptations to their environment.

A. Fournier-Level et al., “A map of local adaptation in Arabidopsis thaliana,” Science, 334:86-9, 2011.

A.M. Hancock et al., “Adaptation to climate across the Arabidopsis thaliana genome,” Science, 334:83-6, 2011.

(Homepage carousel image: Wikimedia Commons, Sui-setz)

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