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Association Studies Provide Clues to Nature of Climate Adaptation in Arabidopsis

NEW YORK (GenomeWeb News) – A pair of genome-wide association studies online today in Science highlight genetic strategies that the model plant Arabidopsis thaliana uses to adapt to changing environmental conditions such as climate change.

Investigators at Brown University and elsewhere did a GWAS of Arabidopsis plants grown in Germany, the UK, Finland, and Spain, sites with a range of climates within the plant's normal range, looking for variants that corresponded to plant survival, fruiting body production (a measure of reproductive success), and local climate adaptation.

Results from their study suggest that genes contributing to fitness and reproduction varied from one region to the next, hinting that the plant has some adaptation strategies that are location-specific.

"We found that the genetic basis of survival and reproduction is almost entirely different in different regions," corresponding author Johanna Schmitt, director of Brown University's Environmental Change Initiative, said in a statement, "which suggests that evolutionary adaptation to one climate may not always result in a tradeoff of poor performance in another climate."

"Thus, the Arabidopsis genome may contain evolutionary flexibility to respond to climate change," she added.

The team genotyped plants grown in field sites in Halle in Germany, Norwich in the UK, Oulu in Finland, and Valencia in Spain at more than 213,000 SNPs in the genome, looking for variants that affect survival and reproductive fitness at each of the sites. They also did analyses on SNPs coinciding with survival and fitness at each location to see how they related to 11 climate-related variables.

In general, the researchers reported, the loci linked to survival and fitness varied depending on the site at which plants were sampled. For instance, just a dozen of the top eight hundred or so fitness-associated SNPs detected were linked to plant fitness at more than one of the sampling sites.

"This result suggests that local adaptation by different genetic mechanisms may facilitate flexible evolutionary response to changing environments across the species range," researchers wrote.

Based on their findings so far, authors of that study argued that "environment-specific fitness may depend more on standing variation than on recent positive selection at specific loci."

Even so, findings from another Science study exploring the genetics of environmental and climate adaptations in Arabidopsis challenge the view that the plant has the genetic capability to keep pace with very rapid changes to their climate or environment.

Researchers from the US and France genotyped 948 Arabidopsis accessions from across the plant's range at around 215,000 SNPs each, looking for SNPs that corresponded to 13 climate variables such seasonal temperature and rainfall and to 107 ecologically-relevant phenotypes.

Among the SNPs associated with climate patterns in general, the researchers found an over-representation of non-synonymous SNPs, especially for variants associated with the amount of precipitation during the wettest and driest months, humidity, growing season length, and levels of so-called photosynthetically active radiation.

Genes involved in processes such as photosynthesis and energy metabolism were among those frequently affected by these non-synonymous changes.

They also found clues that some SNPs contributing to climate response could also be used to help predict plant fitness. For example, using a set of climate-associated genetic variants, the team demonstrated that they could accurately predict fitness for 147 Arabidopsis accessions from a variety of locations that were planted in the same garden in France.

Again, the SNPs involved with adaptation varied by location, with some influencing environmental responses over a broad distribution of sites and others acting more locally.

When they examined the locally distributed SNPs more closely, the team found evidence that at least some of these adaptations were influenced by selective sweeps involving new mutations rather than genetic variants already present in the genome.

While that adaptation strategy is effective, it also takes time, the study authors explained, suggesting it may not be feasible during rapid environmental shifts.

"The contribution of selective sweeps suggests that there will be limits on the rate at which this plant can adapt to climate change," senior author on the study Joy Bergelson, University of Chicago ecology and evolution chair, said in a statement.

"Changing climates may require rapid adaptation," Outi Savolainen explained in a perspectives paper appearing in the same issue of Science. "Adaptation based on selection on new mutations (species-wide or regionally limited selective sweeps) can be slowed down by the lack of suitable mutations, whereas selection on existing low- or intermediate frequency variants can be faster."

Savolainen, a biologist from the University of Oulu in Finland called the two new studies "a major advance toward finding the genomic sites related to climatic adaptation in A. thaliana."

Still, while he said such research may yield insights into predicting plant responses to changing climate conditions, Savolainen also emphasized the need for additional studies to discern the relative importance of new and existing mutations in Arabidopsis adaptation.

He noted that this research is expected to advance as more and more complete Arabidopsis genomes from a range of environments become available.

"SNP-based studies cannot be used to examine all polymorphisms. The effects of the polymorphisms related to climate are only detected if they are correlated with the SNPs that were genotyped," Savolainen wrote. "As the Arabidopsis re-sequencing project advances, these problems will be avoided. Improving genomic resources will also allow genome-wide studies of species with very strong signals of local adaptation."

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