Monthly Archives: November 2011

Genomics in the Brassicales – Arabidopsis as a Model for Climatic Adaptation

I generally don’t work with Arabidopsis, but have used it as a model plant in previous experiments.  I’m currently contributing to a genome sequencing project for a member of the Brassicales, so I’ve been getting up to speed on some of the recent research.  Just in the last year, numerous papers have touched on genome evolution across this important plant family, and I’ll be highlighting a few of these papers in a series of posts on genomics of the Brassicales.

Two recent papers in the journal Science have highlighted the use of Arabidopsis thaliana in understanding genomic responses to climatic and local adaptation.  The paper by Fournier-Level et al “A Map of Local Adaptation in Arabidopsis thaliana” and the paper by Hancock et al “Adaptation to Climate Across the Arabidopsis thaliana Genome” are novel because they correlate well-characterized genome wide analysis of markers, such as SNPs, to estimates of fitness.  Both papers were summarized by Outi Savolainen in a commentary titled “The Genomic Basis of Local Climatic Adaptation” in the same issue.

Fournier-Level et al. estimated survival and reproductive fitness from 150 different reciprocal Arabidopsis transplants from four research sites across Europe.  By measuring SNPs in plants from each environment, the researchers found different polymorphisms associated with fitness for differing environments.  This finding suggests that environmentally induced genomic variation is plastic and that natural selection has a strong effect across these genomes.

In a separate but complimentary study, Hancock et al. observed more than 200,000 SNPs for 1000 Arabidopsis accessions isolated from a wide selection of unique geographic locations.  Using two approaches, the researchers found that, one, there was a correlation between polymorphisms within general protein-coding regions and climate-associated SNPs, and, two, that the climate-associated SNPs could explain some level of fitness in field experiments.

These papers addressed SNP data, but an interesting angle would also be to determine if genomic rearrangements are found in locally adapted populations of Arabidopsis (for a recent study of genomic rearrangements see here).  These types of studies are vital to understanding the genomic foundations underpinning survival in the environment.  With greater and more refined genome-wide resources, especially tied to environmental phenotypic plasticity, researchers are poised to make great contributions to our understanding of the interactions of the genome and environment.