Genetic mechanisms and evolutionary significance of natural variation in Arabidopsis

Abstract

Genomic studies of natural variation in model organisms provide a bridge between molecular analyses of gene function and evolutionary investigations of adaptation and natural selection. In the model plant species Arabidopsis thaliana, recent studies of natural variation have led to the identification of genes underlying ecologically important complex traits, and provided new insights about the processes of genome evolution, geographic population structure, and the selective mechanisms shaping complex trait variation in natural populations. These advances illustrate the potential for a new synthesis to elucidate mechanisms for the adaptive evolution of complex traits from nucleotide sequences to real-world environments.

Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits

“…Like population genomics approaches, both LD and QTL mapping require the survey of a large number of genome-wide molecular markers (Figure 2). Specifically, LD mapping relies on surveys of genetic polymorphism data from a collection of samples (inbred lines, accessions, individuals and populations) to test for statistical associations between these genetic markers and particular phenotypes, again based on the premise that the marker(s) is in LD with the causal locus, or less likely, is in fact the causal mutation itself (Box 1; see Mackay, 2001;Clark, 2003;Mitchell-Olds and Schmitt, 2006). By contrast, in a QTL mapping approach, statistical analyses of genome-wide molecular markers and phenotypes measured in progeny of controlled crosses are used to identify chromosomal regions contributing to phenotypic differentiation (reviewed in Mackay, 2001;Erickson et al, 2004).…”

“…Do these genes show evidence of non-neutral evolution at the sequence level (Stahl et al, 1999;Tian et al, 2002;Mauricio et al, 2003)? What ecological and evolutionary forces lead to the maintenance of variation at these loci (Mitchell-Olds and Schmitt, 2006)? Do ecologically similar environments favor the same genes (Calboli et al, 2003;Colosimo et al, 2004Colosimo et al, , 2005Protas et al, 2006), or is it possible to achieve a similar phenotype with different genetic mechanisms Hoekstra et al, 2006)?…”

Intraspecific variation in expression of candidate genes for osmoregulation, heme biosynthesis and stress resistance suggests local adaptation in European flounder (Platichthys flesus)

“…Acclimation was set to 50 days to assure full acclimation (Deane and Woo, 2004). By applying the reciprocal transplantation experimental design the physical environment can be standardized and allows for studying gene expression variation depending on genetic origin associated with local adaptations (Mitchell-Olds and Schmitt, 2006). Finally, to evaluate whether flounders were in fact stressed in response to salinity changes following reciprocal transfer, we conducted a short-term experiment, where flounders were sampled following 1 day at nonnatural reciprocal salinities to study whether flounders were in fact physiologically stressed following transplantation.…”

Chlorophyll fluorescence emission as a reporter on cold tolerance inArabidopsis thalianaaccessions

“…The contrast in acclimation capacity in A. thaliana accessions has already been extensively exploited in efforts to identify the molecular basis of this trait. [9][10][11] The resulting enhanced capacity of acclimated plants to survive subzero temperatures may be due to freezing tolerance and/or avoidance mechanisms. While freezing tolerant plants do not prevent formation of ice crystals in the extracellular space but, rather, limit the damage to cellular structures by the ice crystals, it has been reported that Arabidopsis survives low temperatures by freezing avoidance, i.e.…”