The genetic basis of complex traits in natural environments

 Screens of natural variation in A. thaliana are widely used as a tool for gene discovery, but have largely been confined to controlled conditions. We therefore study the genetic basis of life history traits in natural environments, using field experiments with inbred lines from natural populations (ecotypes) or recombinant inbred lines (RILs) in different seasons and geographic sites (Weinig et al. 2002.2003a,b, Stinchcombe et al. 2004, 2009, Donohue et al. 2005 a,b,c, Korves et al. 2007, Huang et al. 2010, Fournier-Level et al. 2011). We recently completed a set of large-scale experiments, funded by an NSF FIBR grant,  in which we grew a large panel of ecotypes, mutants, RILs, and near-isogenic lines (NILs) in multiple plantings(synchronized with natural germination in local populations)  in 5 sites spanning the native European climate range (Wilczek et al. 2009, Fournier-Level et al. 2011). Our sites in Spain and Finland represent the species’ southern and northern range limits, respectively, whilst the other three sites lie on a longitudinal transect from the oceanic climate of England to the continental climate of eastern Germany. Our data provide a comprehensive study of the genetic basis of flowering time, life history expression, and fitness in multiple natural environments across the native climate range of A. thaliana. We are now engaged in comprehensive analysis of these unique data, which allow us to address a number of important questions about the genetic basis of adaptation to climate in this model species. 

We continue to conduct field experiments, coupled with controlled chamber manipulations of specific environmental factors, to test functional hypotheses about the effects of allelic variation at specific candidate loci on life history expression in different photothermal environments, and to measure natural selection on that variation.  Because A. thaliana is an inbreeding species, we can combine our field data with genotypes and phenotypic data for the same inbred lines from laboratory studies, as well as geographic and climatic data from the site of origin for ecotypes.  These combined data allow us to address a number of specific questions, such as:How is allelic variation at candidate flowering time loci expressed in different natural conditions, and what are the underlying mechanisms?  How does the expression of genetic variation depend upon genetic background? What is the genome-wide architecture of life history variation in the wild?