Genome evolution and the genetics of abiotic stress tolerance in Arabidopsis thaliana and Arabidopsis lyrata

There has been remarkably little study of nucleotide substitution rate variation among plant nuclear genes or intergenic data. Here, I investigated evolutionary rates in intergenic regions in the model plant genus Arabidopsis. We generated a set of 66 intergenic sequences in Arabidopsis lyrata, a close relative of Arabidopsis thaliana. We compared substitution rates among the 66 intergenic loci, and compared intergenic rates to a set of 64 orthologous coding sequences. Our chief observations were that the average rate of nucleotide substitution is slower in intergenic regions than at synonymous sites, that rate variation in both intergenic and coding regions correlate with GC content. We provide evidence to suggest that transcription-related mutation contributes to rate differences between intergenic and synonymous sites.;Connecting observed phenotypic variation with underlying genetic variants is a primary goal of the study of genetics and evolutionary biology. Here I present a multi-pathway approach to investigating the genetics of abiotic stress tolerance in plants. The model plant species, Arabidopsis thaliana, has long been thought to be a poor model for abiotic stress tolerance studies, as it is considered to be relatively intolerant of most abiotic stresses. We show, perhaps unsurprisingly, A. thaliana, does in fact contain a great deal of naturally occurring variation in abiotic stress tolerance. We then use multiple approaches, including QTL mapping, association mapping, gene expression analysis and population genetics with demographic modeling to generate a picture of the genetic variation underlying the observed phenotypic variation. This work represents the most comprehensive picture of salinity tolerance variation in Arabidopsis to date. We take advantage of this extensive natural variation to map QTL and generate a short list of candidate genes that may explain this phenotypic variation.;Using population genetics and demographic modeling in A. lyrata we further investigate a subset of these candidate loci and identifying candidate genes for abiotic stress tolerance that show evidence of selection in natural populations. This work represents one of the first examples explicitly considering demographic history in tests for local adaptation in plants.