UC Davis

Genetic variation provides the material for evolution, but the variation available to evolutionary processes is itself shaped by biological mechanisms. Mutations determine how genetic differences enter populations, while regulatory systems determine how those differences are expressed. In this dissertation, I use Arabidopsis thaliana to examine these two stages: the generation of genetic variation through mutation and the translation of genetic differences into gene expression plasticity.I investigate the genetic architecture of transcriptomic plasticity in response to salicylic acid using a recombinant inbred population. Although the parental accessions exhibited similar transcriptional responses, their recombinant progeny showed extensive transgressive segregation, with most expression quantitative trait loci acting in trans. These results reveal substantial regulatory variation hidden beneath similar parental phenotypes and suggest that trans-regulatory contributions to plasticity may be underestimated in natural populations. I then investigate how mutation-rate heterogeneity contributes to population genetic variation using forward evolutionary simulations and approximate Bayesian computation. Across genomic regions and modeling conditions, inference consistently supported lower mutation rates in genic sequence. Together, these studies span two fundamental stages in the production of evolutionary variation: how genetic differences arise and how those differences are expressed. They demonstrate that observed patterns of genomic and phenotypic variation depend on the underlying molecular and genetic architectures that generate, regulate, and structure the variation on which evolution acts.