The genetic architecture of quantitative traits in locally adapted plant ecotypes

Locally adapted ecotypes are a common phenomenon generating plant diversity within species, yet we know surprisingly little about the genetic mechanisms that lead to locally adapted traits. The genetic architecture underlying traits can indicate evolutionary history and predict response to selection, with applications in evolutionary ecology, conservation, and crop development. This research broadly investigates the genetic architecture of quantitative traits in paired ecotypes from different plant species. I used multivariate comparative methods and quantitative trait loci (QTL) mapping to quantify genetic correlations and population divergence, between ecologically relevant traits, both at the phenotypic and genotypic level. I tested for adaptive floral trait evolution in a perennial wildflower by comparing differentiation at neutral loci to differentiation in a suite of quantitative floral traits in an Ipomopsis aggregata hybrid zone. I used multivariate comparisons to incorporate the genetic covariance architecture underlying floral display and reward traits, and found a strong signal for divergent selection. Non-neutral divergence for multivariate quantitative traits suggests that selection by pollinators is maintaining a correlation between floral display and reward. In Panicum virgatum, a native perennial grass, I used a genetic mapping population, segregating ecotypic variation, to construct a linkage map, and map QTL for nine ecological traits. Most QTL had intermediate to small effects and clustered on a limited number of linkage groups. I also found over half of the functional allelic effects displayed patterns associated with fixed differences between ecotypes. These results suggest there is considerable standing genetic variation within local populations, as well as between ecotypes for ecologically relevant traits. Lastly, I explored the genetics of plant tissue quality in Panicum hallii, a model lignocellulosic grass system. Cell wall components compose the bulk of lignocellulosic biomass and contribute to the recalcitrance of plant tissue. I characterized the divergence of four major cell wall components between ecotypes, identified 14 QTL, and found half of the QTL localized to a single linkage group. Exploring the genetic architecture of tissue traits in a tractable system will lead to a better understanding of cell wall structure and function as well as provide genomic resources for bioenergy crop improvement.