The molecular genetic basis of natural variation in trichome density in Arabidopsis thaliana : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Biology, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand

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Understanding the genetic basis of natural variation in phenotypes is a central, yet often elusive, goal in evolutionary biology. Trichome density, an herbivory defence trait in Arabidopsis thaliana, is a powerful model for investigating natural phenotypic variation, combining a genetically well characterised developmental pathway with a quantitatively and qualitatively variable phenotype of selective importance. Here, Quantitative Trait Locus (QTL) mapping and candidate gene analyses were undertaken to explore the genetic basis of variation in trichome density in natural accessions of A. thaliana, under an overarching hypothesis that allelic variation in the epidermal development pathway plays a significant role. QTL mapping for constitutive and wounding-induced trichome density and for plasticity of density was undertaken in two newly developed mapping populations, broadening the range of allelic variation sampled in trichome density studies. This study is the first to address the genetic architecture of induced density and plasticity, finding a genetic basis to plasticity and a surprising negative response to wounding among some members of the populations used. Some QTL mapped are unique, while others appear common to both constitutive and induced density phenotypes or to overlap across mapping populations, suggesting particular loci may be key to generating variation for trichome phenotypes. Epistatic interactions and candidate genes for QTL within, up- and downstream of the epidermal development pathway are identified. Candidate gene analyses focussed on genes within the epidermal development pathway: the trichome-specific MYB GL1 and the pleiotropic WD-repeat TTG1. In both GL1 and TTG1, a pattern of high frequency polymorphism correlates with variation in trichome density. In GL1, variation has both qualitative and quantitative effects, with both protein-coding and regulatory changes proposed as underlying bases. The TTG1 coding region is subject to strong purifying selection, and the observed quantitative effect on density appears to be based on variation in regulatory sequence. Both QTL mapping and candidate gene approaches support the hypothesis of a key role for the epidermal development pathway in generating variation in trichome density in A. thaliana, and more generally a role for variation in regulatory genes contributing to natural phenotypic variation.
Arabidopsis thaliana, Molecular genetics, Trichomes, Brassicaceae, Phenotypic variation, Allelic variation, Evolutionary biology