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Subject: search.filters.subject.Evolutionary biology

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    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
    (Massey University, 2013) Bloomer, Rebecca
    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.
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    Within and between whorls: Comparative transcriptional profiling of Aquilegia and Arabidopsis
    (Public Library of Science, 2010) Voelckel C; Borevitz J; Kramer E; Hodges S
    BACKGROUND: The genus Aquilegia is an emerging model system in plant evolutionary biology predominantly because of its wide variation in floral traits and associated floral ecology. The anatomy of the Aquilegia flower is also very distinct. There are two whorls of petaloid organs, the outer whorl of sepals and the second whorl of petals that form nectar spurs, as well as a recently evolved fifth whorl of staminodia inserted between stamens and carpels. METHODOLOGY/PRINCIPAL FINDINGS: We designed an oligonucleotide microarray based on EST sequences from a mixed tissue, normalized cDNA library of an A. formosa x A. pubescens F2 population representing 17,246 unigenes. We then used this array to analyze floral gene expression in late pre-anthesis stage floral organs from a natural A. formosa population. In particular, we tested for gene expression patterns specific to each floral whorl and to combinations of whorls that correspond to traditional and modified ABC model groupings. Similar analyses were performed on gene expression data of Arabidopsis thaliana whorls previously obtained using the Ath1 gene chips (data available through The Arabidopsis Information Resource). CONCLUSIONS/SIGNIFICANCE: Our comparative gene expression analyses suggest that 1) petaloid sepals and petals of A. formosa share gene expression patterns more than either have organ-specific patterns, 2) petals of A. formosa and A. thaliana may be independently derived, 3) staminodia express B and C genes similar to stamens but the staminodium genetic program has also converged on aspects of the carpel program and 4) staminodia have unique up-regulation of regulatory genes and genes that have been implicated with defense against microbial infection and herbivory. Our study also highlights the value of comparative gene expression profiling and the Aquilegia microarray in particular for the study of floral evolution and ecology.