Ecological and functional genomics of plant adaptation

生物学的主要目标之一是描述理解适应性进化的多层次组织：从基因和突变涉及，他们对基因表达和表型的影响，这些特征如何在现实的生态环境中发挥作用。解决这一挑战的一个领域是从营养生长到开花的生活史和发育过渡，由于气候变化和季节性，这通常是在地理上可变的选择。我们已经在一年生植物拟南芥中研究了这一点，拟南芥除了是植物生物学，基因组学和遗传学的杰出模型系统之外，还与重要作物油菜属于同一家族。拟南芥的遗传和基因组资源正越来越多地用于生态学，进化和适应遗传学的研究。拟南芥入侵了北美，并且似乎显示出快速适应性进化的证据。我们小组最近的工作已经确定了53个新的候选基因，这些基因是在引入的范围内进行开花时间分化的基础。这些基因座以前都没有涉及到拟南芥开花时间的变化，这表明后引入的进化使用了新的遗传机制。我将研究这些候选基因变异的表型、生态、进化和转录组学后果。结合敲除实验，近等基因系的研究，生态学研究和转录组学，我们将允许在这些基因的变异的影响大小，优势和生态后果的全面调查。我的具体目标是：1）使用tDNA敲除系验证这些基因的表型效应，2）创建近等基因系以估计这些基因的天然发生突变的效应大小和优势，（3）进行田间实验以验证它们在生态现实环境中的效应，以及（4）检查它们对基因表达变异的贡献，以及表达变异在开花时间群体内变异中的作用。拟议的工作将支持在生态和进化基因组学的快速扩展领域培训几个HQP，并推进我们对开花时间，植物繁殖和入侵物种遗传学的了解，因为它评估了分子遗传和环境变异在塑造复杂性状中的作用。这些结果可能对理解物种对生物入侵和气候变化的适应性反应非常重要。

One of biology's major goals is to describe understand adaptive evolution on multiple levels of organization: from the genes and mutations involved, to their effects on gene expression and phenotypes, to how those traits function in a realistic ecological context. One area to address this challenge is in the life history and developmental transition from vegetative growth to flowering, which is often under geographically variable selection due to climatic variation and seasonality. We have investigated this in the annual plant, Arabidopsis thaliana, which in addition to being the pre-eminent model system for plant biology, genomics, and genetics, is also in the same family as the important crop, Canola. The genetic and genomic resources for Arabidopsis are being increasingly leveraged for studies in the ecology, evolution, and genetics of adaptation.***Arabidopsis thaliana invaded North America, and appears to show evidence of rapid, adaptive evolution. Recent work in our group has identified 53 novel candidate genes underlying flowering time differentiation in the introduced range. None of these loci have been previously implicated as being involved in flowering time variation in Arabidopsis, suggesting that post-introduction evolution has used novel genetic mechanisms.However, these candidates require genetic and ecological validation. I will investigate the phenotypic, ecological, evolutionary, and transcriptomic consequences of variation at these candidate genes. Combining knockout experiments, studies of near-isogenic lines, ecological studies, and transcriptomics we will allow a comprehensive investigation of the effect sizes, dominance, and ecological consequences of variation at these genes. My specific aims are to: 1) Verify the phenotypic effects of these genes, using tDNA knockout lines, 2) Create near isogenic lines to estimate effect sizes and dominance of naturally occurring mutations that these genes, (3) Perform field experiments to validate their effects in ecologically realistic settings, and (4) Examine their contribution to gene expression variation, and the role of expression variation in within-population variation in flowering time.******The proposed work will support training several HQP in the rapidly expanding areas of ecological and evolutionary genomics, and advance our knowledge of flowering time, plant reproduction, and the genetics of invasive species because it evaluates the roles of molecular genetic and environmental variation in shaping complex traits. The results are likely to be of great importance in understanding adaptive responses of species to biological invasion and climate change.**