Ecological and functional genomics of plant adaptation

生物学的主要目标之一是描述和理解组织在多个层面上的适应性进化：从涉及的基因和突变，到它们对基因表达和表型的影响，再到这些特征在现实生态环境中如何发挥作用。解决这一挑战的一个领域是生命史和从营养生长到开花的发育转变，这通常是由于气候变化和季节性而导致的地理变量选择。我们在一年生植物拟南芥中对此进行了研究，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外，还与重要作物油菜籽属于同一科。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（Arabidopsis thaliana）入侵北美，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个新的候选基因在引种范围内的开花时间分化。这些基因座之前都没有被认为与拟南芥开花时间的变化有关，这表明引入后的进化使用了新的遗传机制。然而，这些候选者需要基因和生态验证。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。结合基因敲除实验、近等基因系研究、生态研究和转录组学，我们将对这些基因变异的效应大小、显性和生态后果进行全面调查。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)创建近等基因系来估计这些基因自然发生突变的效应大小和优势，(3)进行实地实验以验证它们在生态现实环境中的影响，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种群内变异中的作用。******这项工作将支持在快速发展的生态和进化基因组学领域培养一些HQP，并提高我们对开花时间、植物繁殖和入侵物种遗传学的认识，因为它评估了分子遗传和环境变化在形成复杂性状中的作用。研究结果可能对了解物种对生物入侵和气候变化的适应性反应具有重要意义

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.**