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，到它们对表型和多效性程度的影响，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。我们随后进行了基因敲除研究，发现了一些有希望进行进一步遗传研究的基因。我们现在正在创建crispr介导的转基因品系，我们将自然发生的开花晚的变体替换为开花早的背景，反之亦然。这些转基因品系需要进行生态验证。我们将研究它们对局灶表型、相关表型和适合度的影响。总的来说，这将是对这些基因变异的效应大小、等位基因频率和生态后果的全面调查。我的具体目标是：1)在一系列室内实验中，在常用的生长条件下验证这些转基因品系的表型效应；2)进行实地实验，在生态现实环境中验证它们的效应，它们是如何在自然选择下的，并将它们与自然发生的变异和选择水平进行定量比较；3)利用群体重测序获得影响开花时间的自然变异的等位基因频率的无偏估计值；4)用数学方法结合这些估计值来评估它们对遗传变异、协方差的贡献，以及等位基因频率的变化如何影响未来的进化反应。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 phenotypes and degree of pleiotropy, 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. We followed this up with knockout studies, which revealed a handful of promising genes for further genetic investigation. We are now creating CRISPR-mediated transgenic lines, in which we are substituting naturally occurring late flowering variants into an early flowering background, and vice-versa. These transgenic lines require ecological verification. We will examine their effects on focal phenotypes, correlated phenotypes, and fitness. Collectively, this will be comprehensive investigation of the effect size, allele frequency, and ecological consequences of variation at these genes. My specific aims are to: 1) Verify the phenotypic effects of these transgenic lines, in a battery of chamber experiments, with commonly used growth conditions, 2) Perform field experiments to validate their effects in ecologically realistic settings, how they are under natural selection, and quantitatively compare them to levels of naturally occurring variation and selection, 3) Use population resequencing to obtain unbiased estimates of allele frequencies for these naturally occurring variants affecting flowering time, and 4) mathematically combine these estimates to evaluate their contribution to genetic variance, covariance, and how changes in allele frequency might affect future evolutionary responses. 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.