Genetic and developmental basis for natural variation in plant stem architecture

植物的高度和形状在很大程度上取决于茎的生长方式。尽管在自然界和栽培植物中茎的高度和形状变化很大，但人们对这种变化背后的基因和机制仍然知之甚少。在过去的几十年里，茎高的变化对于提高作物产量非常重要，但是导致这些变化的突变可能会产生不良的副作用（例如，通过减小种子大小）。因此，了解茎如何形成和新的遗传变化，可以用来修改茎的生长具有基础和实际的兴趣。识别影响茎形成的基因的一种方法是寻找导致来自不同地点和环境的同一物种的植物系之间差异的遗传变化。这有两个好处：自然选择的基因变化不太可能引起负面的副作用，而且比在实验室中诱导和选择的基因变化更多样、更复杂。本项目旨在鉴定在茎发育过程中负责自然变异的新基因及其作用机制。为了实现这一目标，我们将结合最近的两项技术发展。首先，开发了前所未有的资源和方法来分析模式物种拟南芥的自然遗传变异。其次，新的成像和图像分析方法可以更详细和定量地分析植物组织如何生长以及生长与基因活性变化的关系。在与维也纳格雷戈尔孟德尔研究所（Gregor Mendel Institute）的一个实验室的合作中，我们已经建立了许多分析拟南芥自然变异的资源，我们最近确定了拟南芥基因组中与茎宽和长度自然变异相关的小区域。这些区域只包含少数基因，现有的信息表明它们如何影响茎的生长。例如，在茎宽的情况下，三个候选基因中的一个与影响细胞生长方向的基因相似，因此我们假设该基因的变化可能会影响茎形成早期的径向生长。对于茎长，已经提出了两个候选基因中的一个控制茎血管的形成，当血管完全发育时，预计会限制茎的进一步伸长，因此我们假设该基因可能通过血管发育的时间来决定茎的末端长度。我们现在提出要证明哪些候选基因对茎生长的变化负责。为此，我们将在具有不同茎形的拟南芥系之间交换每个候选基因。在确定致病基因后，我们将确定修改基因功能的DNA序列的确切变化。为了充分了解这些基因的功能，我们将研究它们在何时何地表达，并在茎形成的特定组织和发育阶段测试这些基因的开启和关闭的影响。为了详细了解这些基因如何改变干细胞组织的生长，我们将在三个维度上测量自然加入和人为操纵这些基因何时何地起作用后细胞行为（细胞分裂，定向细胞伸长）的差异。最后，我们将把我们的分析从简单的、静态的茎形测量（如宽度和长度）扩展到更复杂但也更有信息的测量，即茎形变化的速度和时间。揭示拟南芥茎形变化背后的遗传变化和机制将是在油菜籽或小麦等作物物种中测试等效遗传变化和机制之前必不可少的第一步。最终，我们的工作将提供知识和遗传工具，了解茎结构如何不仅在作物中被修改，而且在植物进化过程中被修改。

The height and shape of plants depends to a large extent on the way the stem grows. Although stem height and shape varies widely in nature and in cultivated plants, the genes and mechanisms behind this variation are still poorly understood. Changes in stem height have been very important to increase crop yields in the last decades, but the mutations responsible for these changes can have undesirable side effects (for example, by reducing seed size). Therefore, knowledge about how the stem forms and novel genetic changes that can be used to modify stem growth have both fundamental and practical interest. One way to identify genes that affect stem formation is to look for genetic changes responsible for differences seen between plant lines of the same species that have originated from different locations and environments. This has two advantages: naturally selected genetic changes are less likely to cause negative side effects and can be more varied and complex than those induced and selected in the lab. This project aims to identify novel genes responsible for natural variation in stem development, and their mechanisms of action. To achieve this, we will combine two recent technical developments. First, resources and methods of unprecedented power have been developed to analyse natural genetic variation in the model species, Arabidopsis. Second, novel imaging and image analysis methods allow a much more detailed and quantitative analysis of how plant tissues grow and how growth relates to changes in gene activity. In collaboration with a lab at the Gregor Mendel Institute (Vienna), where many of the resources to analyse natural variation in Arabidopsis have been established, we have recently identified small regions of the Arabidopsis genome associated with natural variation in stem width and length. These regions contain only a few genes, for which the available information suggests how they could affect stem growth. For example, in the case of stem width, one of the three candidate genes is similar to genes that affect the orientation of cell growth, so we hypothesize that changes in this gene may affect radial growth at early stages of stem formation. For stem length, one of the two candidate genes has been proposed to control formation of the stem vasculature, which when fully developed is expected to restrict further elongation of the stem, so we hypothesize that this gene may determine terminal stem length through the timing of vascular development. We now propose to prove which candidate genes are responsible for changes in stem growth. For this, we will swap each of the candidate genes between Arabidopsis lines with different stem shapes. After the causative genes are identified, we will determine the exact changes in DNA sequence that modified gene function. To fully understand the functions of these genes, we will then study where and when they are expressed, and test the effect of turning these genes on and off in specific tissues and developmental stages during stem formation. To understand in detail how these genes modify the growth of stem tissues, we will measure in three dimensions the differences in cell behavior (cell division, oriented cell elongation) between natural accessions and after artificially manipulating when and where these genes function. Finally, we will extend our analysis from simple, static measurements of stem shape (such as width and length) to more complex but also more informative measurements of the speed and timing of changes in stem shape. Revealing the genetic changes and mechanisms behind changes in stem shape in Arabidopsis will be an essential first step before equivalent genetic changes and mechanisms can be tested in crop species such as rapeseed or wheat. Ultimately our work will provide knowledge and genetic tools understand how stem architecture can be modified not only in crops, but also during plant evolution.