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。尽管茎的高度和形状在自然界和栽培植物中差异很大，但这种差异背后的基因和机制仍然知之甚少。在过去的几十年里，茎高的变化对提高作物产量非常重要，但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，关于茎的形成和可用于改变茎生长的新的基因变化的知识具有基础和实际意义。识别影响茎形成的基因的一种方法是寻找导致同一物种不同植物品系之间差异的基因变化，这些差异源于不同的地点和环境。这有两个好处：自然选择的基因变化不太可能引起负面副作用，而且可能比实验室诱导和选择的基因变化更多样、更复杂。该项目旨在识别导致茎发育自然变异的新基因，以及它们的作用机制。为了实现这一目标，我们将结合两项最新的技术发展。首先，已经开发出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更定量地分析植物组织是如何生长的，以及生长如何与基因活性的变化有关。在与格雷戈尔·孟德尔研究所(维也纳)的一个实验室的合作下，我们最近发现了与茎宽和茎长的自然变异有关的拟南芥基因组的小区域。这些区域只包含几个基因，现有的信息表明它们可能会如何影响茎的生长。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。对于茎的长度，已经提出了两个候选基因中的一个来控制茎维管系统的形成，当完全发育时，它有望限制茎的进一步伸长，所以我们推测该基因可能通过维管发育的时间来决定末端茎的长度。我们现在建议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状的拟南芥品系之间交换每个候选基因。在确定致病基因后，我们将确定改变基因功能的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，并测试在干细胞形成过程中特定组织和发育阶段开启和关闭这些基因的效果。为了详细了解这些基因如何改变干细胞组织的生长，我们将从三个维度测量天然材料和人工操作这些基因何时何地发挥作用后细胞行为(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、静态的茎形状测量(如宽度和长度)扩展到更复杂但也更有信息量的茎形状变化速度和时间的测量。在油菜籽或小麦等作物物种中测试同等的遗传变化和机制之前，揭示拟南芥茎形状变化背后的遗传变化和机制将是至关重要的第一步。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，而且在植物进化过程中也可以被改变。

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.