Changing fates: rewiring gene expression in barley androgenesis

在大麦中，有可能获得由单个未成熟小孢子衍生的植物，这种细胞类型通常会导致花粉粒的产生。这被称为雄核发育，即获得仅携带父本遗传物质（染色体）的植物的过程。事实上，小孢子只携带一对大麦染色体，与大麦植株中通常携带的染色体相反。如果这种情况在由该小孢子衍生的植物的整个发育过程中保持不变，则将导致这些植物不育。幸运的是，大多数通过雄核发育从未成熟的小孢子再生的植物将经历其染色体的自发加倍，从而恢复育性。这样的植物被称为“双单倍体”，并且在遗传分析和育种中是非常有价值的工具。事实上，雄核发育经常用于植物育种，以加速新品种和改良品种的开发。尽管被广泛使用，但我们对通常注定形成花粉粒的细胞如何经历命运的完全转变并开始以高度组织化的方式分裂以产生胚胎并最终产生新植物的了解相当有限。我们推测，这种命运的戏剧性变化是由于小孢子中表达的基因的深刻而快速的重编程。我们可以想象，需要发生两种类型的过程：1）需要在通往花粉的道路上继续前进的基因产物需要被破坏（石板必须被清理）; 2）为了使小孢子参与产生胚胎的道路，需要表达新的基因（必须给出一套新的指令）。因此，我们预计，细胞中发现的表达基因及其产物的列表必须发生重大变化。我们建议通过一种称为RNA-Seq的技术来研究这些变化（对比导致花粉的路径和导致胚胎的路径中的基因表达），这种方法允许对细胞中表达的所有基因进行广泛的编目。为了进一步探索细胞中必要的周转是如何发生的，我们建议研究在发育中的小孢子中发现的小RNA群体。这种小RNA已被证明在植物和动物的发育中发挥重要作用。已知一些特定类型的小RNA靶向破坏某些基因产物。如果这是小孢子向雄核发育转变时的情况，我们希望找到能够指导消除通常需要“建立”一粒花粉的基因产物的小RNA。一旦一个小孢子被这样去编程，它就可以通过表达一套新的基因来重新编程，发育成一个胚胎。这项工作的结果将增强我们对植物细胞如何重新编程的基本知识，并为优化大麦雄核发育提供有用的工具。

In barley, it is possible to obtain plants derived from a single immature microspore, the type of cell that usually leads to the production of pollen grains. This is termed androgenesis, i.e. the process of obtaining a plant carrying only the genetic material (chromosomes) of the male parent. Indeed, microspores only carry a single copy of each barley chromosome, contrary to the pair normally carried in the barley plant. If this situation remains unchanged throughout the entire development of the plant derived from this microspore, it will result in these plants being sterile. Fortunately, a majority of the plants regenerated from immature microspores via androgenesis will undergo a spontaneous doubling of their chromosomes, thus restoring fertility. Such plants are termed "doubled haploid" and are highly valuable tools in both genetic analysis and breeding. Indeed, androgenesis is often used in plant breeding to expedite the development of new and improved varieties.******Although widely used, we have a rather limited understanding of how it is that a cell, normally destined to form a pollen grain, can undergo a complete shift in fate and start dividing in a highly organized fashion to produce an embryo and eventually a new plant. We hypothesize that this dramatic change in fate is due to a profound and rapid reprogramming of the genes that are expressed in the microspore. One can imagine that two types of processes need to occur: 1) the products of the genes needed to continue on the path towards pollen need to be destroyed (the slate has to be cleaned); and 2) new genes need to be expressed in order for the microspore to engage on the path to producing an embryo (a new set of instructions has to be given). We thus expect that major changes must occur to the list of expressed genes and their products found in the cell. We propose to investigate these changes (contrasting gene expression in both the path leading to pollen and the path leading to embryos) through a technique called RNA-Seq, a method that allow the extensive cataloguing of all the genes that are expressed in a cell.******To further explore how the necessary turnover occurs in the cell, we propose to investigate the population of small RNAs found in developing microspores. Such small RNAs have been shown to play important roles in development, both in plants and animals. Some specific types of small RNAs are known to target the destruction of some gene products. If this is the case when the microspore is undergoing its shift towards androgenesis, we expect to find small RNAs capable of directing the elimination of gene products normally needed to "build" a grain of pollen. Once a microspore has been thus deprogrammed, it can be reprogrammed to develop into an embryo by expressing a new suite of genes.******The results of this work will both enhance our basic knowledge of how plant cells can be reprogrammed and provide useful tools for optimizing androgenesis in barley.