Integrating the genome sequence and genetic linkage map of Physcomitrella patens: a platform for map based gene cloning

整合小立碗藓的基因组序列和遗传连锁图谱：基于图谱的基因克隆平台

• 批准号: BB/F001797/1
• 负责人: Andrew Cuming
• 金额: $ 46.66万
• 依托单位: University of Leeds
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2007
• 资助国家: 英国
• 起止时间: 2007 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FF001797%2F1
• 关键词: Integrating; genome; sequence; genetic; linkage

Our research: BBSRC support of Leeds University over a period of 30 years has led us to pioneer the establishment of the moss Physcomitrella patens as an internationally adopted 'model organism' for the study of plant cell and developmental biology. This support enabled us to (i) develop techniques for the isolation of mutants aberrant in basic plant processes - the first step to identify the genetic basis of biological processes (ii) optimise a technique for genetic engineering by 'gene targeting' - a precision tool not possible in any other plant (iii) initiate a programme of gene discovery that has culminated in the complete sequencing of the Physcomitrella genome by an international consortium. Now we shall establish the final tool to enable the rapid and routine identification of genes that underlie abnormal mutants: the integration of the Physcomitrella genome sequence with its genetic linkage map. This will enable the international and UK plant science community to extract maximum value from the newly released Physcomitrella genome through the application of 'comparative functional genomics' - a BBSRC research priority. The value of comparative studies: Our understanding of complex biological processes has been revolutionised by genetic experiments conducted using a small number of well characterised model organisms. In the Animal Kingdom, the study of the nematode worm, the fruit fly, the zebra fish and the mouse allows analysis of animal development across a wide evolutionary spectrum encompassing increasing levels of complexity. Such wide comparative analysis enables us to discern the evolutionary processes that have generated these disparate creatures, and the ways in which essentially similar genes have been differently utilised in the course of evolution. Within the Plant Kingdom, the comparable model organisms that allow a similarly wide evolutionary perspective to be achieved are the flowering plant, Arabidopsis thaliana, and the moss, Physcomitrella patens. Model organisms are chosen for their experimental tractability. All these organisms have had their whole genome sequences determined. All can be manipulated by the introduction of foreign DNA: in the case of the mouse and the moss, foreign DNA can be introduced to specific sites within their genomes with exquisite precision. In all these organisms, random mutations can be induced that cause radical defects in their normal developmental processes. By identifying the genes in which such mutations have occurred, we identify the genes that normally regulate these processes. This identification is possible only where the sequenced genome is supported by a 'genetic linkage map': a representation of the genome based on the inheritance of large numbers of mutations in a large population. Mutations that lie in adjacent sections of the genome are typically inherited together, and are said to be 'genetically linked'. A gene that is responsible for a mutant trait can be isolated if that trait is co-inherited (genetically linked) with neighbouring, known 'genetic markers' - typically lengths of DNA whose sequence is known. This potent experimental approach allows the functional identification of genes without prior knowledge of their sequence. Such an approach is routine in Arabidopsis. This proposal will make it routine in Physcomitrella and accessible to all plant scientists. Physcomitrella is not a flowering plant. It is a member of the earliest group of land plants - the bryophytes - an ancient and biodiverse group which emerged ca. 300 million years before the flowering plants. It therefore represents an ancestral reference by which divergence in plant gene structure and function has occurred. It also provides insights into 'primitive' plant traits such as enhanced dehydration tolerance (essential for a successful colonisation of the land) and the origins of plant multicellularity, that retain their value for future plant improvement.

我们的研究：BBSRC对利兹大学30年来的支持使我们率先建立了苔藓Physcomitrella patens，成为国际上采用的植物细胞和发育生物学研究的“模式生物”。这项支持使我们能够(I)开发分离植物基本过程中异常突变的技术--这是确定生物过程的遗传基础的第一步；(Ii)通过“基因打靶”--一种在任何其他植物中都不可能实现的精密工具--优化基因工程技术；(Iii)启动一项基因发现计划，最终由一个国际财团对Physcomitrella基因组进行完整测序。现在，我们将建立最终的工具，以实现对异常突变背后的基因的快速和常规鉴定：将Physcomitrella基因组序列与其遗传连锁图整合。这将使国际和英国植物科学界能够通过应用“比较功能基因组学”--BBSRC的研究重点--从新发布的Physcomitrella基因组中提取最大价值。比较研究的价值：我们对复杂生物过程的理解已经通过使用少数特征良好的模式生物进行的基因实验而发生了革命性的变化。在动物界，对线虫、果蝇、斑马鱼和老鼠的研究可以分析动物发育的广泛进化范围，包括日益复杂的水平。这种广泛的比较分析使我们能够辨别产生这些不同生物的进化过程，以及本质上相似的基因在进化过程中被不同地利用的方式。在植物王国内，能够实现类似广泛进化前景的可比模式生物是开花植物拟南芥和苔藓植物。选择模型生物是因为它们在实验上容易驯化。所有这些生物都已经确定了他们的全基因组序列。所有这些都可以通过引入外源DNA来操纵：就老鼠和苔藓而言，外源DNA可以精确地引入到它们基因组中的特定位置。在所有这些生物体中，都可以诱导随机突变，导致它们正常发育过程中的根本性缺陷。通过确定发生这种突变的基因，我们就确定了正常情况下调节这些过程的基因。只有在被测序的基因组得到‘遗传连锁图谱’的支持时，这种鉴定才是可能的。‘遗传连锁图谱’是一种基于大量突变在大种群中的遗传的基因组的表示。位于基因组相邻部分的突变通常是一起遗传的，被认为是“基因联系的”。如果一个突变性状与邻近的已知“遗传标记”--通常是已知序列长度的DNA--共同遗传(遗传关联)，那么就可以分离出该突变性状的基因。这种有效的实验方法允许在不事先知道基因序列的情况下对基因进行功能鉴定。这样的方法在拟南芥中是司空见惯的。这项提议将使它成为Physcomitrella的常规做法，所有植物科学家都可以访问。凤眼莲不是开花植物。它是最早的陆地植物--苔藓植物--的一员，苔藓植物是一种古老的生物多样性物种，大约在开花植物出现前3亿年出现。因此，它代表了一种祖先的参照，通过它，植物基因结构和功能发生了差异。它还提供了对“原始”植物特征的洞察，如增强的脱水耐受性(对土地的成功殖民至关重要)和植物多细胞的起源，这些特征保留了它们对未来植物改良的价值。

项目成果

Origin and function of stomata in the moss Physcomitrella patens.

• DOI: 10.1038/nplants.2016.179
• 发表时间: 2016-11-28
• 期刊: Nature plants
• 影响因子: 18

A minus-end directed kinesin motor directs gravitropism in Physcomitrella patens.

• DOI: 10.1038/s41467-021-24546-2
• 发表时间: 2021-07-22
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Li Y;Deng Z;Kamisugi Y;Chen Z;Wang J;Han X;Wei Y;He H;Terzaghi W;Cove DJ;Cuming AC;Chen H
• 通讯作者: Chen H