Ecological consequences of plant parasitism in Euphrasia

寄生是自然界中普遍存在的现象，对寄主和寄生虫都有显著的进化和生态后果。有超过3000种已知的寄生植物，包括通过阻碍其他草本植物的生长来维持草原生态系统的莱茵草，以及每年摧毁价值120亿美元的水稻作物的斯特里加。虽然植物寄生对自然生态系统有重大影响，但我们对植物寄生生态学的了解却令人惊讶地贫乏。为了了解植物寄生的起源和维持，有必要研究寄主附着对植物寄生的适应性利益，以及与寄生植物综合征相关的基因。该项目研究了寄生在胡杨属植物中的生态后果，胡杨属植物是一组多能植物寄生虫，它们可以独立生长，但当附着在合适的寄主植物上时生长得更旺盛。该属在英国包括约20个物种，每个物种都表现出显著的栖息地偏好（例如沿海，山地，草甸），因此也可能不同的本地宿主偏好。我们最近收集了来自英国各地种群的种子，并开发了新的基因组资源（全基因组草图序列），使我们能够研究寄生和寄主偏好的生态意义和基因组基础。本项目结合大规模植物生长试验和前沿基因表达数据来解决以下研究问题：1)适应不同生境（山地与沿海）的胡杨物种是否对不同寄主物种有偏好？2)不同寄主附着的表型和生理生态变化是什么？3)附着在不同寄主植物上是否存在主要的基因表达变化？除了回答这些研究问题外，该项目还将涉及与CASE合作伙伴Scotia Seeds的工业安置，Scotia Seeds是苏格兰领先的野花种子生产商。在整个博士学位的一系列短期实习中，学生将测试发芽协议和将胡杨作为野花种子混合物的商业作物种植的程序。总的来说，这个项目代表了一个令人兴奋的例子，在这个例子中，生长试验和基因组工具的结合可能会为进化生物学和粮食安全挑战的问题提供见解。该项目的核心是在爱丁堡皇家植物园（RBGE）的一个大型普通花园实验中分析不同寄主生长的植物的适应性，并在Scotia种子站点进行了额外的试验。来自不同栖息地的种子将根据营养活力和种子设置进行评分，以了解与本地与非本地寄主植物一起生长时的适应性。项目中使用的其他方法将根据学生的兴趣发展。对基因组学有浓厚兴趣的个人将能够使用激光解剖显微镜和组织特异性RNA测序来研究宿主-寄生虫界面的基因表达变化。这将揭示与寄主附着相关的基因表达变化。另外，对生态学感兴趣的学生将使用新的工具来量化与宿主附着相关的生态生理变化。叶绿素荧光是一个强有力的工具，可以用来研究寄主如何破坏寄主植物的光合器官，并有可能提高寄主植物的光合能力。将提供一项全面的培训方案，包括专门的科学培训和一般的可转移技能和专业技能。学生将学习普通园林生长研究的实验设计，如何产生下一代测序数据，各种遗传分析（与基因表达数据分析相关），以及与植物进化生物学实验相关的技能

Parasitism is a ubiquitous phenomenon in the natural world, with dramatic evolutionary and ecological consequences for both the host and the parasite. There are over 3000 described parasitic plant species, including Rhinanthus, which maintains grassland ecosystems by stunting the growth of other herbaceous plants, and Striga, which decimates 12 billion dollars' worth of rice crops each year. While plant parasitism has a major effect on natural ecosystems, our understanding of the ecology of plant parasitism is surprisingly poor. In order to understand the origin and maintenance of plant parasitism, it is necessary to study the fitness benefit plant parasites receive from host attachment, and the genes associated with the parasitic plant syndrome.This project investigates the ecological consequences of parasitism in Euphrasia, a group of generalist plant parasites which can grow independently, but grow more vigorously when attached to a suitable host plant. The genus includes c. 20 species in the UK, with each species showing notable habitat preferences (e.g. coastal, montane, meadow), and thus potentially different local host preferences, too. We have recently made seed collections from populations across the UK, as well as developed new genomic resources (whole draft-genome sequences), enabling us to investigate the ecological significance and genomic basis of parasitism and host preferences.This project incorporates large-scale plant growth trials and cutting-edge gene expression data to address the following research questions:1) Do Euphrasia species adapted to different habitats (montane vs coastal) have preferences for different host species?2) What are the phenotypic and ecophysiological changes with alternative host attachment?3) Are there major gene expression changes associated with attaching to different host plants?In addition to answering these research questions, this project will also involve an industrial placement with CASE partner Scotia Seeds, the leading producer of wildflower seeds in Scotland. During a series of short placements throughout the PhD, the student will test germination protocols and procedures for growing Euphrasia as a commercial crop for wildflower seed mixes.Overall, this project represents an exciting example of where the combination of growth trials and genomic tools may give insight into questions in evolutionary biology and food security challenges.The core of this project relies on analysing fitness of plants grown with different hosts, in a large common garden experiment based at the Royal Botanic Garden Edinburgh (RBGE), and with additional trials at the Scotia Seed site. Seeds sourced from different habitats will be scored for vegetative vigour and seed set, to understand fitness when grown with a local vs. non-local host plant.Other methods used in the project will be developed in line with the students' interests. Individuals with a strong interest in genomics will be able to use laser-dissection microscopy and tissue-specific RNA sequencing to study the gene expression changes at the host-parasite interface. This will reveal gene expression changes associated with host attachment. Alternatively, or in addition, students interested in ecology will use new tools to quantify ecophysiological changes associated with host attachment. Chlorophyll fluorescence is a powerful tool which could be used to investigate how parasitism could damage the photosynthetic apparatus of the host plant, and potentially enhance the photosynthetic capacity of the parasite. A comprehensive training programme will be provided comprising both specialist scientific training and generic transferable and professional skills. The student will be taught experimental design for common garden growth studies, how to produce next-generation sequencing data, a variety of genetic analyses (related to the analysis of gene expression data), and skills related to experiments in plant evolutionary biolo