Ecological consequences of plant parasitism in Euphrasia

寄生虫是自然界中普遍存在的一种现象，对寄主和寄生虫都有戏剧性的进化和生态后果。有3000多种被描述的寄生植物，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犀牛，以及每年导致价值120亿美元的水稻作物大量死亡的斯特里加。虽然植物寄生对自然生态系统有很大的影响，但我们对植物寄生的生态学的了解却出人意料地差。为了了解植物寄生的起源和维持，有必要研究植物寄生虫从寄主依附中获得的适合度收益，以及与寄生植物综合症相关的基因。本项目研究了寄生在大叶植物上的寄生的生态后果。大叶寄生是一组通用的植物寄生虫，可以独立生长，但附着在合适的宿主植物上时生长更旺盛。该属包括英国的约20种，每一种都表现出显著的栖息地偏好(例如海岸、山地、草甸)，因此可能也有不同的当地宿主偏好。我们最近从英国各地的种群中收集了种子，并开发了新的基因组资源(全基因组草图序列)，使我们能够调查寄生和寄主偏好的生态意义和基因组基础。这个项目结合了大规模的植物生长试验和前沿的基因表达数据来解决以下研究问题：1)适应不同生境(山地和沿海)的大戟树种对不同的寄主物种有偏好吗？2)不同的寄主附着有什么表型和生态生理变化？3)与附着不同的寄主植物有关的主要基因表达变化？除了回答这些研究问题外，该项目还将涉及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，学生将测试将大戟作为商业作物种植野花种子的发芽方案和程序。总的来说，这个项目代表了一个令人兴奋的例子，即生长试验和基因组工具的结合可以洞察进化生物学和食品安全挑战中的问题。这个项目的核心是分析不同寄主植物的适合性，在爱丁堡皇家植物园(RBGE)的一个大型普通花园实验中，以及在斯科舍省种子基地的其他试验。来自不同生境的种子将根据营养活力和种子结实情况进行评分，以了解与本地寄主植物和非本地寄主植物一起生长时的适应性。该项目中使用的其他方法将根据学生的兴趣开发。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。这将揭示与宿主依附相关的基因表达变化。或者，或者另外，对生态学感兴趣的学生将使用新的工具来量化与宿主依恋相关的生态生理变化。叶绿素荧光是一个强大的工具，可以用来研究寄生如何破坏寄主植物的光合作用装置，并潜在地提高寄生植物的光合作用能力。将提供一个全面的培训方案，包括专门的科学培训以及通用的可转让和专业技能。学生将学习常见花园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有关)，以及与植物进化生物实验相关的技能。

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