Quantifying how host genotype and microbiome composition combine to influence susceptibility to Dothistroma needle blight disease in pine trees.

植物病害研究中的一个关键挑战是了解植物寄主与其相关微生物群(植物内/植物上存在的细菌、真菌和病毒)之间的相互作用如何影响植物病害的发病率和严重程度。这些相互作用受到宿主的遗传变异、环境条件和宿主微生物群中各种微生物的影响。在这个项目中，我们主要关注松树的针叶枯萎病(DNB)，它对全世界松树物种的生长和寿命都有不利影响。由于树木还将在应对当前的生物多样性和气候危机方面发挥关键作用，因此，了解影响树木疾病到达和传播的因素以及它们如何影响树木健康是重要的政策战略。我们项目中提出的关于树木健康的创新研究将提供给这些战略。DNB是由Dothistroma Septosporum引起的，Dothistroma Septosporum是一种英国列出的检疫真菌，目前在世界各地都有发现，它影响了100多种树种，包括商业用材树种苏格兰松、科西嘉松和罗奇波尔松。DNB是一种影响松针的叶部疾病，会导致包括过早失针在内的各种症状。这些症状会导致木材产量下降，并可能导致树木死亡。目前，对DNB的唯一治疗方法是对林木进行管理，以减少在苗圃树上传播和使用杀菌剂的有利条件。在这个项目中，我们将检验我们的假设，即寄主树木的遗传驱动微生物群落的组成和松针的相互作用，以改变树木对DNB的敏感性。为了实现这一点，我们将结合我们已建立的苏格兰松树试验中现有的宿主遗传数据和关于松针微生物组的新的核酸测序信息。我们将使用元基因组和元转录组测序。元基因组测序提供了一份微生物清单(“有什么？”)元转录测序告诉我们哪些社区成员是活跃的(“他们在做什么？”)。我们有三个具体目标，1)量化宿主遗传变异解释微生物群落组成和对DNB敏感性变化的程度，(2)评估在间隔孢子菌感染期间微生物群落组成和功能的时间变化，以及(3)预测哪些微生物群落成员与间隔孢子菌相互作用，以及哪些影响宿主对DNB的易感性。我们的建议解决了BBSRC综合微生物组研究重点中的关键挑战(1)将宿主基因与微生物组组成和健康状况联系起来，以及(2)表征微生物组的功能特性和驱动微生物组-宿主关系的基因。这一建议的好处有两个：(A)我们将了解寄主遗传学和微生物组组成如何结合在一起影响松树对DNB病的易感性，以及(B)我们将开发公开可用的方法来整合多组学(元基因组学、元转录组和基因分型)数据，这些数据将直接适用于从植物到人类的许多不同的宿主-微生物组系统。该项目将使对树木病害管理感兴趣的森林研究人员和对作物遗传学对微生物群和作物病害发病率和严重性的影响感兴趣的农业研究人员受益。该项目还将使计算生物学家和生物学家受益，他们整合了元基因组学、转录组学和基因分型数据集，以回答各种生物学问题。

A key challenge in plant disease research is to understand how the interactions between the plant host and its associated microbiome (the bacteria, fungi and viruses that exist within/on the plant) affect plant disease incidence and severity. These interactions are affected by genetic variation in the host, environmental conditions, and the variety microbes in the host's microbiome. For this project we focus on the pine tree disease Dothistroma needle blight (DNB), that detrimentally affects the growth and life span of pine species worldwide. As trees will also play a critical role in combatting our current biodiversity and climate crises, an understanding of the factors governing the arrival and spread of tree diseases, and how they impact tree health, are important policy strategies. Innovative research on tree health, as proposed in our project, will deliver to these strategies.DNB is caused by Dothistroma septosporum, a UK listed quarantine fungus that is now found worldwide, where it affects more than 100 tree species including the commercial timber species Scots pine, Corsican pine and Lodgepole pine. DNB is a foliar disease affecting the pine needles that causes a variety of symptoms including premature needle loss. These symptoms result in reduced timber yields and can cause tree death. Currently the only treatment for DNB is tree stand management to reduce the favourable conditions for spread and the use of fungicides on nursery trees. In this project we will test our hypothesis that the genetics of the host tree drives microbiome composition and interactions of the pine needles to alter the trees susceptibility to DNB. To achieve this we will combine existing host genetic data from our established Scots pine tree trial with new nucleic acid sequencing information on the pine needle microbiome. We will use meta-genomic and meta-transcriptomic sequencing. Meta-genomic sequencing provides a microbe inventory ("what is there?") and meta-transcriptomic sequencing tell us which community members are active ("what are they doing?"). We have three specific objectives 1) quantify the extent to which host genetic variation explains variation in microbial community composition and susceptibility to DNB, (2) evaluate temporal variation in microbiome composition and function during D. septosporum infection and (3) predict which microbiome community members interact with D. septosporum and which impact on host susceptibility to DNB.Our proposal addresses key challenges within the BBSRC integrative microbiome research priority (1) relating host genotype to microbiome composition and health status, and (2) characterising functional properties of the microbiome and the genes driving the microbiome-host relationship. The benefits of this proposal are two-fold: (a) we will understand how host genetics and microbiome composition combine to influence susceptibility to DNB disease in pine trees and (b) we will develop publicly available methods to integrate multi-omics (metagenomics, meta-transcriptomics and genotyping) data which will be directly applicable to many different host-microbiome systems, from plants to humans. The project will benefit forest researchers with interests in tree disease management and agricultural researchers with interests in the effect of crop genetics on microbiomes and crop disease incidence and severity. The project will also benefit computational biologists and biologists integrating metagenomics, transcriptomics and genotyping datasets to answers diverse biological questions.