Fusarium disease of wheat - exploring tissue specific host-pathogen interactions using a systems biology approach

小麦赤霉病（Fusarium graminearum）是一种具有高度破坏性的真菌病——赤霉病（Fusarium Head Blight， FHB）的致病菌，主要侵染小麦和其他谷物。它在收获前显著降低粮食质量，造成毁灭性的作物损失。此外，这种病原体会产生有害的毒素，使谷物不适合人类或动物食用。面对不断增长的人口、气候变化、环境压力和杀菌剂耐药性；控制植物真菌病原体的能力已成为全球关注的问题，需要紧急解决。作为最具经济价值的植物病原真菌之一，发展我们对其感染和致病能力的理解是至关重要的。随着真菌基因组学和测序技术的发展，人们对禾谷真菌及其寄主在感染过程中的遗传相互作用进行了大量的研究。在发展生物信息学管道和网络分析方面也取得了进展，以预测和识别微生物中的疾病相关基因。在本项目中，学生将与禾本科真菌微生物学和新兴生物信息学分析技术领域的专家合作，开发不同的生物信息学管道来研究禾本科真菌与小麦之间的宿主-病原体相互作用。为了预测和鉴定关键的疾病相关基因和基因复合物，转录组表达网络将被开发。首先将建立一个网络，单独研究F. graminearum基因在植物感染期间的表达，并将其与体外生长期间的表达进行比较。然而，本项目还旨在开发一个双重病原体-宿主联合表达网络。这将说明禾粒镰刀菌与小麦之间的遗传相互作用。F. graminearum网络将使用未发表的内部和已发表的公共rna测序（RNA-seq）数据集生成。可能会产生额外的RNA-seq数据集来研究感染过程的独特方面。通过网络分析或其他途径确定的预测毒性和疾病相关基因将使用分裂标记删除策略在真菌中删除。然后在小麦开花期将突变体接种到小麦穗上，以测定毒力水平的变化并进行一系列表型试验。参与毒力的基因将进一步功能表征，以了解它们在细胞过程中的参与。小麦中选定的潜在抗性或易感基因也可以通过过表达和病毒诱导的基因沉默来检测。总之，该项目将对禾粒镰刀菌的侵染过程产生新的认识，这对开发作物保护的化学和生物手段具有重要意义。网络分析和其他生物信息学管道也可以被其他研究人员用于进一步推进该领域的研究。

Fusarium graminearum is the causative agent of the highly destructive fungal disease Fusarium Head Blight (FHB), which infects wheat and other cereals. It causes devastating crop losses by dramatically decreasing grain quality before harvest. Furthermore, the pathogen produces harmful toxins which deem grains unfit for human or animal consumption. Faced with a growing population, climate change, environmental pressures, and fungicide resistance; the ability to control fungal plant pathogens has become a global concern requiring urgent solutions. With F. graminearum being one of the most economically important plant pathogenic fungi, developing our understanding of its ability to infect and inflict disease is paramount. Following the advances of fungal genomics and sequencing technologies, there have been a substantial number of studies investigating the genetic interaction between F. graminearum and its cereal hosts during infection. There has also been progress in the development of bioinformatic pipelines and network analyses to predict and identify disease-related genes in microorganisms. In this project, the student will work with experts in both fields of F. graminearum microbiology and emerging bioinformatic analysis technologies to develop different bioinformatic pipelines to study the host-pathogen interaction between F. graminearum and wheat. To predict and identify key disease-related genes and gene complexes a transcriptomic expression network will be developed. Initially a network will be generated to solely study the expression of F. graminearum genes during in planta infections and compare this with expression during in vitro growth. However, this project also aims to develop a dual pathogen-host combined expression network. This will illustrate genetic interactions between F. graminearum and Wheat. The F. graminearum networks will be generated using both unpublished in-house and published public RNA-sequencing (RNA-seq) datasets. Additional RNA-seq datasets may be generated to study unique aspects of the infection process. Predicted virulence and disease-related genes identified through the network analyses or other pipelines, will be deleted in the fungus using a split-marker deletion strategy. The mutants will then be inoculated onto wheat heads at anthesis to assay for changes in virulence levels and undergo a range of phenotypic tests. Genes involved in virulence will then be further functionally characterised to understand their involvement in cellular processes. Selected potential resistance or susceptibility genes in wheat could also be tested using overexpression and virus induce gene silencing. Overall, this project will generate novel insight on the infection process of F. graminearum, which is imperative for developing chemical and biological means of crop protection. The network analysis and other bioinformatics pipelines can also be used by other researchers to further advance research in the field.