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

禾谷镰刀菌是一种侵染小麦和其他谷物的极具破坏性的真菌病害--赤霉病的病原。它会在收获前大幅降低谷物质量，从而造成毁灭性的农作物损失。此外，病原体还会产生有害的毒素，认为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、环境压力和杀菌剂抗药性，控制真菌植物病原菌的能力已成为全球关注的问题，迫切需要解决。禾谷镰刀菌是经济上最重要的植物病原真菌之一，发展对其侵染和致病能力的了解是至关重要的。随着真菌基因组学和测序技术的发展，已有大量研究探讨了禾谷镰刀菌在侵染过程中与其寄主之间的遗传相互作用。在开发生物信息管道和网络分析以预测和识别微生物中与疾病有关的基因方面也取得了进展。在这个项目中，学生将与禾谷镰刀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管道来研究禾谷镰刀菌与小麦之间的寄主-病原菌相互作用。为了预测和识别与疾病相关的关键基因和基因复合体，将建立一个转录表达网络。最初，将建立一个网络来单独研究禾谷镰刀菌在植物感染过程中的基因表达，并将其与体外生长过程中的表达进行比较。然而，本项目还旨在开发一个双病原-宿主联合表达网络。这将说明禾谷镰刀菌与小麦之间的遗传互作。将使用未公布的内部和已公布的公开RNA测序(RNA-seq)数据集来生成禾谷镰刀菌网络。可以生成额外的RNA-SEQ数据集，以研究感染过程的独特方面。通过网络分析或其他管道确定的预测毒力和疾病相关基因，将使用分裂标记删除策略在真菌中删除。然后在开花期将突变株接种到小麦头上，以检测毒力水平的变化，并进行一系列表型测试。参与毒力的基因随后将进一步从功能上描述，以了解它们参与细胞过程的情况。还可以利用过表达和病毒诱导的基因沉默来检测小麦中选定的潜在抗性或感病基因。总体而言，该项目将对禾谷镰刀菌的感染过程产生新的见解，这对于开发作物保护的化学和生物手段至关重要。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来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.