Molecular characterisation of plant disease resistance genes through novel Next-Generation Sequencing applications

该博士项目将为马铃薯遗传学(二倍体和四倍体)以及植物病原菌基因组学/共同进化方面的成功候选人提供全面的培训。学生将生成和分析最先进的下一代测序(NGS)数据，用于在已建立的分离种群中绘制遗传图谱和克隆对晚疫病病原菌马铃薯晚疫病菌有效的抗性。此外，学生将通过细胞生物学分析，包括报告基因、下拉图、共聚焦成像和效应器识别，描述已经分离的功能抗性基因及其变体的作用模式。学生将有机会通过牛津纳米孔MinION开发NGS技术，重点是高分子DNA测序。学生将成为Dundee Effector Consortium(DEC)的正式成员，该联盟联合了50多名植物-病原菌共同进化各方面(包括计算遗传学/基因组学)的研究人员。DEC将提供一个论坛，以便在友好的环境中交流成果，并就博士学位的进展和方向接受批评但具有建设性的反馈。一般背景：数据分析将集中在研究致病疫霉和马铃薯之间的相互作用。卵菌病原菌P.infestans是对全球农作物生产的广泛和重大的经济威胁。疫霉具有很强的破坏性，能够迅速适应现代农业带来的新的选择压力。在分子水平上，病原菌对自然发生或部署的寄主抗病的无毒或毒力是由效应器决定的。基于效应器识别的诱导植物防御反应通常由核苷酸结合，富含亮氨酸重复序列(NLR)的抗病蛋白控制。我们已经成功地开发了马铃薯NLRs以及致病疫霉病原体效应物的靶标浓缩测序，它们决定了植物的识别能力，从而决定了抗药性。我们创造了这些新的方法RenSeq[1-2]和PenSeq。

This PhD project will provide comprehensive training for the successful candidate in potato genetics (diploid and tetraploid) as well as plant-pathogen genomics/co-evolution. The student will generate and analyse state-of-the-art Next Generation Sequencing (NGS) data for the genetic mapping and the cloning of resistances effective against the late blight pathogen Phytophthora infestans in established segregating populations. In addition, the student will characterise the mode-of-action of already isolated functional resistance genes and their variants through cell-biological assays including report genes, pull-downs, confocal imaging, and effector recognition. The student will have the opportunity to develop NGS techniques with a focus on high-molecular DNA sequencing through Oxford Nanopore MinION.The student will be a full member of the Dundee Effector Consortium (DEC), which unites more than 50 researchers on all aspects (including computational genetics/genomics) of plant-pathogen co-evolution. DEC will provide a forum to gain experience in communicating results in a friendly environment and receiving critical but constructive feedback on progress and direction of the PhD. General Background: The data analyses will be focused on studying the interaction between Phytophthora infestans and potato. The oomycete pathogen P. infestans is a widespread and economically significant threat to global crop production. Phytophthora species are very destructive and can adapt rapidly to new selection pressures imposed by modern agriculture. On a molecular level pathogen avirulence or virulence to naturally occurring or deployed host disease resistances is determined by effectors. The effector recognition-based inducible plant defense response is often governed by nucleotide-binding, leucine-rich repeat (NLR) disease resistance proteins. We have successfully developed target enrichment sequencing for potato NLRs as well as pathogen effectors from P. infestans that determine recognition in the plants and therefore resistance. We have coined these novel methods RenSeq [1-2] and PenSeq.