Using population genomics to predict the epidemiology and evolution of R. solanacearum plant pathogen in the UK

利用群体基因组学预测英国青枯菌植物病原体的流行病学和进化

• 批准号: 2108489
• 金额: --
• 依托单位: University of York
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2018
• 资助国家: 英国
• 起止时间: 2018 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-2108489
• 关键词: Using; population; genomics; predict; epidemiology

Plant pathogenic bacteria cause considerable economic losses globally due to damage to crops.Bacterial wilt, caused by the Gram-negative quarantine bacterium Ralstonia solanacearum, is one ofthe most important bacterial crop diseases. In the UK, R. solanacearum causes potato brown rot. UKoutbreaks have been associated with flooding or irrigation of potato crops from contaminated riverwater sources where it can persist by overwintering in the roots of its secondary host plant, WoodyNightshade. It is currently known that R. solanacearum densities peak in July-September when thewater temperatures are high and that the strains isolated from disease outbreaks are highly related tothe environmental strains isolated from water and alternative hosts upstream of the infested potatofields. While these findings suggest that environmental reservoirs play important roles in the diseaseoutbreaks, it is still unclear how the R. solanacearum population has dispersed, expanded and evolvedsince the first disease finding in 1992.This project will use population genomics and a collection of time sampled pathogen isolates tounderstand the epidemiology and genomic evolution of R. solanacearum in the UK river system. Thestudentship will address three research areas:1) Global pathogen dispersal: comparison of UK isolates with an existing sequence database of R.solanacearum genomes to determine whether the UK population is genetically unique and locallyadapted and to estimate the frequency of international dispersal.2) Evolutionary dynamics: to what extent has R. solanacearum changed during the UK diseaseoutbreaks since 1992? Can we identify quantitative traits that are important for pathogenic vs.environmental isolates by using genome-wide association approaches (GWAS)? Can we use genomedifference to infer something about pathogen ecology and adaptation in environmental reservoirs andis R. solanacearum still evolving in the UK?3) Spatial and temporal distribution of R. solanacearum genotypes: We will develop a genomicdatabase that will help in identifying novel outbreak strains, to infer the likely geographic source of their2origin and to match specific control management strategies against the given outbreak strain.The project combines next-generation genome sequencing, bioinformatics and evolutionary biology tounderstand the dynamics of concurrent plant pathogen outbreaks.

植物病原菌对农作物造成巨大的经济损失。青枯病是由革兰氏阴性检疫菌青枯菌引起的，是最重要的细菌性农作物病害之一。在英国，青枯菌会导致马铃薯褐腐病。英国的疫情爆发与受污染的河水源对马铃薯作物的洪水或灌溉有关，马铃薯作物可以通过在其次要寄主植物茄属植物的根部越冬而持续存在。目前已知，青枯菌密度在7月至9月水温较高时达到峰值，从疾病暴发中分离出的菌株与从受侵染马铃薯田上游的水和替代宿主中分离出的环境菌株高度相关。虽然这些发现表明环境储存库在疾病暴发中发挥着重要作用，但自 1992 年首次发现疾病以来，目前尚不清楚青枯菌种群如何扩散、扩展和进化。该项目将利用种群基因组学和时间采样的病原体分离株集合来了解英国河流系统中青枯菌的流行病学和基因组进化。该奖学金将涉及三个研究领域：1）全球病原体传播：将英国分离株与现有的青枯菌基因组序列数据库进行比较，以确定英国种群是否具有遗传独特性和本地适应能力，并估计国际传播的频率。2）进化动力学：自1992年以来，在英国疾病暴发期间，青枯菌发生了多大程度的变化？我们能否通过使用全基因组关联方法（GWAS）来识别对致病性与环境分离株重要的数量性状？我们能否利用基因组差异来推断有关环境储存库的病原体生态和适应情况，以及在英国仍在进化的青枯菌？3）青枯菌基因型的时空分布：我们将开发一个基因组数据库，该数据库将有助于识别新的爆发菌株，推断其起源的可能地理来源，并针对给定的爆发菌株匹配特定的控制管理策略。 结合下一代基因组测序、生物信息学和进化生物学，以了解同时发生的植物病原体爆发的动态。