Using field pathogenomics to study wheat yellow rust dispersal and population dynamics at a national and international scale

小麦条锈菌是由小麦条锈菌（Puccinia striiformis f.）小麦赤星病对全世界小麦生产是一个重大威胁，最近又重新成为英国农业的主要制约因素。它对全球粮食安全的重要性反映在小麦对人类卡路里和蛋白质摄入量的重大贡献（约20%）上。这种疾病的破坏性影响使育种者、农民和最终用户产生了加强监测的紧迫感。为了解决这个问题，我们最近开发了一种新的方法，称为“现场病原体组学”的病原体种群监测。这种基于新的基因测序技术的方法使我们能够直接从锈菌感染的小麦的田间样品中获得数据。通过实施这种方法，我们发现近年来英国各地的黄锈病种群发生了重大变化。遗传分析揭示了四个不同的谱系，通过传统的病理学为基础的毒力测定确定的表型组相关。该项目的总体目标是将基因测序技术应用于黄锈病的监测，并对这一重要植物病原体进行全面的全球群体遗传分析。目前，基因型多样性的评估不包括在英国小麦锈病的国家监测活动。我们的新方法能够将高分辨率基因型数据整合到病原体监测活动中，这对于提高我们对人群遗传子结构的理解至关重要。拟议的研究旨在：（1）通过绘制全球种群结构图，分析小麦黄锈病潜在外来入侵对英国的威胁，（2）利用锈病基因型数据，（目的1）为了确认特定小麦品种上的爆发，并寻找病原基因型与宿主谱系之间的关联，（3）产生关于基因型多样性在一个地点是否随时间推移而变化以及早期出现的锈病基因型是否预示晚季基因型的信息，以及（4）开发适当的开源工具，以确保本文生成的所有数据尽快以适合育种者，病理学家和更广泛人口的格式发布到公共领域。该项目旨在为英国提供最新的基因组工具，促进育种者更有效地开发品种，并帮助降低与杀菌剂应用相关的环境和经济成本，所有这些都将对英国耕地产业的整体竞争力和可持续性产生积极影响。这将通过与6大洲的13个锈病病理学实验室的合作以及来自6个育种，农学和化学公司以及HGCA的工业支持来实现。

Wheat yellow rust caused by the fungus Puccinia striiformis f. sp tritici is a substantial threat to wheat production worldwide and recently re-emerged as a major constraint on UK agriculture. Its importance to global food security is reflected by the significant contribution of wheat to the calorific and protein intake of human kind (approximately 20%). The devastating impact of this disease gives a deep sense of urgency to breeders, farmers and end users to improve surveillance. To address this, we recently developed a novel approach called "field pathogenomics" for pathogen population surveillance. This method, based on new gene sequencing technology, allows us to acquire data directly from field samples of rust-infected wheat. By implementing this approach we found that the yellow rust population across the UK underwent a major shift in recent years. Genetic analyses revealed four distinct lineages that correlated to the phenotypic groups determined through traditional pathology-based virulence assays. The overall aim of this project is to apply gene-sequencing technology to the surveillance of yellow rust and undertake comprehensive global population genetic analyses of this important plant pathogen. Currently, the assessment of genotypic diversity is not included within UK national surveillance activities for wheat rust. Our new approach enables the integration of high-resolution genotypic data into pathogen surveillance activities that is vital to improve our understanding of the genetic sub-structure within a population. The proposed research aims to: (1) Analyze the threat of potential exotic incursions of wheat yellow rust to the UK by mapping the global population structure, (2) exploit the rust genotype data (Obj. 1) to confirm outbreaks on particular wheat varieties and look for associations between pathogen genotypes and host pedigrees, (3) generate information on whether genotypic diversity shifts over time at a locality and whether early appearing rust genotypes are predictive of late season genotypes and (4) develop appropriate open-source tools to ensure all data generated herein is released into the public domain as soon as possible and in a format that is suitable for breeders, pathologists and the wider demographic. This project aims to equip the UK with the latest genomic tools, facilitate more efficient varietal development by breeders, and help reduce the environmental and economic costs associated with fungicide applications, all of which will have a positive impact on the overall competitiveness and sustainability of the UK arable industry. This will be achieved through collaboration with 13 rust pathology laboratories across 6 continents and industrial support from 6 breeding, agronomy and chemical companies and the HGCA.