Potato PCN Resistance: Cloning effective resistances against potato cyst nematodes

马铃薯 PCN 抗性：克隆对马铃薯胞囊线虫的有效抗性

• 批准号: BB/X009068/1
• 负责人: Ingo Hein
• 金额: $ 60.69万
• 依托单位: James Hutton Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2023
• 资助国家: 英国
• 起止时间: 2023 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FX009068%2F1
• 关键词: Potato; PCN; Resistance; Cloning; effective

Potato is the world's most important non-cereal food crop and production is threatened by pathogens that severely reduce crop yield, quality, and impede seed potato production. Potato Cyst Nematodes (PCN) are widespread pathogens of potato that are difficult to eradicate once established. The potato industry is dependent on access to PCN-free land to produce healthy seed tubers as well as PCN resistant potato varieties to suppress populations of this economically damaging pest.Current control methods for PCN often depend on nematicides which can be environmentally damaging and are consequently being phased out in many potato producing countries. Further, crop rotations, which in the UK typically span between six to seven years, can help reduce the disease pressure, but fail to clean-up contaminated land as PCN cysts in the soil can remain viable for over 20 years. The realisation that cultivated potatoes can be protected from pathogens such as PCN by the introduction of disease resistance genes from wild species led to the deployment into cultivars of the H1 resistance effective against the PCN species Globodera rostochiensis and Gpa5 and Gpa4 that are effective against G. pallida. Previous genetic mapping studies of these resistances have provided evidence that the hitherto elusive genes are likely members of the plant nucleotide-binding, leucine-rich-repeat gene family (NLRs). This project aims to identify the functional NLRs that are responsible for the resistances against both nematode species and to understand the molecular mechanism by which these genes provide protection upon recognition of pathogen molecules known as effectors. It is this combined knowledge about the host and pathogen molecules that determine the ability of potatoes to be infected or to defend themselves that breeders require to develop resistant potato varieties for the future. Our consortium brings together experts on potato NLRs from The James Hutton Institute and The Sainsbury Laboratory alongside PCN experts from The James Hutton Institute and the University of Cambridge. We have obtained support from the international companies PepsiCo Solynta and Averis, as well as the 2Blades foundation to ensure immediate impact of the research. Key resources for this project are already in place. For potatoes, this includes our ability to preferentially re-sequence NLRs using a technology known as RenSeq that was jointly developed by members of this consortium. Using RenSeq, we have been able to represent the NLRs in existing potato varieties that contain the genes H1, Gpa5 and Gpa4. This enables powerful association studies to identify gene candidates. By taking advantage of existing high-throughput transformation capabilities, these candidate NLRs can be assessed quickly to identify the functional nematode resistance genes. For PCN, we have in place genomic resources such as genome assemblies of both PCN species and established pipelines to identify likely candidate effector genes. In addition, we have PCN populations of G. rostochiensis and G. pallida that have been selected for virulence on potato plants carrying H1, Gpa5 or Gpa4, respectively. These populations will allow us to prioritise candidate avirulence genes that trigger the potato resistance responses upon detection. Through Solynta and Averis we have access to PCN populations that can evade Gpa5 resistance and allow us to study virulence.These resources combined make the project extremely timely and feasible. The knowledge generated in this project will a) address a scientific gap in our understanding of resistances against plant-parasitic nematodes and b) will deliver an applied outcome to protect potato production. Indeed, we anticipate reaching a position where we can inform breeders about the nature of resistances that can be combined and predict their effectiveness by considering pathogen effector diversity including changes to bona fide avirulence genes.

马铃薯是世界上最重要的非谷物粮食作物，其生产受到病原菌的威胁，严重降低了作物的产量和品质，并阻碍了马铃薯的种薯生产。马铃薯孢囊线虫(PCN)是马铃薯上分布广泛的病原菌，一旦发现就很难根除。马铃薯产业依赖于获得无PCN的土地来生产健康的块茎种子，以及抗PCN的马铃薯品种来抑制这种具有经济破坏性的害虫的种群。目前对PCN的控制方法通常依赖于可能对环境造成破坏的杀线虫剂，因此在许多马铃薯生产国正在逐步淘汰。此外，在英国，轮作通常持续六到七年，可以帮助减轻疾病压力，但无法清理受污染的土地，因为土壤中的PCN孢子可以存活20多年。意识到通过从野生物种导入抗病基因可以保护栽培马铃薯免受PCN等病原体的侵染，导致H1抗性的品种被部署到对PCN物种轮纹夜蛾和Gpa5和Gpa4有效的品种中，Gpa5和Gpa4对灰霉病菌有效。以前对这些抗性的遗传作图研究已经提供了证据，表明到目前为止难以捉摸的基因很可能是植物核苷酸结合富含亮氨酸重复基因家族(NLRs)的成员。本项目旨在确定对这两个线虫物种产生抗性的功能NLR，并了解这些基因在识别病原体分子(称为效应器)时提供保护的分子机制。正是这种关于寄主和病原体分子的综合知识决定了土豆被感染或自卫的能力，育种者要求为未来培育出抗病的土豆品种。我们的联盟汇集了来自詹姆斯·赫顿研究所和塞恩斯伯里实验室的马铃薯NLR专家以及来自詹姆斯·赫顿研究所和剑桥大学的PCN专家。我们已经得到了国际公司百事Solynta和Averis以及2Blade基金会的支持，以确保研究立即产生影响。这个项目的关键资源已经到位。对于土豆，这包括我们使用由该联盟成员共同开发的名为RenSeq的技术优先重新排序NLR的能力。使用RenSeq，我们已经能够表示包含H1、Gpa5和Gpa4基因的现有马铃薯品种的NLR。这使得强大的关联性研究能够识别候选基因。通过利用现有的高通量转化能力，可以快速评估这些候选NLR以鉴定功能上的线虫抗性基因。对于PCN，我们有适当的基因组资源，如PCN物种的基因组组装和已建立的管道，以确定可能的候选效应基因。此外，我们还发现了罗氏棉铃虫和青枯棉的PCN种群，它们分别被选为对携带H1、Gpa5或Gpa4的马铃薯植株具有致病力。这些种群将使我们能够优先选择候选无毒基因，这些基因在检测到后会触发马铃薯的抗性反应。通过Solynta和Averis，我们可以接触到可以逃避Gpa5抗性的PCN种群，并使我们能够研究毒力。这些资源结合在一起，使该项目非常及时和可行。该项目产生的知识将a)解决我们对植物寄生线虫抗性认识上的科学空白，b)将提供保护马铃薯生产的应用成果。事实上，我们预计可以通过考虑病原体效应多样性，包括真正无毒基因的变化，来告知育种者可以组合的抗性的性质，并预测它们的有效性。

项目成果

Identification and mapping of Rpi-blb4 in diploid wild potato species Solanum bulbocastanum

二倍体野生马铃薯品种 Solanum tubecastanum 中 Rpi-blb4 的鉴定和定位

• DOI: 10.1016/j.cj.2023.08.005
• 发表时间: 2023
• 期刊: The Crop Journal
• 作者: Li J

HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes.

• DOI: 10.1186/s12859-023-05335-8
• 发表时间: 2023-05-17
• 期刊: BMC bioinformatics
• 影响因子: 3

Resistify - A rapid and accurate annotation tool to identify NLRs and study their genomic organisation

• DOI: 10.1101/2024.02.14.580321
• 发表时间: 2024-04
• 期刊: bioRxiv
• 作者: Moray Smith;John T. Jones;Ingo Hein