Controlling important diseases in potato by cloning functional NB-LRR-type resistance genes

克隆功能性NB-LRR型抗性基因防治马铃薯重要病害

• 批准号: BB/L008025/1
• 负责人: Ingo Hein
• 金额: $ 77.73万
• 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: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FL008025%2F1
• 关键词: Controlling; important; diseases; potato; cloning

Potato is one of the world's most important food crops, and production is threatened by several pests and pathogens that severely reduce crop yield and quality. These pathogens include late blight, the organism that caused the infamous Irish potato famine, soil-dwelling cyst nematodes that attack the roots, and a number of bacteria and viruses. Current control methods for many of these pathogens in most parts of the world are based mainly on the use of chemical sprays which are both environmentally hazardous and often ineffective. Moreover, some of these chemicals, for example nematicides, are being removed from use by EU legislation, severely limiting the ability of growers to control cyst nematodes. Modelling suggests that global potato production could increase by up to a third if the diseases that reduce yields could be controlled. It is widely thought that the most promising and environmentally benign route for combating crop pests and diseases is by deployment of naturally-occurring plant resistance genes. In plants, including potato, disease resistance is typically controlled by resistance genes, known as 'R genes' that have a recognizable DNA 'domain' structure. In the plant innate immune system, the R proteins encoded by R genes provide resistance by recognising 'effector' molecules produced by the pathogen and then activating various defence processes. Hence R genes are key players in plant disease resistance, and they are effective towards diverse pathogens of all major types (oomycetes, fungi, viruses, nematodes and bacteria). We recently analysed the published potato genome and identified ~760 R genes using a novel technique we have developed for rapid isolation of all R genes from potato varieties or wild species. This new method, called RenSeq (R gene enrichment sequencing), takes advantage of recent developments in genome sequencing and in 'capturing' targeted DNA sequences from complex mixtures. Using this technique we can now sequence the R genes, which represent only about 0.24% of the DNA in the potato genome, from any potato or closely related plant in an efficient and cost effective manner. Moreover, given the appropriate sequence information, this method can be easily applied to other crop species.This project makes use of the wide diversity of R genes present in wild potatoes and other Solanaceae. The main aims of this project are to combine the RenSeq method with the latest sequencing technologies to determine the R gene complements of selected Solanum species harbouring functionally effective resistances against one or more potato pathogen. We will use the sequence data generated to identify markers and gene candidates for functional resistances using an efficient genetic pooling approach. This will make use of existing crosses between resistant and susceptible plants to map the functional resistances to a chromosomal position in the plant genome. RenSeq will be deployed to sequence all R genes in the parents of crosses as well as pools of offspring plants that are resistant and susceptible. Comparing these sequence data using new bioinformatics approaches we will develop genetic markers that are within or immediately flanking the genes conferring resistance. Markers will be deployed via conventional plant breeding to select for resistance and candidate genes will be subjected to functional studies for potential future biotechnological deployment. A key aspect of this project is the partnership between the JHI, UoD and TSL, the plant genome sequencing expertise of TGAC as well as the link with Simplot, who will test resistance genes in field trials in the USA.

马铃薯是世界上最重要的粮食作物之一，生产受到多种害虫和病原菌的威胁，严重降低了作物的产量和质量。这些病原体包括晚疫病、导致臭名昭著的爱尔兰土豆饥荒的有机体、攻击根部的土生孢囊线虫，以及一些细菌和病毒。在世界大多数地区，目前对许多此类病原体的控制方法主要是基于使用化学喷雾，这种喷雾对环境有害，而且往往无效。此外，欧盟立法正在停止使用其中一些化学物质，例如杀线虫剂，这严重限制了种植者控制孢囊线虫的能力。模型表明，如果降低产量的疾病得到控制，全球马铃薯产量可能会增加多达三分之一。人们普遍认为，利用自然产生的植物抗性基因来抗击作物病虫害是最有前途和对环境最有利的途径。在包括马铃薯在内的植物中，抗病通常由抗病基因控制，这种抗病基因被称为“R基因”，具有可识别的DNA“结构域”结构。在植物的天然免疫系统中，由R基因编码的R蛋白通过识别病原体产生的“效应器”分子，然后激活各种防御过程来提供抗性。因此，R基因在植物抗病中起关键作用，它们对所有主要类型的各种病原体(卵菌、真菌、病毒、线虫和细菌)都有效。我们最近分析了已发表的马铃薯基因组，并利用我们开发的一种新技术从马铃薯品种或野生物种中快速分离所有R基因，鉴定了约760个R基因。这种新方法被称为RenSeq(R基因浓缩测序)，它利用了基因组测序和从复杂混合物中‘捕获’目标DNA序列的最新发展。利用这项技术，我们现在可以以高效和经济高效的方式对任何马铃薯或近缘植物的R基因进行测序，这些基因仅占马铃薯基因组DNA的0.24%。此外，在给定适当的序列信息的情况下，该方法可以很容易地应用于其他作物物种。该项目利用了野生马铃薯和其他茄科植物中存在的广泛的R基因多样性。本项目的主要目的是将RenSeq方法与最新的测序技术相结合，以确定对一种或多种马铃薯病原菌具有功能有效抗性的选定茄属物种的R基因互补序列。我们将使用生成的序列数据，通过一种有效的基因池方法来识别功能抗性的标记和基因候选。这将利用抗性和感病植物之间的现有杂交，将功能抗性映射到植物基因组中的染色体位置。RenSeq将被用于对杂交亲本以及抗性和感病后代植物池中的所有R基因进行测序。使用新的生物信息学方法比较这些序列数据，我们将开发出位于抗药性基因内或直接位于抗药性基因两侧的遗传标记。将通过传统的植物育种部署标记以选择抗性，并将对候选基因进行功能研究，以便在未来进行潜在的生物技术部署。该项目的一个关键方面是JHI、UOD和TSL之间的合作，TGAC的植物基因组测序专业知识以及与Simplot的联系，Simplot将在美国进行田间试验测试抗性基因。

项目成果

Identification of Resistance Genes Using Diagnostic R-Gene Enrichment Sequencing (dRenSeq).

使用诊断 R 基因富集测序 (dRenSeq) 鉴定耐药基因。

• DOI: 10.1007/978-1-0716-1609-3_10
• 发表时间: 2021
• 期刊: Methods in molecular biology (Clifton, N.J.)
• 作者: Armstrong M

BLASTmap: A Shiny-Based Application to Visualize BLAST Results as Interactive Heat Maps and a Tool to Design Gene-Specific Baits for Bespoke Target Enrichment Sequencing.

• DOI: 10.1007/978-1-4939-8724-5_14
• 发表时间: 2018
• 期刊: Methods in molecular biology
• 作者: Katie Baker;Gordon Stephen;Shona M Strachan;M. Armstrong;I. Hein

A Phytophthora infestans RXLR effector targets plant PP1c isoforms that promote late blight disease.

• DOI: 10.1038/ncomms10311
• 发表时间: 2016-01-29
• 期刊: Nature communications
• 影响因子: 16.6
• 作者: Boevink PC;Wang X;McLellan H;He Q;Naqvi S;Armstrong MR;Zhang W;Hein I;Gilroy EM;Tian Z;Birch PRJ
• 通讯作者: Birch PRJ

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

HISS：基于 Snakemake 的工作流程，用于执行 SMRT-RenSeq 组装、AgRenSeq 和 dRenSeq，用于发现新型植物抗病基因

• DOI: 10.1101/2022.11.01.514708
• 发表时间: 2022
• 作者: Adams T

Tracking disease resistance deployment in potato breeding by enrichment sequencing.

• DOI: 10.1111/pbi.12997
• 发表时间: 2019-03
• 期刊: Plant biotechnology journal
• 影响因子: 13.8
• 作者: Armstrong MR;Vossen J;Lim TY;Hutten RCB;Xu J;Strachan SM;Harrower B;Champouret N;Gilroy EM;Hein I
• 通讯作者: Hein I