Identifying genomic resources against pests and pathogens in tree genera: a case study in Fraxinus

识别树属害虫和病原体的基因组资源：白蜡树案例研究

• 批准号: BB/L012162/1
• 负责人: Richard Buggs
• 金额: $ 66.4万
• 依托单位: Queen Mary University of London
• 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%2FL012162%2F1
• 关键词: Identifying; genomic; resources; against; pests

British ash trees are threatened by the fungal disease ash dieback, which has already arrived in the UK, and by the emerald ash borer (EAB), a beetle found in the USA and Russia. Scientists are currently seeking to develop ash trees resistant to ash dieback, using genetic information already present in European ash trees. In the longer term, Britain and the World need ash trees that are resistant to both ash dieback and EAB. To achieve this, we may need to study not just in Fraxinus excelsior -- the ash species most common in Britain -- but in the whole ash genus, which consists of about 50 species worldwide. Preliminary studies suggest that some of these species are resistant to one or both of these problems, due to co-evolution. Looking in the whole genus may help us (i) to identify genes in Fraxinus excelsior that can give resistance to these threats, which would otherwise have been hard to find, and (ii) reveal genes in other ash species that give resistance but are not found in Fraxinus excelsior. This consortium is an international team of leaders in research on ash trees, ash dieback, the EAB, ash taxonomy and phylogenetics, ash genomics, tree breeding, phylogenomics and social framings of nature. It is led by Dr Richard Buggs (Queen Mary, University of London) who is currently sequencing a Fraxinus excelsior genome funded by NERC. It will pioneer the application of a new method for finding genes responsible for traits developed by Dr Steve Rossiter's group (Queen Mary, University of London), funded by BBSRC, that has not been used before in tree health contexts. This works by building evolutionary trees for thousands of genes in the ash genus, and examining how the patterns of evolution seen in them fit with patterns of susceptibility/resistance to ash dieback and EAB. This evolutionary approach allows us to identify genes or gene variants that may be involved in resistance.For this method to work, we need accurate information about the susceptibility of different ash species to ash dieback and the EAB. Our current knowledge of this is patchy and largely anecdotal, so we need to fill this gap. At the moment we do not even have good data on how susceptible the British ash species, Fraxinus excelsior, is to the EAB. We therefore propose an experiment on susceptibility of ash species to the EAB to be carried out in the USA, in an area where this pest is killing thousands of trees. This will be conducted by Dr Jennifer Koch (US Forest Service), who has years of experience and well developed protocols in testing ash trees for EAB susceptibility, but has not carried out a systematic study of the whole genus. This experiment will be carried out on clones of all ash species currently available in American living collections.A similar experiment will be carried out in the UK, testing the susceptibility of all ash species currently available in British and Irish living collections to ash dieback. This experiment will be led by Dr Steve Lee (Forest Research) who is currently leading a project screening thousands of F. excelsior genotypes for resistance to ash dieback, funded by Defra. This proposal provides a logical extension to that project to include other ash species.Whilst we carry out experimental work to identify genes for pest and pathogen resistance, a social science study will be conducted by Dr Paul Jepson (Oxford University) about how they might be used in a tree health context in a manner that is socially and politically acceptable. Could we develop ash populations resistant to EAB and ash dieback by planting other ash species? By hybrid breeding programes? By genetic modification? This study will seek answers to these questions in a social and political sense.This project will pioneer new methods and approaches to tackling both a fungal pathogen and an invertebrate pest in a widespread tree genus. If successful these approaches can be used to tackle tree health issues in other tree genera.

英国的白蜡树受到真菌疾病白蜡树枯死的威胁，这种疾病已经到达英国，还有一种在美国和俄罗斯发现的甲虫--绿白蜡虫（EAB）。科学家们目前正在利用欧洲白蜡树中已经存在的遗传信息，寻求开发抗白蜡树枯梢病的白蜡树。从长远来看，英国和世界需要灰树，是既抗灰枯死和EAB。为了实现这一目标，我们可能不仅需要研究英国最常见的白蜡树，而且需要研究全世界约有50种的白蜡树属。初步研究表明，由于共同进化，这些物种中的一些对这些问题中的一个或两个都有抵抗力。在整个属中寻找可能有助于我们（i）确定白蜡树中可以抵抗这些威胁的基因，否则很难找到，（ii）揭示其他白蜡树物种中具有抵抗力但在白蜡树中没有发现的基因。该联盟是一个国际领导团队，研究白蜡树、白蜡树顶枯病、EAB、白蜡树分类学和白蜡树遗传学、白蜡树基因组学、树木育种、白蜡树基因组学和自然界的社会框架。它由理查德·布格斯博士（玛丽女王，伦敦大学）领导，他目前正在测序由NERC资助的白蜡树基因组。它将开创一种新方法的应用，该方法用于寻找由史蒂夫罗西特博士的小组（玛丽皇后，伦敦大学）开发的负责性状的基因，由BBSRC资助，以前从未在树木健康方面使用过。这是通过为白蜡树属中的数千个基因构建进化树，并研究它们中的进化模式如何与白蜡树顶枯和EAB的易感性/抗性模式相适应。这种进化方法使我们能够识别可能参与抗性的基因或基因变体。为了使这种方法发挥作用，我们需要关于不同白蜡物种对白蜡枯梢病和EAB的易感性的准确信息。我们目前对这方面的知识是零散的，而且大部分是轶事，所以我们需要填补这一空白。目前，我们甚至没有关于英国白蜡树物种（白蜡树）对EAB的敏感性的良好数据。因此，我们建议在美国进行一项关于白蜡树物种对EAB敏感性的实验，在该地区，这种害虫正在杀死数千棵树。这将由Jennifer Koch博士（美国林务局）进行，他在测试白蜡树对EAB的敏感性方面拥有多年的经验和完善的方案，但尚未对整个属进行系统的研究。这项实验将在美国现有的所有白蜡树物种的克隆上进行，类似的实验将在英国进行，测试英国和爱尔兰现有的所有白蜡树物种对白蜡树枯梢病的敏感性。这项实验将由史蒂夫·李博士（森林研究）领导，他目前正在领导一个筛选数千种F。由Defra资助的抗白蜡树枯梢病基因型。这项建议提供了一个合乎逻辑的扩展，该项目包括其他白蜡树物种。我们进行实验工作，以确定抗害虫和病原体的基因，将进行一项社会科学研究，由保罗杰普森博士（牛津大学）关于如何在树木健康的情况下，在社会和政治上可接受的方式使用。我们能否通过种植其他白蜡树品种来培育抗EAB和白蜡树枯梢病的白蜡树种群？通过杂交育种计划？通过基因改造？本研究将从社会和政治的角度寻求这些问题的答案。本项目将开创新的方法和途径，以解决广泛分布的树木属中的真菌病原体和无脊椎动物害虫。如果成功的话，这些方法可以用来解决其他树种的树木健康问题。

项目成果

State of the World's Fungi 2018

2018 年世界真菌状况

• 发表时间: 2018
• 作者: Buggs RJA

Genes for ash tree resistance to an insect pest identified via comparative genomics

• DOI: 10.1101/772913
• 发表时间: 2019-09
• 期刊: bioRxiv
• 作者: L. J. Kelly;W. Plumb;D. Carey;M. Mason;E. Cooper;William Crowther;A. Whittemore;S. Rossiter

Molecular markers for tolerance of European ash (Fraxinus excelsior) to dieback disease identified using Associative Transcriptomics.

使用联想转录组学鉴定的欧洲灰分（fraxinus excelsior）耐受性疾病的耐受性的分子标记。

• DOI: 10.1038/srep19335
• 发表时间: 2016-01-13
• 期刊: Scientific reports
• 影响因子: 4.6
• 作者: Harper AL;McKinney LV;Nielsen LR;Havlickova L;Li Y;Trick M;Fraser F;Wang L;Fellgett A;Sollars ES;Janacek SH;Downie JA;Buggs RJ;Kjær ED;Bancroft I
• 通讯作者: Bancroft I

Convergent molecular evolution among ash species resistant to the emerald ash borer.

对翡翠灰钻的灰分物种之间的融合分子进化。

• DOI: 10.1038/s41559-020-1209-3
• 发表时间: 2020-08
• 期刊: Nature ecology & evolution
• 影响因子: 16.8
• 作者: Kelly LJ;Plumb WJ;Carey DW;Mason ME;Cooper ED;Crowther W;Whittemore AT;Rossiter SJ;Koch JL;Buggs RJA
• 通讯作者: Buggs RJA

A high-quality reference genome for Fraxinus pennsylvanica for ash species restoration and research.

宾夕法尼亚州弗拉金斯的高质量参考基因组，用于灰分恢复和研究。

• DOI: 10.1111/1755-0998.13545
• 发表时间: 2022-05
• 期刊: MOLECULAR ECOLOGY RESOURCES
• 影响因子: 7.7
• 作者: Huff, Matt;Seaman, Josiah;Di, Wu;Zhebentyayeva, Tetyana;Kelly, Laura J.;Faridi, Nurul;Nelson, Charles D.;Cooper, Endymion;Best, Teodora;Steiner, Kim;Koch, Jennifer;Severson, Jeanne Romero;Carlson, John E.;Buggs, Richard;Staton, Margaret
• 通讯作者: Staton, Margaret