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

英国的白蜡树受到真菌病白蜡树枯梢病的威胁，白蜡树枯梢病已经在英国蔓延，翠绿白蜡树蛀虫（EAB）是一种在美国和俄罗斯发现的甲虫。科学家们目前正在利用已经存在于欧洲白蜡树中的遗传信息，寻求培育出抗白蜡树枯梢病的白蜡树。从长远来看，英国和世界需要既能抵抗白蜡树枯梢病又能抵抗EAB的白蜡树。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（Fraxinus excelsior），还需要研究整个白蜡树属，这一属在全世界约有50种。初步研究表明，由于共同进化，其中一些物种对其中一种或两种问题都有抵抗力。在整个属中进行研究可以帮助我们(i)鉴定出在黄曲霉中可以抵抗这些威胁的基因，否则这些基因很难被发现，（ii）揭示出在其他白蜡树物种中具有抗性但在黄曲霉中没有发现的基因。该联盟是一个研究白灰树、白灰枯梢病、EAB、白灰分类和系统发育、白灰基因组学、树木育种、系统基因组学和自然社会框架的国际领导团队。该项目由理查德·巴格斯博士（伦敦大学玛丽女王学院）领导，他目前正在对NERC资助的一种黄曲星（Fraxinus excelsior）基因组进行测序。它将率先应用史蒂夫·罗西特博士的团队（伦敦大学玛丽女王学院）开发的一种新方法来寻找负责性状的基因，该方法由BBSRC资助，以前从未在树木健康环境中使用过。这项工作通过为白蜡树属的数千个基因建立进化树，并检查它们的进化模式如何与白蜡树枯梢病和EAB的易感性/抗性模式相匹配。这种进化方法使我们能够识别可能与耐药性有关的基因或基因变异。为了使这种方法有效，我们需要关于不同白蜡树种对白蜡树枯梢病和EAB的敏感性的准确信息。我们目前对这方面的了解是不完整的，很大程度上是道听途说，所以我们需要填补这一空白。目前，我们甚至还没有关于英国白蜡树（Fraxinus excelsior）对EAB有多敏感的可靠数据。因此，我们建议在美国进行一项关于白蜡树对EAB的敏感性的实验，在这个害虫杀死成千上万棵树的地区。这将由Jennifer Koch博士（美国林业局）进行，她在测试白蜡树EAB易感性方面有多年的经验和完善的方案，但尚未对整个属进行系统研究。这项实验将在目前美国活体收集的所有白蜡树品种的克隆上进行。英国也将进行类似的实验，测试英国和爱尔兰现有的所有白蜡树品种对白蜡树枯梢病的易感性。这项实验将由Steve Lee博士（森林研究）领导，他目前正在领导一个由Defra资助的项目，筛选数千种F. excelsior基因型，以抵抗白蜡树枯梢病。该提案为该项目提供了一个合理的扩展，以包括其他灰种。在我们开展鉴定抗虫害和病原体基因的实验工作的同时，Paul Jepson博士（牛津大学）将开展一项社会科学研究，研究如何以社会和政治上可接受的方式在树木健康环境中使用这些基因。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？这项研究将在社会和政治意义上寻求这些问题的答案。该项目将开拓新的方法和途径来解决真菌病原体和无脊椎害虫在一个广泛的树种。如果成功，这些方法可用于解决其他树种的树木健康问题。

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.