Identifying genetic variation associated with pathogen susceptibility in pines using population genomics

由于气候变化、入侵昆虫的引入和干扰，加拿大的森林正面临来自害虫和病原体的越来越大的压力。这些害虫/病原体的负面影响很难管理，因为干扰可能发生在大范围内。我的研究计划的总体目标是深入了解树木-病虫害/病原体的复杂相互作用，以及气候如何影响这种相互作用。这项研究将结合一套方法(群体基因组学、景观遗传学和分子生物学)来帮助解决关于病原体和宿主之间共同进化关系的基本问题。最终，所获得的知识将用于森林的政策和管理。我将使用两个害虫/病原体系统，在当前的赠款周期中使用山松甲虫(Dendroctonus Ponderosae)，在未来的资助周期中使用西部锈菌(Cronartium Harkiessii)。我之所以选择这些系统，是因为它们有不同的致病生活史，这将使我的实验室能够识别它们的两个寄主--小叶松(Pinus trorta var.)的不同防御反应。Latifolia)和短叶松(P.bansiana)。我还将调查东部白松(P.strobus)和红松(P.resinosa)，因为随着这种昆虫的范围继续扩大，它们未来可能会受到山松甲虫的影响。我的研究计划将首先确定树木对害虫/病原体的反应，这可以分为三个目标：(1)为四个松树物种开发新的基因组资源，这将调查很大一部分编码基因组。基因组学方法现在正被应用于非模式生物，但松树是一个额外的挑战，因为它们的基因组非常大和复杂。因此，我的实验室将使用杂交来定位基因组的相关部分。(2)通过检测与病原菌攻击状态相关的等位基因来识别与防御反应相关的遗传变异。我们还将研究攻击相关的等位基因是否也会随着气候变量的变化而变化，因为防御反应和树木管理环境应激源的能力是相关的。(3)最后，我们将开发一份遗传信息的易感图谱。利用景观遗传学方法，我们将研究所有四种松树病原菌相关等位基因的空间分布，以绘制范围广泛的风险图。这项工作的研究成果将包括更好地了解林木防御和气候适应，这些可以用来更好地预测气候变化对这些经济和生态重要物种的影响。最后，管理人员可以利用为主要森林干扰因素开发的标准风险图来确定缓解战略的优先次序。

Canada's forests are facing increasing pressures from pests and pathogens as a result of climate change, introduction of invasive insects, and disturbances. The negative impacts from these pests/pathogens is difficult to manage as the disturbance can occur over large scales. The overall goal of my research program is to gain insight into the complex tree-pest/pathogen interaction, and how climate influences this interaction. This research will incorporate a suite of approaches (population genomics, landscape genetics, and molecular biology) to help address fundamental questions regarding the co-evolutionary relationship between pathogen and host. Ultimately the knowledge gained will be used to inform policy and management of forests. I will use two pest/pathogen systems, mountain pine beetle (Dendroctonus ponderosae) for the current grant cycle, and western gall rust (Cronartium harknessii) in the future. I have chosen these systems as they have different pathogenic life-histories, which will allow my lab to identify different defense responses in two of their hosts, lodgepole pine (Pinus contorta var. latifolia), and jack pine (P. banksiana). I will also investigate eastern white-pine (P. strobus), and red pine (P. resinosa), as they will potentially be affected by mountain pine beetle in the future as the insect's range continues to expand. My research program will first begin with identifying how the tree responds to the pest/pathogen, which can be broken into three objectives: (1) Develop new genomic resources for the four pine species that will survey a large portion of the coding genome. Genomic approaches are now being applied to non-model organisms, but pine trees represent an additional challenge as their genomes are very large and complex. Therefore, my lab will use hybridization to target the relevant portions of the genome. (2) Identify genetic variation associated with defense response by detecting alleles that co-vary with pathogen attack status. We will also examine whether attack-associated alleles also vary with climatic variables, as defense response and a tree's ability to manage environmental stressors is linked. (3) Finally, we will develop a genomically informed map of susceptibility. Using landscape genetics approaches, we will examine the spatial distribution of pathogen-associated alleles for all four pine species to develop range-wide risk maps. Research outcomes from this work will include a better understanding of forest tree defense, and climatic adaptations which can be used to better predict climate change impacts on these economically and ecologically important species. Finally, the development of a stand-risk map for a major forest disturbance agent can be used by managers to prioritize mitigation strategies.