RESEARCH-PGR: QTL Analyses Identify Genetic Components Regulating the Interactions between Plants, Pathogens and the Environment in the Face of Climate Change

生物体对环境的反应能力是其生存的基础。当感兴趣的生物体参与宿主-病原体相互作用时，“环境”变得复杂，不仅包括外力，还包括相互作用伙伴施加的条件。还有两个基因组在起作用，每一个都影响两种生物体的行为。此外，外部环境力量施加了额外的压力，每个基因组都可以影响伴侣双方的反应。本项目研究宿主基因组在环境胁迫下改变宿主和病原体行为中的作用。它利用了一个与农业相关的系统，番茄的线虫感染。寄生线虫造成全球每年约1250亿美元的作物损失，其中番茄产量损失高达80%以上。可供选择的控制方法有限，而农业中一个新出现的问题使情况更加恶化：夜间气温升高的影响。这一前所未有的趋势给农作物带来了严峻的挑战。这项工作更广泛的未来影响包括开发新的方法来检查宿主-病原体相互作用以及它们如何受到外部条件的影响。这将导致鉴定出更能适应非生物和生物胁迫的植物品系。重要的是，通过阐明WNT下寄生虫对这些植物的反应背后的分子生物学，本研究将超越仅仅识别相关的宿主基因，从而为这些基因改变线虫生物学的机制提供新的见解。除了了解植物外，还了解线虫为直接针对寄生虫进行作物改良铺平了道路。这个项目的目标与遗传学的一个首要问题一致：识别影响个体如何对环境做出反应的DNA变异。在这里，“个体”和“环境”的概念是复杂的。一个物种的DNA变异将被确定，与外部环境条件相结合，影响另一个相互作用的物种的反应。考虑的环境背景是夜间温度升高（WNT），这是一个关键的、高度相关的、当前的环境问题。由栽培品系和野生品系杂交而来的遗传变异的番茄植株将被遗传同质的寄生线虫感染。还将对未感染的植株进行对照试验。这些早期、晚期和对照实验将在两种温度制度下进行：正常夜间温度和WNT。对于每种处理组合，将收集与感染和植物健康相关的表型，以及植物和线虫的基因表达数据。通过这种设计，番茄基因组中的DNA变异与线虫和植物的分子反应之间的联系将被建立起来，WNT对这些联系的影响将通过一系列遗传作图实验被揭示。利用以这种方式确定的联系，随后可以推断出更复杂的基因型-表达-表型途径，为植物-寄生虫相互作用对WNT的反应提供分子生物学的详细视图。它还将确定有希望的候选基因，这些基因将在功能上得到验证。所有项目成果都将通过出版物和在长期存储库中存放数据和资源的方式向公众开放。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

An organism’s ability to respond to its environment is fundamental to its survival. When the organism of interest is involved in a host-pathogen interaction, “the environment” becomes complex, including includes not only external forces, but also the conditions imposed by the interacting partner. There are also two genomes at play, each of which affects the behavior of both organisms. In addition, external environmental forces impose additional pressures, and each genome can affect how both partners respond. This project examines the role the host genome plays in altering behavior of both host and pathogen under environmental stress. It leverages an agriculturally relevant system, nematode infection of tomato. Parasitic nematodes are responsible for around $125 billion in annual crop loss worldwide with yield loss upwards of 80% for tomato. Limited control options are available, and the situation is exacerbated by an emerging concern in agriculture: the effect of warming nighttime temperatures (WNT). This unprecedented trend is causing critical challenges to crops. Broader, future impacts of this work include the development of novel approaches to examine host-pathogen interactions and how they are affected by external conditions. This then will lead to the identification of plant lines that are more resilient to both abiotic and biotic stresses. Importantly, by elucidating the molecular biology behind the parasite response to those plants under WNT, this study will go beyond merely identifying relevant host genes to contribute new insight into the mechanisms by which those genes alter the nematode biology. Understanding the nematode in addition to the plant paves the way towards targeting the parasite directly for crop improvement.The goals of this project align with an overarching concern in genetics: to identify DNA variants that influence how individuals respond to their environment. Here, the concept of “individuals” and “environment” are complex. DNA variants in one species will be identified that, in tandem with external environmental conditions, affect how another, interacting species responds. The environmental context considered is warming nighttime temperatures (WNT), a critical, highly relevant, and current environmental concern. Genetically variable tomato plants derived from a cross between a cultivated line and a wild line will be infected with a genetically homogeneous strain of parasitic nematodes. A control experiment will also be performed with uninfected plants. These early, late, and control experiments will be carried out under two temperature regimes: normal nighttime temperatures and WNT. For each treatment combination, phenotypes related to infection and plant health will be collected, along with gene expression data for both plant and nematode. With this design, connections between DNA variants in the tomato genome and molecular responses of the nematode as well as the plant will be made, and the effect of WNT on these connections will be uncovered through via a series of genetic mapping experiments. Leveraging the connections identified in this way, more complex genotype-expression-phenotype pathways can subsequently be inferred, providing a detailed view of the molecular biology of the plant-parasite interaction response to WNT. It will also pinpoint promising candidate genes, which will be functionally validated. All project outcomes will be made publicly accessible through publications and deposition of data and resources in long-term repositories.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.