Collaborative Research: Assessing the connections between genetic interactions, environments, and phenotypes in Arabidopsis thaliana

合作研究：评估拟南芥遗传相互作用、环境和表型之间的联系

• 批准号: 2210431
• 负责人: Shin-Han Shiu
• 金额: $ 90万
• 依托单位: Michigan State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2210431&HistoricalAwards=false
• 关键词: Collaborative; Research; Assessing; connections; between

Organismal complexity is due in large part to genes working not in isolation but with each other. Knowledge of such interactions will facilitate improving plant productivity and resilience to increasingly extreme conditions. However, studying the impacts of gene interactions on plant traits is challenging for two reasons. First, there can be millions of possible interactions to sieve through. Second, both nature (i.e., genes and gene interactions) and nurture (i.e., the environment) are important. Even when a gene interaction is identified as being important, its relevance is frequently known only for one environment. This project will address these challenges by investigating the question of how nature and nurture jointly impact plant traits. Specifically, interactions between hundreds of pairs of genes in the model plant Arabidopsis will be examined by measuring survival traits under different temperatures. Artificial intelligence-based approaches will be used to measure traits and to build models that predict gene interactions under different environments. These prediction models will also incorporate existing knowledge of interactions among similar genes from non-plant species. The predictions will be tested experimentally and will provide insight into how nature and nurture jointly influence plant survival and fitness. Such insight will facilitate better predictions of gene functions in both model and crop plants and provide candidate genes for engineering productive and resilient plants. Findings from this project will serve as examples illustrating to the scientific community and the public the benefits of integrating experimental and computational approaches. Advances in genetics and genomics have led to an unprecedented understanding of how genotypes connect with phenotypes and the roles of genetic interactions and the environment in controlling phenotype. However, the environmental dependency of gene × gene interactions is frequently not considered, particularly in multicellular species. The goal of this project is to better understand the connection between genotypes and phenotype by assessing the impact of environmental perturbation on genetic interactions and by identifying the genetic components underlying this plasticity in the model plant Arabidopsis thaliana using protein kinase genes as examples. This will be accomplished through phenotyping experiments coupled with computational modeling. First, models predicting genetic interactions specific to an environmental context will be generated through multi-omics data integration and the use of existing genetic interaction data from Arabidopsis and other model species (e.g., yeast and worm) and new experimental data generated from 150–200 pairs of single and double kinase mutants grown in 3–5 different environmental contexts (i.e., temperature regimes), yielding multiple trait values, which will be used to calculate quantitative measures of genetic interactions between gene pairs and the environment. Next, model predictions will be validated using the experimental data, and the results will be used to further refine the models. The refined models will be dissected using model interpretation methods to reveal the molecular features important for specifying context-specific genetic interactions.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.

有机体的复杂性在很大程度上是由于基因不是孤立地工作，而是相互作用的。了解这种相互作用将有助于提高植物生产力和对日益极端条件的适应能力。然而，研究基因相互作用对植物性状的影响具有挑战性，原因有两个。首先，可能有数百万种可能的交互需要筛选。第二，两种性质（即，基因和基因相互作用）和养育（即，环境）很重要。即使一个基因的相互作用被认为是重要的，它的相关性往往是已知的只有一个环境。这个项目将通过调查自然和养育如何共同影响植物性状的问题来解决这些挑战。具体而言，将通过测量不同温度下的存活性状来检查模式植物拟南芥中数百对基因之间的相互作用。基于人工智能的方法将用于测量性状，并建立预测不同环境下基因相互作用的模型。这些预测模型还将结合现有的知识，从非植物物种的类似基因之间的相互作用。这些预测将通过实验进行测试，并将深入了解自然和养育如何共同影响植物的生存和健康。这样的洞察力将有助于更好地预测模型和作物植物中的基因功能，并为工程生产和弹性植物提供候选基因。该项目的研究结果将作为例子，向科学界和公众说明实验和计算方法相结合的好处。遗传学和基因组学的进步使人们对基因型与表型的联系以及遗传相互作用和环境在控制表型中的作用有了前所未有的了解。然而，基因×基因相互作用的环境依赖性往往没有考虑，特别是在多细胞物种。该项目的目标是更好地了解基因型和表型之间的联系，通过评估环境干扰对遗传相互作用的影响，并通过识别基因组件的可塑性，在模式植物拟南芥蛋白激酶基因为例。这将通过表型实验结合计算建模来实现。首先，预测特定于环境背景的遗传相互作用的模型将通过多组学数据整合和使用来自拟南芥和其他模式物种的现有遗传相互作用数据（例如，酵母和蠕虫）和由在3-5种不同环境条件下生长的150-200对单激酶和双激酶突变体产生的新实验数据（即，温度制度），产生多个性状值，这将被用来计算基因对和环境之间的遗传相互作用的定量措施。接下来，将使用实验数据验证模型预测，并将结果用于进一步完善模型。该奖项反映了NSF的法定使命，并已被认为是值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估的支持。

项目成果

Evolutionary analysis of the LORELEI gene family in plants reveals regulatory subfunctionalization

植物 LORELEI 基因家族的进化分析揭示了调控亚功能化

• DOI: 10.1093/plphys/kiac444
• 发表时间: 2022
• 期刊: Plant Physiology
• 影响因子: 7.4
• 作者: Noble, Jennifer A.;Bielski, Nicholas V.;Liu, Ming-Che James;DeFalco, Thomas A.;Stegmann, Martin;Nelson, Andrew D. L.;McNamara, Kara;Sullivan, Brooke;Dinh, Khanhlinh K.;Khuu, Nicholas
• 通讯作者: Khuu, Nicholas

Challenges and opportunities to build quantitative self-confidence in biologists

• DOI: 10.1093/biosci/biad015
• 发表时间: 2023-04-29
• 期刊: BIOSCIENCE
• 影响因子: 10.1
• 作者: Cuddington，Kim;Abbott，Karen C.;White，Easton R.
• 通讯作者: White，Easton R.