RESEARCH-PGR: Atomic Numbers: Identifying the conserved genes driving element accumulation in plants

元素是物质的基本组成部分，不能在化学上相互转换。它们的获取和利用对所有生命都是必不可少的。然而，许多参与元件获得过程的基因是未知的。在这个提议中测试的假设是，潜在的元件获取基因可以通过使用它们的进化守恒来检测。本研究使用来自5个不同物种（模式植物拟南芥、玉米、高粱、大豆和水稻）的植物遗传数据集来鉴定基因组保守区域中直接元素积累的基因。这些基因在拟南芥、玉米和高粱中的突变体将被鉴定和表征，以确定元素积累的机制。将表征实验的结果与预测进行比较将使比较方法得到改进。该方法还将扩展到利用来自每个物种不同环境的数据，允许探索任何生物体中基因和环境之间的相互作用。这种方法可以扩展到所有可以测序的物种，包括其他作物。元素平衡机制的知识是理解植物适应的关键，也是减少作物肥料需求的必要条件。为了扩大科学家群体，我们将把生物信息学和遗传学研究纳入本科课堂，让本科生进入实验室，为中学生开展课外活动，并为科学学员和研究界制作播客。元素的获取和利用是所有细胞生命代谢的基础。植物改变它们的代谢和生理以适应元素有效性的许多倍差异。先前的研究使用了5个物种元素积累的全基因组关联研究（GWAS），并确定，在这些数量性状位点的置信区间内，同源基因的存在频率比预期的要高。为了验证基因功能的预测，本项目将分析拟南芥、高粱和玉米序列索引突变群体中功能缺失的等位基因对元素谱的影响。在GWAS实验中的同源基因中，可能涉及元素运输和该过程的转录调节因子。该项目将探索候选基因子集的生物学，以确定它们控制的细胞生物学和基因表达方面。该项目将根据这些基因的功能注释（如转录因子、转运蛋白）对其进行机制研究。同源方法不仅允许跨物种组合多个GWAS实验，而且可以创建影响环境偶然或种群特异性变异的同源物列表。该项目将扩展该方法，将跨多种环境和多种人口类型的实验纳入基于正字法的方法。这将扩展方法，允许未来探索元素稳态中基因与环境的相互作用，并提高定量遗传实验中致病基因的准确鉴定。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。

Elements are building blocks of matter that cannot be chemically interconverted. Their acquisition and utilization are essential for all life. Yet, many genes involved in the process of element acquisition are unknown. The hypothesis tested in this proposal is that genes underlying element acquisition can be detected by using their evolutionary conservation. This research uses plant genetic datasets from five diverse species (the model plant Arabidopsis, maize, sorghum, soybean, and rice) to identify genes in conserved regions of genomes that direct elemental accumulation. Mutants in these genes in Arabidopsis, maize and sorghum will be identified and characterized to determine the mechanisms of element accumulation. Comparing the results of the characterization experiments to the predictions will enable refinement of the comparative approach. The approach will also be extended to utilize data from different environments in each species permitting exploration of interactions between genes and environments in any organism. This approach is extendable to all species that can be sequenced, including other crops. Knowledge of the mechanisms of elemental homeostasis is critical to understanding plant adaptation and necessary to reduce fertilizer requirements in crops. To expand the community of scientists, we will integrate our bioinformatics and genetics research into undergraduate classrooms, bring undergraduates into the lab, conduct after-school activities for middle schoolers, and produce a podcast for scientific trainees and the research community.Elemental acquisition and utilization are fundamental to metabolism in all cellular life. Plants change their metabolism and physiology to accommodate many-fold differences in element availability. Previous work used genome-wide association studies (GWAS) of elemental accumulation across five species and determined that, more often than expected, orthologous genes are present within confidence intervals of these quantitative trait loci. To validate the predictions of gene function, this project will analyze loss-of-function alleles from sequence-indexed mutant populations of Arabidopsis, sorghum, and maize for effects on elemental profiles. Among the orthologs in the GWAS experiments are genes likely involved in elemental transport and transcriptional regulators of this process. This project will explore the biology of a subset of candidate genes to determine the aspects of cell biology and gene expression they control. The project will carry out mechanistic investigations of these genes consistent with their functional annotation (e.g., transcription factor; transporter). The orthologous approach not only permits the combining of multiple GWAS experiments across species, but also can create lists of orthologs affecting environmentally contingent or population-specific variation. The project will extend the method to incorporate experiments across multiple environments and multiple population types into the orthology-based approach. This will extend the approach to permit future exploration of gene-by-environment interactions in elemental homeostasis and improve the accurate identification of causative genes from quantitative genetic experiments.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.