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

元素是无法进行化学相互转化的物质的组成部分。它们的获取和利用对所有生命都是必不可少的。然而，许多参与元素获得过程的基因还不清楚。在这项提议中检验的假设是，通过使用它们的进化保守性可以检测到潜在的元素获取的基因。这项研究使用了来自五个不同物种(模式植物拟南芥、玉米、高粱、大豆和水稻)的植物遗传数据集，以确定基因组保守区域中指导元素积累的基因。这些基因在拟南芥、玉米和高粱中的突变体将被鉴定和鉴定，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，将能够改进比较方法。该方法还将扩展到利用来自每个物种不同环境的数据，从而探索任何生物体中基因和环境之间的相互作用。这种方法可以推广到所有可以测序的物种，包括其他作物。对元素动态平衡机制的了解对于了解植物的适应性和减少作物的化肥需求是至关重要的。为了扩大科学家群体，我们将把我们的生物信息学和遗传学研究整合到本科课堂，把本科生带进实验室，为中学生开展课外活动，并为科学实习生和研究界制作播客。元素的获取和利用是所有细胞生命新陈代谢的基础。植物改变它们的新陈代谢和生理，以适应元素可利用性的许多倍的差异。之前的工作使用了五个物种的元素积累的全基因组关联研究(GWAS)，并确定在这些数量性状基因座的可信区间内存在直源基因的情况比预期的要多。为了验证基因功能的预测，该项目将分析拟南芥、高粱和玉米的序列索引突变群体中功能丧失的等位基因对元素谱的影响。在GWAS实验中的同源基因中，有可能参与这一过程的元素运输和转录调节的基因。这个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的方面。该项目将对这些基因进行与其功能注释一致的机制研究(例如，转录因子；转运蛋白)。同源方法不仅允许跨物种的多个GWAS实验的组合，而且还可以创建影响环境条件或特定于种群的变异的同源列表。该项目将扩展该方法，将跨多个环境和多个种群类型的实验纳入基于正畸的方法。这将扩展方法，允许未来探索元素动态平衡中基因与环境的相互作用，并提高从定量基因实验中准确识别致病基因。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.