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

研究-PGR：原子序数：识别驱动植物元素积累的保守基因

• 批准号: 2309932
• 负责人: Ivan Baxter
• 金额: $ 250万
• 依托单位: Donald Danforth Plant Science Center
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-06-01 至 2027-05-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2309932&HistoricalAwards=false
• 关键词: RESEARCH; PGR; Atomic; Numbers; Identifying

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.

元素是物质的组成部分，不能通过化学反应相互转化。它们的获得和利用对所有生命都是必不可少的。然而，许多参与元素获取过程的基因是未知的。在这个建议中测试的假设是，基因的元素获取可以通过使用它们的进化保守性来检测。这项研究使用来自五个不同物种（模式植物拟南芥，玉米，高粱，大豆和水稻）的植物遗传数据集来识别基因组保守区域中指导元素积累的基因。将对拟南芥、玉米和高粱中这些基因的突变体进行鉴定和表征，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，以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。了解元素稳态的机制对于理解植物的适应性是至关重要的，并且对于减少作物的肥料需求是必要的。为了扩大科学家的社区，我们将把我们的生物信息学和遗传学研究融入本科生课堂，把本科生带到实验室，为中学生开展课后活动，并为科学培训生和研究社区制作播客。元素的获取和利用是所有细胞生命代谢的基础。植物改变它们的新陈代谢和生理以适应元素可用性的许多倍差异。以前的工作使用全基因组关联研究（GWAS）的元素积累在五个物种，并确定，更经常比预期的，orthopathic基因存在于这些数量性状位点的置信区间内。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的功能丧失等位基因对元素配置文件的影响。在GWAS实验中的直系同源物中，有可能参与元素转运和该过程的转录调节因子的基因。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）。直向同源方法不仅允许跨物种的多个GWAS实验的组合，而且可以创建影响环境偶然性或群体特异性变异的直向同源物的列表。该项目将扩展该方法，将跨多个环境和多个人群类型的实验纳入基于直系亲属的方法。这将扩展的方法，使未来的探索基因与环境的相互作用，在元素的稳态和提高准确识别致病基因的定量遗传experiments.This奖项反映了NSF的法定使命，并已被认为是值得通过评估使用基金会的智力价值和更广泛的影响审查标准的支持。