RESEARCH-PGR: Uncovering the molecular mechanisms that integrate nutrient and water dose sensing and impact crop production

研究-PGR：揭示整合养分和水剂量传感并影响作物生产的分子机制

• 批准号: 1840761
• 负责人: Gloria Coruzzi
• 金额: $ 240.3万
• 依托单位: New York University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-06-01 至 2025-05-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1840761&HistoricalAwards=false
• 关键词: RESEARCH; PGR; Uncovering; molecular; mechanisms

Two resources critical to plant growth, Nitrogen (N) and Water (W), are limited in soils globally, creating marginal soils that are agriculturally unproductive. To engineer or breed crop varieties that can thrive in marginal environments, it must first be understood how plants sense and integrate responses to Nitrogen (N) and Water (W). Detecting the genes and gene regulatory mechanisms plants rely on to sense and respond to multiple environmental inputs is at the leading edge of efforts to adapt crops to a changing climate. Thus, this award resides in Pasteur's quadrant, the scientific space where fundamental scientific discoveries have applied outcomes. The researchers will discover the molecular mechanisms plants rely on to perceive and integrate the abiotic signals N and W using mutant/transgenic analysis on the genetically tractable model plant Arabidopsis thaliana. Initial testing in Arabidopsis will prioritize candidate genes to test in rice. This discovery will be exploited to engineer or breed rice adapted to low-N low-W marginal soils. The research will be linked to the International Rice Research Institute in the Philippines (IRRI), which is the primary source of new breeding material for stress-prone regions of Asia. Outcomes of this project have a high probability of impact through immediate consideration for deployment into the IRRI trait development pipeline for marginal soil environments. This project offers a unique application of genomics and systems biology approaches to improve crop performance under stress in translating network knowledge from well-studied models to crops. While efforts have focused on how plants signal either N or W status, how plants integrate these two abiotic signals remains unexplored. Whether organisms respond to changes in absolute nutrient amount (moles) vs. its concentration in water (molarity) is particularly relevant in agriculture, as soil drying can alter nutrient concentration, without changing its absolute amount. To compare effects of amount vs. concentration, rice was exposed to a factorial matrix varying nitrogen dose (N) and water (W) in range of combinations, and transcriptome and phenotype responses quantified. Using linear models, researchers identified distinct dose responses to either N-moles, W-volume, N-molarity (N/W), or their synergistic interaction (NxW). Importantly, genes whose expression is best explained by N-dose and W interactions (N/W or NxW) were associated with crop outcomes in field trials. The goal of this grant is to uncover the molecular basis for these N-by-W interactions that affect crop yield. To this end, a collaborative effort between New York University, University of Wisconsin-Madison, and the International Rice Research Institute (IRRI) in the Philippines proposes to discover the genes responsible for the integration of N and W inputs in the genetically tractable model plant Arabidopsis thaliana and in rice, one of the world's most important crops. This project will use a multidisciplinary approach that combines genomics, bioinformatics, statistical modeling, and plant physiology to understand how plant genomes sense and integrate N and W signals to optimize plant biomass and grain production.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.

对植物生长至关重要的两种资源，氮（N）和水（W），在全球范围内都受到土壤的限制，从而产生了农业上不生产的边缘土壤。为了设计或培育能够在边缘环境中茁壮成长的作物品种，首先必须了解植物如何感知和整合对氮（N）和水（W）的反应。检测植物所依赖的基因和基因调控机制来感知和响应多种环境输入，是使作物适应气候变化的前沿工作。因此，该奖项属于巴斯德象限，即基础科学发现应用成果的科学空间。研究人员将发现植物依赖于感知和整合非生物信号N和W的分子机制，使用遗传上易处理的模式植物拟南芥的突变/转基因分析。在拟南芥中的初步测试将优先考虑在水稻中测试的候选基因。这一发现将被用来设计或培育适应低氮低水边际土壤的水稻。该研究将与菲律宾国际水稻研究所（IRRI）联系起来，该研究所是亚洲易受压力地区新育种材料的主要来源。该项目的结果有很高的可能性，通过立即考虑部署到IRRI性状发展管道边缘土壤环境的影响。该项目提供了基因组学和系统生物学方法的独特应用，以改善作物在压力下的表现，将网络知识从经过充分研究的模型转化为作物。虽然努力集中在植物如何信号N或W状态，植物如何整合这两个非生物信号仍然没有探索。生物体是否对绝对营养量（摩尔）与其在水中的浓度（摩尔浓度）的变化做出反应在农业中特别相关，因为土壤干燥可以改变营养浓度，而不会改变其绝对量。为了比较量与浓度的影响，将水稻暴露于在组合范围内改变氮剂量（N）和水（W）的析因矩阵，并量化转录组和表型响应。使用线性模型，研究人员确定了对N-摩尔，W-体积，N-摩尔浓度（N/W）或其协同作用（NxW）的不同剂量反应。重要的是，基因的表达是最好的解释N-剂量和W的相互作用（N/W或NxW）与作物的田间试验结果。 这项资助的目标是揭示这些影响作物产量的N-W相互作用的分子基础。 为此，纽约大学、威斯康星大学麦迪逊分校和菲律宾的国际水稻研究所（IRRI）之间的合作努力提出了在遗传上易于处理的模式植物拟南芥和世界上最重要的作物之一水稻中发现负责N和W输入整合的基因。该项目将采用多学科方法，结合基因组学、生物信息学、统计建模和植物生理学，了解植物基因组如何感知和整合N和W信号，以优化植物生物量和谷物产量。该奖项反映了NSF的法定使命，并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，被认为值得支持。

项目成果

Water impacts nutrient dose responses genome-wide to affect crop production

• DOI: 10.1038/s41467-019-09287-7
• 发表时间: 2019-03
• 期刊: Nature Communications
• 影响因子: 16.6
• 作者: Joseph Swift;Mark Adame;D. Tranchina;A. Henry;G. Coruzzi

Forgetful Forests: Data Structures for Machine Learning on Streaming Data under Concept Drift

• DOI: 10.3390/a16060278
• 发表时间: 2023-05
• 期刊: Algorithms
• 影响因子: 2.3
• 作者: Zhehu Yuan;Yinqi Sun;D. Shasha

Molecular mechanisms underlying nitrate responses in plants

• DOI: 10.1016/j.cub.2022.03.022
• 发表时间: 2022-05
• 期刊: Current Biology
• 影响因子: 9.2
• 作者: Liliana Lamig;S. Moreno;J. M. Álvarez;R. Gutiérrez