RESEARCH-PGR: Comparative developmental dynamics: single-cell analysis of maize meristem trajectories

研究-PGR：比较发育动力学：玉米分生组织轨迹的单细胞分析

• 批准号: 1934388
• 负责人: Kenneth Birnbaum
• 金额: $ 435.7万
• 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: 2019-11-01 至 2024-10-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1934388&HistoricalAwards=false
• 关键词: RESEARCH; PGR; Comparative; developmental; dynamics

Maize is one of the most important crops in the United States and plays a major role in the country's food production and its economy. The ability of maize to produce and grow robustly is dependent on growth centers within the plant known as meristems. This study examines two meristem types in detail -- the inflorescence meristem, which ultimately produces all the edible grain, and the root meristem, which forages nutrients and water from the soil. While these meristems are located at opposite ends of the plant, they express many of the same genes and share functional properties. This project takes advantage of new techniques, developed in medical research, called single-cell RNA-sequencing that can dissect an entire organ, like a meristem, one cell at a time, to find which genes are active in a given cell. After such cell-by-cell analysis in root and shoot meristems, the project will use computational techniques to reconstruct each meristem from individual cells, like assembling a tile mosaic. The project will use another set of computational techniques to identify common aspects of gene regulation among cells of the different meristems, analogous to finding common patterns across mosaics. In biological terms, these common patterns represent a core, conserved set of functions that control important traits such as growth. Knowledge of such core gene regulators could be used by breeders to improve traits like grain yield in the shoot and drought resistance in the root. The project will also train junior researchers in these emerging techniques.Root and shoot meristems are traditionally studied separately, but aspects of their organization are in fact similar. In both root and shoot meristems, pluripotent stem cells signal back and forth with 'organizer' cells (the quiescent center in the root and the organizing center in the shoot) within the stem cell niche. In addition, they share a number of common or paralogous gene regulators. The premise of the project is that a detailed dissection of shoot and root meristems will identify key shared components that control meristem organization and maintenance. In addition, while forward genetics has uncovered many key regulators, genetic redundancy has been a barrier to a more comprehensive understanding of meristems. The project takes advantage of advances in single-cell RNA-seq that now permit a cell-by-cell reconstruction of several different types of shoot and root meristems. A computational analysis will be employed to map equivalent cells among the meristems using the MetaNeighbor approach, accounting for potentially paralogous genes with homologous function across meristems. Machine learning approaches will be used to generate models of the genetic circuitry shared across many or a subset of meristems. The goal is to identify common circuits (and their potentially redundant components) across meristems that could represent a core circuitry needed for the maintenance of meristems. CRISPR knockouts will then be used to test the models of core meristem circuitry, addressing redundancy with guideRNA constructs that target multiple paralogs at once.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.

玉米是美国最重要的农作物之一，在该国的粮食生产和经济中发挥着重要作用。玉米生产和强劲生长的能力取决于植物内称为分生组织的生长中心。这项研究详细研究了两种分生组织——花序分生组织（最终产生所有可食用谷物）和根分生组织（从土壤中获取养分和水）。虽然这些分生组织位于植物的两端，但它们表达许多相同的基因并具有相同的功能特性。该项目利用了医学研究中开发的新技术，称为单细胞 RNA 测序，可以解剖整个器官，例如分生组织，一次一个细胞，以找出给定细胞中哪些基因处于活跃状态。在对根和芽分生组织进行逐个细胞分析后，该项目将使用计算技术从单个细胞重建每个分生组织，就像组装瓷砖马赛克一样。该项目将使用另一组计算技术来识别不同分生组织细胞之间基因调控的共同方面，类似于寻找嵌合体的共同模式。从生物学角度来看，这些常见模式代表了一组控制重要性状（例如生长）的核心、保守的功能。育种者可以利用此类核心基因调控因子的知识来改善芽的谷物产量和根的抗旱性等性状。该项目还将培训初级研究人员掌握这些新兴技术。根和芽分生组织传统上是分开研究的，但它们的组织实际上是相似的。在根和芽分生组织中，多能干细胞与干细胞生态位内的“组织者”细胞（根中的静止中心和芽中的组织中心）来回发出信号。此外，它们共享许多共同或旁系同源的基因调节因子。该项目的前提是对芽和根分生组织的详细解剖将确定控制分生组织组织和维护的关键共享组件。此外，虽然正向遗传学发现了许多关键的调控因子，但遗传冗余一直是更全面地了解分生组织的障碍。该项目利用了单细胞 RNA 测序技术的进步，现在可以对几种不同类型的芽和根分生组织进行逐细胞重建。将使用 MetaNeighbor 方法进行计算分析来绘制分生组织之间的等效细胞图，从而解释在分生组织之间具有同源功能的潜在旁系同源基因。机器学习方法将用于生成许多分生组织或分生组织子集共享的遗传电路模型。目标是识别分生组织中的常见电路（及其潜在的冗余组件），这些电路可以代表维持分生组织所需的核心电路。然后，CRISPR 敲除将用于测试核心分生组织电路模型，通过同时针对多个旁系同源物的guideRNA构建体解决冗余问题。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

A pan-grass transcriptome reveals patterns of cellular divergence in crops

• DOI: 10.1038/s41586-023-06053-0
• 发表时间: 2023-05-10
• 期刊: NATURE
• 影响因子: 64.8
• 作者: Guillotin, Bruno;Rahni, Ramin;Birnbaum, Kenneth D.
• 通讯作者: Birnbaum, Kenneth D.