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作物之一，在美国的粮食生产和经济中发挥着重要作用。玉米的生产能力和生长健壮依赖于植物内的生长中心，称为分生组织。这项研究详细研究了两种分生组织类型-花序分生组织，最终产生所有可食用的谷物，和根分生组织，从土壤中获取营养和水分。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共享功能特性。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，如分生组织，一次一个细胞，以发现特定细胞中哪些基因是活跃的。在对根和茎分生组织进行逐个细胞的分析之后，该项目将使用计算技术从单个细胞中重建每个分生组织，就像组装瓷砖马赛克一样。该项目将使用另一套计算技术来确定不同分生组织细胞之间基因调控的共同方面，类似于在马赛克中找到共同模式。从生物学的角度来看，这些共同的模式代表了一组核心的、保守的功能，这些功能控制着重要的性状，如生长。育种者可以利用这些核心基因调控因子的知识来改善作物的性状，如地上部的谷物产量和根部的抗旱性。该项目还将培训这些新兴技术的初级研究人员。根和茎分生组织传统上是分开研究的，但它们的组织结构实际上是相似的。在根和茎分生组织中，多能干细胞与干细胞龛内的“组织者”细胞（根中的静止中心和茎中的组织中心）来回传递信号。此外，它们还具有许多共同或旁系同源的基因调控因子。该项目的前提是，茎和根分生组织的详细解剖将确定控制分生组织的组织和维护的关键共享组件。此外，虽然正向遗传学已经发现了许多关键的调控因子，但遗传冗余一直是更全面了解分生组织的障碍。该项目利用了单细胞RNA-seq的进步，现在可以逐个细胞重建几种不同类型的芽和根分生组织。计算分析将被用来映射等效细胞之间的分生组织使用的MetaNeighbor的方法，占潜在的旁系同源基因与同源功能的分生组织。机器学习方法将用于生成在许多分生组织或分生组织子集中共享的遗传电路的模型。我们的目标是确定共同的电路（和他们潜在的冗余组件）在分生组织，可以代表一个核心电路需要维护的分生组织。CRISPR基因敲除将用于测试核心分生组织电路模型，解决guideRNA构建的冗余问题，同时靶向多个旁系同源物。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.