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

玉米是美国最重要的作物之一，在该国的粮食生产和经济中发挥着重要作用。玉米生产和健壮生长的能力依赖于植物内部被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类型——花序分生组织，它最终产生所有可食用的谷物，而根分生组织，它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。这个项目利用了医学研究中发展起来的新技术，称为单细胞rna测序，它可以解剖整个器官，如分生组织，一次一个细胞，以发现在给定细胞中哪些基因是活跃的。在对根和芽的分生组织进行逐个细胞的分析后，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。该项目将使用另一套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，类似于在马赛克中寻找共同模式。在生物学术语中，这些共同模式代表了一组核心的、保守的功能，这些功能控制着诸如生长等重要特征。这些核心基因调控的知识可以被育种者用来提高诸如茎部产量和根部抗旱性等性状。该项目还将培训这些新兴技术的初级研究人员。根和芽的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。在根和茎分生组织中，多能干细胞与干细胞生态位内的“组织者”细胞（根的静止中心和茎的组织中心）相互传递信号。此外，它们有许多共同的或同源的基因调控因子。该项目的前提是对茎和根分生组织的详细解剖将确定控制分生组织和维持的关键共享成分。此外，虽然正向遗传学已经发现了许多关键的调控因子，但遗传冗余一直是对分生组织更全面理解的障碍。该项目利用了单细胞rna测序技术的进步，现在可以逐细胞重建几种不同类型的茎和根分生组织。计算分析将使用metanneighbor方法来绘制分生组织之间的等效细胞，考虑到分生组织中具有同源功能的潜在同源基因。机器学习方法将用于生成在许多或一部分分生组织中共享的遗传电路模型。目标是识别跨分生系统的公共电路（及其潜在的冗余组件），这些电路可以代表维护分生系统所需的核心电路。CRISPR敲除将被用于测试核心分生系统电路的模型，解决guideRNA结构的冗余问题，该结构同时针对多个类似物。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

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.