RESEARCH-PGR: Single-cell Transcriptomic Analyses of Shoot Meristem Ontogeny and Function

由于被称为茎分生组织的植物特异性干细胞的活性和增殖，构成成年玉米植株的绝大多数细胞、组织和器官都是在胚胎阶段很久之后形成的。茎分生组织产生器官初始细胞，这些细胞在生长发育过程中经历特定的基因表达模式，形成成熟植物体中复杂的细胞和组织模式。通过这种方式，芽部分生组织在胚胎阶段产生，并产生玉米芽部的所有营养结构。基因组技术的新进展现在可以分析在玉米发育的各个阶段获得的单个细胞内的基因表达，这有望对这种具有重要农学意义的作物植物的茎发育的遗传和基因组机制产生新的见解。胚形成芽分生组织，芽分生组织形成器官。本研究将研究在芽发育过程中单个细胞的特定基因表达模式，从芽分生组织形成之前、期间和之后的早期胚胎阶段，以及在营养器官（如叶、茎和枝）形成过程中。这些研究将有助于我们进一步了解玉米营养芽形态形成的细胞特异性机制，以及芽分生组织的结构和功能。该项目将生成公开发布的原始数据，同时为研究生、在科学领域代表性不足的本科生和被关押在纽约州北部监狱的人提供科学培训和教学框架。玉米茎部的模式形成始于胚胎发生的早期，并发生在多个尺度上，从单个细胞和组织到植物内的所有器官。最近的进展现在可以在单细胞分辨率上分析玉米图案的形成。玉米茎尖分生组织（SAM）是一个干细胞库，负责所有茎源器官的发育。本研究将从发育中的玉米茎的单个细胞中获得转录组学数据，并将破译细胞位置、细胞信号、罕见细胞类型和随机性对单细胞基因表达的影响。单细胞转录组学数据将从关键的个体发生阶段获得，从胚胎轴的建立，到SAM和茎的第一个侧面器官的形成，到幼苗SAM和叶片原基的发育，以及最终产生穗的侧枝分生组织的形态发生。同样，该项目将在单细胞分辨率下研究营养SAM特定功能域内的单细胞转录组网络，以及野生型和突变型叶片外生缺陷的茎尖，以研究在茎个体发育过程中玉米茎型形成的转录组网络。这些研究将提供科学训练和原始数据的发布，并将接待少数民族本科生和高中生进行暑期研究实习。最后，作为康奈尔监狱教育项目的一部分，斯坎伦实验室将继续在埃尔米拉惩教设施进行教学。该奖项由植物基因组研究计划和综合有机体系统部的植物、真菌和微生物发育机制计划共同资助。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。

The vast majority of cells, tissues and organs that comprise the adult maize plant are formed long after embryonic stages, due to the activity and proliferation of plant-specific stem cells called shoot meristems. Shoot meristems generate organ initial cells, which undergo specific patterns of gene expression during growth and development to give rise to the complex pattern of cells and tissues found in the mature plant body. In this way, shoot meristems arise during embryonic stages and generate all the vegetative structures of the maize shoot. New advances in genomic technology now enable analyses of gene expression within individual cells obtained at all stages of maize development, which promises to generate novel insight into the genetic and genomic mechanisms of shoot development in this agronomically important crop plant. Embryos make shoot meristems and shoot meristems make organs. This study will examine the specific patterns of gene expression in individual cells throughout shoot development, from early embryonic stages before, during and after shoot meristem initiation, and during formation of vegetative organs such as leaves, stems, and branches. These studies will advance our understanding of the cell-specific mechanisms underlying pattern formation in the maize vegetative shoot, and of the structure and function of shoot meristems. This project will generate original data for public release, while providing a framework for scientific training and teaching of graduate students, undergraduates who are under-represented in science, and people incarcerated in upstate New York State prisons.Pattern formation in the maize shoot begins early in embryogenesis and occurs across multiple scales, from individual cells and tissues, to all the organs within the plant. Recent advances now enable analyses of maize pattern formation at single-cell resolution. The maize shoot apical meristem (SAM) is a stem cell reservoir responsible for the development of all shoot-derived organs. This study will generate transcriptomic data from individual cells in the developing maize shoot, and will decipher the effects of cell position, cell signaling, rare cell types, and stochasticity on single-cell gene expression. Single-cell transcriptomic data will be obtained from key ontogenetic stages ranging from the establishment of embryonic axes, to formation of the SAM and the first lateral organs of the shoot, to the development of the seedling SAM and foliar leaf primordia, and during morphogenesis of the lateral branch meristems that will ultimately give rise to ears. Likewise, this project will investigate the single-cell transcriptomic networks within specific, functional domains of the vegetative SAM, and in wild type versus mutant shoot apices defective in leaf outgrowth to investigate the transcriptomic networks underlying maize shoot pattern formation throughout shoot ontogeny, at single-cell resolution. These studies will provide scientific training and release of original data, and will host minority undergraduate and high school students for summer research internships. Lastly, the Scanlon lab will continue teaching at the Elmira Correctional Facility, as part of the Cornell Prison Education Program.This award was co-funded by the Plant Genome Research Program and the Plant, Fungal and Microbial Developmental Mechanisms Program in the Division of Integrative Organismal Systems.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.