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

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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.