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.

Agency
National Science Foundation (NSF)
Institute
Division of Integrative Organismal Systems (IOS)
Type
Standard Grant (Standard)
Application #
1934388
Program Officer
Diane Okamuro
Project Start
Project End
Budget Start
2019-11-01
Budget End
2023-10-31
Support Year
Fiscal Year
2019
Total Cost
$4,356,988
Indirect Cost
Name
New York University
Department
Type
DUNS #
City
New York
State
NY
Country
United States
Zip Code
10012