A Single-Cell Map of Corn’s Root Identifies a Cellular Diversity Regulator

Plants add additional cell layers to help them endure climate stressors like drought and flooding, according to a new study that uses revolutionary single-cell profiling techniques. The study focuses on corn, a globally significant crop, in order to build a cell-by-cell map of the plant’s root system, which handles drought stress and collects nutrients and fertilizer from the soil.

“We discovered how corn expands its cortex tissue, which makes up much of the crop’s root system. Adding layers to the cortex tissue is a key evolutionary feature that generates ways for plants to tolerate drought and flooding and improve nutrient uptake,” said Kenneth Birnbaum, a professor in New York University’s Department of Biology and Center for Genomics and Systems Biology and the senior author of the paper, which appears in the journal Science.

“These traits will be critical targets to allow plants to withstand global warming and reduce the carbon footprint of crops,” added Birnbaum, whose lab at NYU led the project in collaboration with researchers at Cold Spring Harbor Laboratory and the University of Pennsylvania.

The researchers used cell-wall digesting enzymes to break apart the corn root into single, free-floating cells in order to construct a per-cell map of the root. Using tiny droplet-based single cell-sequencing techniques, they were able to evaluate the mRNA content of individual cells, differentiating molecular traits that lead to specific types of specialized cells.

The cells were then traced back to their original locations in the corn root, similar to putting together a 10,000-piece jigsaw puzzle without a guide. To solve the conundrum, the researchers utilized fluorescent dyes that penetrated root tissues at varying depths to label and isolate different layers, similar to how onion layers are separated, providing gene landmarks to map single cells.

We discovered how corn expands its cortex tissue, which makes up much of the crop’s root system. Adding layers to the cortex tissue is a key evolutionary feature that generates ways for plants to tolerate drought and flooding and improve nutrient uptake.

Kenneth Birnbaum

“This second layer of information essentially gave us the puzzle box that allowed us to precisely map cells to their appropriate location in order to recreate a 3D model of gene expression throughout the entire corn root,” said Carlos Ortiz Ramirez of the NYU Center for Genomics and Systems Biology and UGA Laboratorio Nacional de Genómica para la Biodiversidad in Mexico, who was the first author of the study.

The new corn root map shows previously unknown cellular specialization in the root’s cortex. The cortex is especially essential because it makes up the majority of the early corn root and contains over ten layers.

Furthermore, the cortical cellular subtypes are crucial for features that aid crop plants in dealing with environmental stresses. The inner cortical layer, for example, is where symbiotic fungus exchange nutrients with the plant and improved collaboration could help reduce agriculture’s carbon footprint.

The brain’s middle layers form air tunnels that allow gas exchange during flooding, and on-demand cortex enlargement can prevent water loss during drought stress.

“Using our 3D model of the corn root, we mapped out four distinct cortex layer signatures that could provide important genetic targets for further improvement in symbiosis, flooding, and drought,” said Ortiz Ramirez.

Furthermore, the team discovered indications about how corn could develop the extra layers of cortex in the new root map. SHORT ROOT (SHR), a crucial gene regulator with a function that is consistent among plants, was at an unusual position that was distinct from other plants with only one layer of cortex.

SHR was one of the first transcription factors discovered to transfer from cell to cell in Arabidopsis, a small flowering plant frequently used as a model organism in plant biology. This allowed inner cell types to provide instructions to middle layers to build new tissue. As a result, SHR acts as a local organizer, driving root tissues to form a core pattern.

In corn, however, the single-cell map revealed that SHR had moved to a new location exactly next to the several layers of cortex, providing a perfect “jumping off” point for expanding the multiple layers of cortex. SHR protein was shown to be hypermobile, traveling not just one layer but numerous layers through the cortex, according to the researchers.

Furthermore, mutations that disrupted SHR function in corn and its related foxtail millet resulted in a significant reduction in the number of cortical layers. This indicates how SHR maintained its basic function of expanding tissue layers and establishing new cell identities while shifting its position to allow corn to adapt with environmental challenges.

“Identifying SHR has a key regulator of cortex expansion is an important first step,” said Birnbaum. “Moving forward, tweaking these regulators could provide tools to alter the number of cortex layers or subtypes that could enhance their ability to withstand climate stressors like drought, or improve nitrogen uptake, allowing plants to use less fertilizer or grow in nutrient-poor soil.”

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