ScBdLR init 2025

Single-cell transcriptomic landscape of lateral root initiation in Brachypodium distachyon

Author

Affiliation

Corentin Maslard, PhD

UniNE

Abstract

Lateral root (LR) formation is a critical process in shaping plant root architecture, requiring the emerging organ to breach surrounding tissues through tightly regulated cell wall (CW) remodeling. In dicots, this spatial accommodation involves coordinated modification of pectins and hemicelluloses. However, the molecular and structural dynamics underlying this process in monocots, especially grasses with compositionally distinct Type II cell walls, remain largely unexplored. Here, we combine high-resolution immunolocalization and single-cell RNA sequencing to construct a spatiotemporal atlas of CW remodeling during LR development in Brachypodium distachyon, a model grass. Using a comprehensive panel of glycan-directed antibodies, we reveal dynamic and tissue-specific reorganization of hemicellulose and pectin epitopes. Xyloglucan remodeling at the LRP-parent root interface and arabinoxylan modifications in overlying cortical layers suggest coordinated enzymatic activity facilitating primordium emergence. Although overall pectin levels are low, localized deposition and remodeling of rhamnogalacturonan-I and xylogalacturonan in specific LRP and cortical domains point to precise functional roles for distinct pectic substructures. Integration with single-cell transcriptomic data identifies candidate enzymes, including glycosyltransferases, hydrolases, driving these structural transitions. Together, our findings uncover a modular and layered CW remodeling program in a grass species.

Preface

Contributors: Kevin Beland / Thomas Badet / Corentin Maslard / Joop E.M Vermeer

This project is an extension of the research work carried out by the Laboratory of cell and molecular biology, with several publications directly related to this subject, presented below:

• Bellande et al. (n.d.)

• De Jesus Vieira Teixeira (2024)

• Bellande, Teixeira, and Vermeer (2025)

Guide being written

This guide is still incomplete. The complete repository (documentation, data, script, etc.) will be available shortly at this link: https://github.com/cmaslard/ScBdLR_2025.

More informations about my work :

• Personal website
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• Github
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• ORCID
• ResearchGate
• Google Scholar

• X (Twitter)
• HAL
• CV

Licence

This document is made available under the terms of the Licence Creative Commons Attribution - Non Commercial Use - Share Alike 4.0 International.

Package used in this quarto document

library(renv) # install.packages("renv")
library(dplyr)

deps <- renv::dependencies(path = ".", progress = F, quiet = T)

unique_packages <- unique(deps$Package)
writeLines(unique_packages, here::here("src/packages_use_in_this_quarto.txt"))

data.frame(
  Package = unique_packages,
  Version = sapply(unique_packages, function(pkg) {
    tryCatch(as.character(packageVersion(pkg)), error = function(e) NA)
  }),
  stringsAsFactors = FALSE
) %>% 
  #knitr::kable(caption = "List of packages used in this document", row.names = FALSE)
  DT::datatable(.,
  filter = "top",
  class = 'cell-border stripe',
  rownames = FALSE
)

Bellande, Kevin, Richard Sibout, Anne Roulin, Joop E M Vermeer, and Thomas Badet. n.d. “Exodermis Lignification Impacts Lateral Root Emergence in Brachypodium Distachyon.”

Bellande, Kevin, Cristovāo De Jesus Vieira Teixeira, and Joop E. M. Vermeer. 2025. “Auxin Signaling Mediated Spatial Accommodation Mechanisms During Lateral Root Development.” Physiologia Plantarum 177 (5): e70481. https://doi.org/10.1111/ppl.70481.

De Jesus Vieira Teixeira, Cristóvâo. 2024. “Lateral Root Formation in "Arabidopsis Thaliana" and "Brachypodium Distachyon": Comparison of Spatial Accommodating Responses.” PhD thesis, Université de Neuchâtel. https://doi.org/10.35662/unine-thesis-3140.