Reconstruction of lateral root formation through single-cell RNA sequencing reveals order of tissue initiation

Laura Serrano-Ron, Pablo Perez-Garcia, Alvaro Sanchez-Corrionero, Inmaculada Gude, Javier Cabrera, Pui Leng Ip, Kenneth D. Birnbaum, Miguel A. Moreno-Risueno

Research output: Contribution to journalArticlepeer-review


Postembryonic organogenesis is critical for plant development. Underground, lateral roots (LRs) form the bulk of mature root systems, yet the ontogeny of the LR primordium (LRP) is not clear. In this study, we performed the single-cell RNA sequencing through the first four stages of LR formation in Arabidopsis. Our analysis led to a model in which a single group of precursor cells, with a cell identity different from their pericycle origins, rapidly reprograms and splits into a mixed ground tissue/stem cell niche fate and a vascular precursor fate. The ground tissue and stem cell niche fates soon separate and a subset of more specialized vascular cells form sucrose transporting phloem cells that appear to connect to the primary root. We did not detect cells resembling epidermis or root cap, suggesting that outer tissues may form later, preceding LR emergence. At this stage, some remaining initial precursor cells form the primordium flanks, while the rest create a reservoir of pluripotent cells that are able to replace the LR if damaged. Laser ablation of the central and lateral LRP regions showed that remaining cells restart the sequence of tissue initiation to form a LR. Collectively, our study reveals an ontological hierarchy for LR formation with an early and sequential split of main root tissues and stem cells.

Original languageEnglish (US)
Pages (from-to)1362-1378
Number of pages17
JournalMolecular Plant
Issue number8
StatePublished - Aug 2 2021


  • cell fate
  • organogenesis
  • patterning
  • regeneration
  • single-cell RNA-seq
  • stem cells

ASJC Scopus subject areas

  • Molecular Biology
  • Plant Science


Dive into the research topics of 'Reconstruction of lateral root formation through single-cell RNA sequencing reveals order of tissue initiation'. Together they form a unique fingerprint.

Cite this