A conserved superlocus regulates above- and belowground root initiation

Abstract

Plants continuously form new organs in different developmental contexts in response to environmental cues. Underground lateral roots initiate from prepatterned cells in the main root, but cells can also bypass the root-shoot trajectory separation and generate shoot-borne roots through an unknown mechanism. We mapped tomato ( Solanum lycopersicum ) shoot-borne root development at single-cell resolution and showed that these roots initiate from phloem-associated cells through a unique transition state. This state requires the activity of a transcription factor that we named SHOOTBORNE ROOTLESS ( SBRL ) . Evolutionary analysis reveals that SBRL ’s function and cis regulation are conserved in angiosperms and that it arose as an ancient duplication, with paralogs controlling wound-induced and lateral root initiation. We propose that the activation of a common transition state by context-specific regulators underlies the plasticity of plant root systems.

Genome-Wide Identification and Characterization of the Calmodulin-Binding Transcription Activator (CAMTA) Gene Family in Plants and the Expression Pattern Analysis of CAMTA3/SR1 in Tomato under Abiotic Stress

“…There was a slight increase but no significant expression difference compared with the control in the root at the flowering and fruiting stages. Plants continuously adjust their body plans to adapt to the local environment by forming new organs in various developmental stages [ 50 ]. We speculate that the high expression of SlCAMTA3/SR1 in the root during the seedling stage was diminished in the leaf because of the plant’s need to absorb sufficient nutrients to maintain plant development and metabolic homeostasis strategies, and this gene should be involved and play a vital role in this process.…”

Advances and applications of single‐cell omics technologies in plant research

“…Since protoplasts must remain alive and be subjected to a minimal level of disturbance during isolation, the cell wall digestion procedure requires optimization for suitability to the tissue under study. Accordingly, different cell wall digestion protocols have been developed to release protoplasts from different tissue types in a range of plant species, including Arabidopsis (Birnbaum et al., 2003), tomato ( Solanum lycopersicum ) (Omary et al., 2022), rice ( Oryza sativa ) (Liu et al., 2021), and maize (Bezrutczyk et al., 2021). Efforts have also been made to find more broadly applicable protocols for protoplast isolation (Wang et al., 2022).…”

“…Efforts have also been made to find more broadly applicable protocols for protoplast isolation (Wang et al., 2022). In comparison with protoplast isolation, nucleus isolation is more robust and can be adapted to a wider range of tissue types and species (Farmer et al., 2021; Marand et al., 2021; Omary et al., 2022; Tian et al., 2020). Tissues can be frozen in liquid nitrogen (Mo et al., 2021) or even fixed prior to nucleus isolation, preventing the induction of stress‐responsive and other genes by the isolation procedure (Xu et al., 2021b).…”

The biology of time: dynamic responses of cell types to developmental, circadian and environmental cues

“…For example, pseudotime was able to capture very early and transient transcriptional states that occur when lateral root primordia cells arise from xylem pole pericycle cells (Gala et al., 2021), or as mature conductive cells arise from the root stem cell niche (Roszak et al., 2021). In another example, when applied to tomato shoots, pseudotime was able to detect transitions in cell identity that lead to shoot‐borne roots (Omary et al., 2020). In each of these studies, pseudotime led to the identification and functional validation of key candidate genes involved in these phenotypes.…”