ArticleGenome biology2023
Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers, 1 of them a synthesis that pooled it.
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Who cites it
48 citing papers in PubMed, 1 synthesis or guideline pooled it, 83 citations in OpenAlex.
- A systematic review of single-cell RNA sequencing applications and insights in Oryza sativa response to environmental stresses.Molecular biology reports · 2025Pooled it
- Multi-organ single-cell transcriptomic atlas identifies QrIAA14 as a candidate negative regulator of adventitious root development in Quercus robur.PLoS genetics · 2026Article
- Single-Cell and Spatial Omics Technologies in Rice Abiotic Stress Biology: A Methodological Review.International journal of molecular sciences · 2026Review
- Single-cell insights into plant growth, adaptation, and evolution.Journal of integrative plant biology · 2026Review
- Single-nucleus RNA-seq and ATAC-seq analyses provide molecular insights into cadmium-stress response in alfalfa roots.Horticulture research · 2026Article
- Integrative transcriptional regulatory networks governing cereal root responses to heavy metals and drought.Plant cell reports · 2026Review
- Single-cell RNA-sequencing profiles reveal the developmental landscape of hawthorn leaves.BMC plant biology · 2026Article
- Biotic Stress Resistance in Sweet Potato: Mechanisms, Perspectives, and Sustainable Production Strategies.Plants (Basel, Switzerland) · 2026Review
- The potential of wheat spatial omics.Nature genetics · 2026Review
- Single-cell chromatin accessibility and cis-regulatory element analyses in plants using the scPlantReg platform.Nature plants · 2026Article
- Article
- Dynamic and cell-type specific transcriptional reprogramming underlies the floral transition in the maize shoot apical meristem.Genome biology · 2026Article
- Cell-Type-Specific and Variety-Specific Responses to Salt Stress in Wheat Root Revealed by Single-Cell Transcriptomics.Plant biotechnology journal · 2026Article
- The sucrose-trehalose 6-phosphate nexus is conserved in flowering plants with different phloem loading and carbon storage strategies.Journal of experimental botany · 2026Article
- Integrated single cell transcriptomics analysis for unraveling heterogeneity and plasticity of root cells for sustainable and regenerative agriculture.Frontiers in plant science · 2026Review
- Wheat Plasma Membrane Receptors: Orchestrating Immunity and Bridging to Crop Improvement.Current issues in molecular biology · 2025Review
- Trehalose 6-phosphate - a central regulator at the crossroads of sugar signalling, metabolism, and development.The New phytologist · 2025Review
- Integrated single-cell transcriptomics and spatial metabolomics unveil cellular differentiation and ginsenosides biosynthesis inHorticulture research · 2025Article
- A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution.Nature plants · 2025Article
- The impact of asymmetrical gene expression on the development of spike morphology iniMetaOmics · 2025Article
Corrections and comments
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Authors and funding
17 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHomoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs to the transcriptome, is critical for determining the traits that influence wheat growth and development. Asymmetric transcription of homoeologs has been so far investigated in a tissue or organ-specific manner, which could be misleading due to a mixture of cell types.
resultsHere, we perform single nuclei RNA sequencing and ATAC sequencing of wheat root to study the asymmetric gene transcription, reconstruct cell differentiation trajectories and cell-type-specific gene regulatory networks. We identify 22 cell types. We then reconstruct cell differentiation trajectories that suggest different origins between epidermis/cortex and endodermis, distinguishing bread wheat from Arabidopsis. We show that the ratio of asymmetrically transcribed triads varies greatly when analyzing at the single-cell level. Hub transcription factors determining cell type identity are also identified. In particular, we demonstrate that TaSPL14 participates in vasculature development by regulating the expression of BAM1. Combining single-cell transcription and chromatin accessibility data, we construct the pseudo-time regulatory network driving root hair differentiation. We find MYB3R4, REF6, HDG1, and GATAs as key regulators in this process.
conclusionsOur findings reveal the transcriptional landscape of root organization and asymmetric gene transcription at single-cell resolution in polyploid wheat.
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