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Single-cell resolution analysis reveals the preparation for reprogramming the fate of stem cell niche in cotton lateral meristem.

Zhu, X; Xu, Z; Wang, G; Cong, Y; Yu, L; Jia, R; Qin, Y; Zhang, G; Li, B; Yuan, D; Tu, L; Yang, X; Lindsey, K; Zhang, X; Jin, S

Single-cell resolution analysis reveals the preparation for reprogramming the fate of stem cell niche in cotton lateral meristem. Thumbnail


Authors

X Zhu

Z Xu

G Wang

Y Cong

L Yu

R Jia

Y Qin

G Zhang

B Li

D Yuan

L Tu

X Yang

X Zhang

S Jin



Abstract

Background
Somatic embryogenesis is a major process for plant regeneration. However, cell communication and the gene regulatory network responsible for cell reprogramming during somatic embryogenesis are still largely unclear. Recent advances in single-cell technologies enable us to explore the mechanism of plant regeneration at single-cell resolution.

Results
We generate a high-resolution single-cell transcriptomic landscape of hypocotyl tissue from the highly regenerable cotton genotype Jin668 and the recalcitrant TM-1. We identify nine putative cell clusters and 23 cluster-specific marker genes for both cultivars. We find that the primary vascular cell is the major cell type that undergoes cell fate transition in response to external stimulation. Further developmental trajectory and gene regulatory network analysis of these cell clusters reveals that a total of 41 hormone response-related genes, including LAX2, LAX1, and LOX3, exhibit different expression patterns in the primary xylem and cambium region of Jin668 and TM-1. We also identify novel genes, including CSEF, PIS1, AFB2, ATHB2, PLC2, and PLT3, that are involved in regeneration. We demonstrate that LAX2, LAX1 and LOX3 play important roles in callus proliferation and plant regeneration by CRISPR/Cas9 editing and overexpression assay.

Conclusions
This study provides novel insights on the role of the regulatory network in cell fate transition and reprogramming during plant regeneration driven by somatic embryogenesis.

Citation

Zhu, X., Xu, Z., Wang, G., Cong, Y., Yu, L., Jia, R., …Jin, S. (2023). Single-cell resolution analysis reveals the preparation for reprogramming the fate of stem cell niche in cotton lateral meristem. Genome Biology, 24, Article 194. https://doi.org/10.1186/s13059-023-03032-6

Journal Article Type Article
Acceptance Date Aug 6, 2023
Online Publication Date Aug 25, 2023
Publication Date 2023
Deposit Date Sep 12, 2023
Publicly Available Date Sep 12, 2023
Journal Genome Biology
Print ISSN 1474-760X
Publisher BioMed Central
Peer Reviewed Peer Reviewed
Volume 24
Article Number 194
DOI https://doi.org/10.1186/s13059-023-03032-6
Public URL https://durham-repository.worktribe.com/output/1735204

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Licence
http://creativecommons.org/licenses/by/4.0/

Publisher Licence URL
http://creativecommons.org/licenses/by/4.0/

Copyright Statement
This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.




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