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

Genome Biology

Research

Keith Lindsey¹  Lili Tu²  Xianlong Zhang²  Daojun Yuan²  Guanying Wang²  Ruoyu Jia²  Yuan Qin²  Xiangqian Zhu²  Yulong Cong²  Shuangxia Jin²  Zhongping Xu²  Xiyan Yang²  Lu Yu²  Guangyu Zhang²  Bo Li³ 

[1] Department of Biosciences, Durham University, DH1 3LE, Durham, UK;Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, Hubei, China;Xinjiang Key Laboratory of Crop Biotechnology, Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, 830000, Wulumuqi, Xinjiang, China;

关键词: Cotton;    Plant regeneration;    scRNA-seq;    Gene regulatory network;    Gene functional verification;   

DOI  :  10.1186/s13059-023-03032-6

 received in 2023-01-29, accepted in 2023-08-06,  发布年份 2023

来源: Springer

【 摘 要 】

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

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

【 图 表 】

Fig. 1

40517_2023_266_Article_IEq1.gif

40517_2023_266_Article_IEq52.gif

40517_2023_266_Article_IEq49.gif

Fig. 2

Fig. 2

Fig. 6

13690_2023_1147_Article_IEq4.gif

Fig. 6

Fig. 1

Fig. 1