Single-cell transcriptomic analysis of flowering regulation and vernalization in Chinese cabbage shoot apex

Abstract

In Chinese cabbage development the interplay between shoot apex activity and vernalization is pivotal for flowering timing. The intricate relationship between various cell types in the shoot apex meristem and their roles in regulating flowering gene expression in Chinese cabbage is not yet fully understood. A thorough analysis of single-cell types in the Chinese cabbage shoot apex and their influence on flowering genes and vernalization is essential for deeper insight. Our study first established a single-cell transcriptomic atlas of Chinese cabbage after 25 days of non-vernalization. Analyzing 19 602 single cells, we differentiated them into 15 distinct cell clusters using established marker genes. We found that key genes in shoot apex development and flowering were primarily present in shoot meristematic cells (SMCs), companion cells (CCs), and mesophyll cells (MCs). MADS-box protein FLOWERING LOCUS C 2 (BrFLC2), a gene suppressing flowering, was observed in CCs, mirroring patterns found in Arabidopsis. By mapping developmental trajectories of SMCs, CCs, and MCs, we elucidated the evolutionary pathways of crucial genes in shoot apex development and flowering. The creation of a single-cell transcriptional atlas of the Chinese cabbage shoot apex under vernalization revealed distinct alterations in the expression of known flowering genes, such as VERNALIZATION INSENSITIVE 3 (VIN3), VERNALIZATION 1 (VRN1), VERNALIZATION 2 (VRN2), BrFLC, and FLOWERING LOCUS T (FT), which varied by cell type. Our study underscores the transformative impact of single-cell RNA sequencing (scRNA-seq) for unraveling the complex differentiation and vernalization processes in the Chinese cabbage shoot apex. These insights are pivotal for enhancing breeding strategies and cultivation management of this vital vegetable.

Acknowledgements

This research was supported by the National Key Research and Development Program of China (2023YFD1201504), the China Agriculture Research System (CARS-23-A-14), the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS-ASTIP-IVFCAAS), and the National Natural Science Foundation of China (32102373 and 32172562).

Author contributions

S.Z. (Shujiang Zhang), F.L., and R.S. designed the experiments. Y.D., S.Z. (Shifan Zhang), S.W., H.Z., and G.L. conducted the experiments and carried out the data analysis. Y.D., S.Z. (Shifan Zhang), and J.G. wrote the manuscript.

Data availability

The raw sequence data from this research have been submitted to the Genome Sequence Archive (GSA: CRA014199). The GSA is maintained by the National Genomics Data Center, which is part of the China National Center for Bioinformation and the Beijing Institute of Genomics. These institutions are affiliated with the Chinese Academy of Sciences. The data are publicly accessible at the following URL: https://ngdc.cncb.ac.cn/gsa.

Conflict of interests

The authors confirm that they have no conflicts of interest concerning this research.

Supplementary information

The supplementary tables associated with this study have been uploaded to Zenodo for open access. These tables include detailed statistical data and analysis results that support the findings of this paper. The data can be accessed via the following DOI: https://doi.org/10.5281/zenodo.12759721. Supplementary figures are available at Horticulture Research online.

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