Unlocking vernalization response at the cellular level in cabbage
image: Differential gene expression patterns across various cell types during vernalization. A Chinese cabbage shoot apex sample pattern maps for control and vernalization treatments Short scale bar, 200 μm; long scale bar, 1000 μm; le, leaf or leaf primordium. B DEGs between control and vernalization treatments in different cell types. C Average expression and flowchart of each gene of the vernalization pathway in different cell types. V represents vernalization; NV represents non-vernalization. Red and blue represent high and low expression levels, respectively. D Venn diagram showing the distribution of overlapping DEGs between different cell types. E Relative expression of TFs in two samples in each cell type. Red signifies high expression levels, while blue indicates low expression levels. F GO-annotated DEG information related to flowering and shoot development and expression levels of SOBIR1 genes in different cell types of the two samples. The depth of red represents the number of DEGs.
Credit: Horticulture Research
Understanding how environmental signals regulate flowering is crucial for crop improvement. This study presents a high-resolution single-cell transcriptomic atlas of the shoot apex in Chinese cabbage (Brassica rapa), revealing how distinct cell types coordinate flowering control and vernalization response. By analyzing over 19,000 single cells, researchers identified 15 major cell clusters, with flowering-related genes such as BrFLC2 specifically expressed in companion cells (CCs), mesophyll cells (MCs), and shoot meristematic cells (SMCs). The findings underscore the importance of cell-type-specific gene regulation in flowering and provide new molecular targets to manipulate bolting time and improve breeding strategies in cruciferous vegetables.
In temperate crops, vernalization—the prolonged exposure to cold—serves as a key environmental cue to induce flowering. The shoot apical meristem (SAM) integrates environmental signals and developmental programs, but the role of individual cell types in this transition remains unclear, especially in crops like Chinese cabbage. While core vernalization genes such as FLC, VRN1, and FT have been well studied in Arabidopsis, their cell-specific expression and functional conservation in Brassica species have not been fully elucidated. Due to these challenges, there is a pressing need to conduct in-depth studies to understand how vernalization shapes gene expression dynamics across distinct cell populations in the shoot apex of Chinese cabbage.
Researchers from the Chinese Academy of Agricultural Sciences have published a comprehensive single-cell transcriptomic study (DOI: 10.1093/hr/uhae214) of Chinese cabbage in Horticulture Research on July 30, 2024. By integrating single-cell RNA sequencing (scRNA-seq) with developmental and vernalization analyses, the team identified key flowering regulators and mapped their expression across cell types, offering new insights into how vernalization influences flowering at single-cell resolution.
Using the 10× Genomics platform, the authors analyzed 19,602 single cells from the shoot apex of Chinese cabbage under non-vernalized (N25) and vernalized (V25) conditions. Cells were grouped into 15 clusters, including shoot meristematic cells (SMCs), companion cells (CCs), and mesophyll cells (MCs). Key flowering genes such as BrFLC2, FT, and SOC were predominantly expressed in the CC population. Notably, BrFLC2, a homolog of FLC in Arabidopsis, showed a conserved expression pattern and acted as a floral repressor when overexpressed in Arabidopsis, delaying flowering and reducing FT and SOC expression.
Pseudotime trajectory analyses revealed that CCs may differentiate from both SMCs and MCs, and CCs exhibited high expression of flowering-related genes during specific developmental states. During vernalization, the expression of BrFLC2 decreased, while flowering-promoting genes such as FT increased, indicating a cell-type-specific regulatory shift. Furthermore, comparative analysis with Arabidopsis scRNA-seq data revealed conserved gene expression networks across species, particularly within CC, MC, and SMC populations. These findings highlight the central role of CCs in integrating developmental and environmental signals to regulate flowering and underscore the power of scRNA-seq in plant developmental research.
“Our study reveals that CCs are not merely structural or supportive—they are regulatory hubs for flowering signals,” said Dr. Shujiang Zhang, co-corresponding author of the study. “By leveraging single-cell transcriptomics, we demonstrated how BrFLC2 functions as a key repressor and how vernalization triggers its downregulation to promote flowering. These discoveries offer new molecular entry points for breeding Chinese cabbage varieties with tailored flowering times and broader climate adaptability.”
The single-cell atlas of the Chinese cabbage shoot apex offers valuable resources for studying flowering and shoot development in cruciferous crops. The identification of BrFLC2 as a central floral repressor and its dynamic regulation during vernalization suggests promising avenues for crop improvement. By targeting BrFLC2 and related genes in specific cell types like CCs, breeders may develop varieties with optimized bolting and flowering schedules. Additionally, the conservation of regulatory networks between Brassica and Arabidopsis enhances our understanding of plant development and opens up translational research opportunities across species.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhae214
Funding information
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).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.