Transcriptomic analyses to summarize gene expression patterns that occur during leaf initiation of Chinese cabbage

Abstract

In Chinese cabbage, rosette leaves expose their adaxial side to the light converting light energy into chemical energy, acting as a source for the growth of the leafy head. In the leafy head, the outer heading leaves expose their abaxial side to the light while the inner leaves are shielded from the light and have become a sink organ of the growing Chinese cabbage plant. Interestingly, variation in several ad/abaxial polarity genes is associated with the typical leafy head morphotype. The initiation of leaf primordia and the establishment of leaf ad/abaxial polarity are essential steps in the initiation of marginal meristem activity leading to leaf formation. Understanding the molecular genetic mechanisms of leaf primordia formation, polar differentiation, and leaf expansion is thus relevant to understand leafy head formation. As Brassica’s are mesa-hexaploids, many genes have multiple paralogues, complicating analysis of the genetic regulation of leaf development. In this study, we used laser dissection of Chinese cabbage leaf primordia and the shoot apical meristem (SAM) to compare gene expression profiles between both adaxial and abaxial sides and the SAM aiming to capture transcriptome changes underlying leaf primordia development. We highlight genes with roles in hormone pathways and transcription factors. We also assessed gene expression gradients along expanded leaf blades from the same plants to analyze regulatory links between SAM, leaf primordia and the expanding rosette leaf. The catalogue of differentially expressed genes provides insights in gene expression patterns involved in leaf development and form a starting point to unravel leafy head formation.

Acknowledgements

This study was supported by the National Natural Science Foundation of China (grant 32330096, 32002054, 3217180965), the Dutch Royal Academy of Sciences China Exchange Program (grant 530-4CDP08), Project of Hebei Provincial Department of Human Resources and Social Security (C20210363).

Author contributions

X.S. performed the experiments, data analysis and contributed to manuscript writing. Z.L. performed the experiments and conducted data collection. J.B. conducted greenhouse experiment. G.B., J.Z., and R.V. supervised the whole experiment and amended the manuscript. All authors have read and approved the final manuscript.

Data availability statement

The data underlying this article are available in the article and in its online supplementary material. The raw sequence data reported in this paper have been deposited in the Genome Sequence Archive (Genomics, Proteomics & Bioinformatics 2021) in National Genomics Data Center (Nucleic Acids Res 2022), China National Center for Bioinformation / Beijing Institute of Genomics, Chinese Academy of Sciences (GSA: CRA013309) that are publicly accessible at https://ngdc.cncb.ac.cn/gsa.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary information

Supplementary data is available at Horticulture Research online.

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