Single-cell transcriptome reveals dominant subgenome expression and transcriptional response to heat stress in Chinese cabbage

Abstract

Background Chinese cabbage (Brassica rapa ssp. pekinensis) experienced a whole-genome triplication event and thus has three subgenomes: least fractioned, medium fractioned, and most fractioned subgenome. Environmental changes affect leaf development, which in turn influence the yield. To improve the yield and resistance to different climate scenarios, a comprehensive understanding of leaf development is required including insights into the full diversity of cell types and transcriptional networks underlying their specificity. Results Here, we generate the transcriptional landscape of Chinese cabbage leaf at single-cell resolution by performing single-cell RNA sequencing of 30,000 individual cells. We characterize seven major cell types with 19 transcriptionally distinct cell clusters based on the expression of the reported marker genes. We find that genes in the least fractioned subgenome are predominantly expressed compared with those in the medium and most fractioned subgenomes in different cell types. Moreover, we generate a single-cell transcriptional map of leaves in response to high temperature. We find that heat stress not only affects gene expression in a cell type-specific manner but also impacts subgenome dominance. Conclusions Our study highlights the transcriptional networks in different cell types and provides a better understanding of transcriptional regulation during leaf development and transcriptional response to heat stress in Chinese cabbage.

Single‐cell transcriptomic analysis of pea shoot development and cell‐type‐specific responses to boron deficiency

“…Currently, several studies have applied scRNA‐seq or single‐nucleus RNA‐seq (snRNA‐seq) to explore differences in cell types and developmental and differentiation trajectories in various plant species and tissues, including A. thaliana shoots and roots (Denyer et al., 2019; Zhang, Chen, & Wang, 2021), maize ( Z. mays ) shoots (Satterlee et al., 2020), rice ( Oryza sativa ) shoots and roots (Liu, Liang, et al., 2021; Wang et al., 2021), poplar ( Populus ) stems and shoots (Chen et al., 2021; Conde et al., 2022), peanut ( Arachis hypogaea ) leaves (Liu, Hu, et al., 2021), tea ( Camellia sinensis ) leaves (Wang et al., 2022), Medicago truncatula root nodules (Ye et al., 2022), soybean ( Glycine max ) nodules (Liu et al., 2023) and wheat ( Triticum aestivum ) roots (Zhang et al., 2023). A few studies have also focused on the heterogeneous response of plant tissues under stress which include Z. mays roots in response to nitrate (Li et al., 2022), strawberry ( Fragaria vesca ) leaves in response to Botrytis cinerea infection (Bai et al., 2022), Chinese cabbage ( Brassica rapa ) leaves in response to heat stress (Sun, Feng, et al., 2022), rubber tree ( Hevea brasiliensis ) leaves in response to powdery mildew infection (Liang et al., 2023). However, the application of single‐cell sequencing technology in the response of shoots to nutrient stress needs further investigation.…”

Single‐cell transcriptome analyses reveal cellular and molecular responses to low nitrogen in burley tobacco leaves

“…scRNA‐seq has been mostly applied to animal tissues, albeit a fast‐growing number of applications to plants have been implemented since 2019. Its high‐resolution molecular information contributes to elucidating cellular heterogeneity and molecular processes specific to cell types in complex tissues, such as flowers (Kang et al, 2022, leaves Sun et al, 2022), shoot apical meristems (Zhang et al, 2021), roots (Dorrity et al, 2021). Many single‐cell transcriptomic atlases have been established successfully for various crops, including Arabidopsis thaliana (Kim et al, 2021), allotetraploid peanut ( Arachis hypogaea L .…”

“…Many single‐cell transcriptomic atlases have been established successfully for various crops, including Arabidopsis thaliana (Kim et al, 2021), allotetraploid peanut ( Arachis hypogaea L . ; Liu et al, 2021, Chinese cabbage Sun et al, 2022, rice Wang et al, 2021 and maize Marand et al, 2021). These atlases lay the foundation for the functional characterization and manipulation of candidate genes that are needed to develop elite cultivars.…”

“…These atlases lay the foundation for the functional characterization and manipulation of candidate genes that are needed to develop elite cultivars. In addition to revealing the gene expression atlas, single‐cell transcriptomics is also used to investigate plant responses to biotic and abiotic stresses (Bai et al, 2022; Liang et al, 2023; Sun et al, 2022). This technology has provided a previously unattainable view of gene expression dynamics in plant tissues and the alteration of these dynamics under various physiological conditions (Rich‐Griffin et al, 2020).…”

“…Its high-resolution molecular information contributes to elucidating cellular heterogeneity and molecular processes specific to cell types in complex tissues, such as flowers (Kang et al, 2022, leaves Sun et al, 2022, shoot apical meristems (Zhang et al, 2021), roots (Dorrity et al, 2021). Many single-cell transcriptomic atlases have been established successfully for various crops, including Arabidopsis thaliana (Kim et al, 2021), allotetraploid peanut (Arachis hypogaea L.; Liu et al, 2021, Chinese cabbage Sun et al, 2022, rice Wang et al, 2021and maize Marand et al, 2021. These atlases lay the foundation for the functional characterization and manipulation of candidate genes that are needed to develop elite cultivars.…”