Single-cell omics in plant biology: mechanistic insights and applications for crop improvement

Abstract

In recent years, single-cell omics technologies have significantly advanced plant and agricultural research, providing transformative insights into plant development, cellular heterogeneity, and environmental response mechanisms. Traditional bulk-level analyses often obscure differences between individual cells, whereas single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq) now reveal unique expression profiles across distinct cell populations, facilitating the identification of novel cell types and elucidation of gene regulatory networks. Additionally, epigenomic approaches like single-nucleus ATAC sequencing (snATAC-seq) offer a deeper understanding of chromatin accessibility and its complex relationship with gene regulation. These technologies have seen widespread application in model plants such as Arabidopsis thaliana, as well as in major crops and horticultural plants, providing essential data for crop improvement and breeding strategies. Moving forward, with the continued development and integration of single-cell multi-omics technologies, there will be greater depth of insight into cell-type-specific regulation and complex trait analysis, bringing new opportunities for sustainable agriculture and crop improvement.

Keywords

Plant single-cell omics / Single-cell transcriptomics / Biology Findings / Plants / Crops / Horticultural plants

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Funding

National Natural Science Foundation of China(32470346)

Project of National Key Laboratory for Tropical Crop Breeding(NKLTCBCXTD26)

Central Public-interest Scientific Institution Basal Research Fund for Chinese Academy of Tropical Agricultural Sciences(1630052024024)

Key Technologies Research and Development Program(2024YFD1200800)

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