Application prospect of single-cell and spatial transcriptomics in horticultural plants

Single-cell and spatial transcriptomics technologies hold great potential in horticultural plant research, enabling the analysis of cellular heterogeneity, spatial gene expression distribution, and cell-cell interactions. Although these technologies are relatively mature in animal studies, their application in plant research still faces numerous challenges, including difficulties in single-cell isolation, metabolite interference, perennial growth cycles, and a lack of genomic resources. This review summarizes the application of single-cell and spatial transcriptomics in plant research from 2017 to 2025, as well as their respective applications in horticultural plants, including regeneration, vegetative organ development, floral organ development, fruit development, disease resistance, abiotic stress responses, plant-microorganism interactions, and phylogenetic relationship analysis. Furthermore, the current limitations, as well as the future development of these two technologies are also discussed, with a view to informing applications on horticultural plants.