Single-cell and spatial transcriptomics technologies have significantly advanced our understanding of the molecular mechanisms underlying crop biology. This review presents an update on the application of these technologies in crop improvement. The heterogeneity of different cell populations within a tissue plays a crucial role in the coordinated response of an organism to its environment. Single-cell transcriptomics enables the dissection of this heterogeneity, offering insights into the cell-specific transcriptomic responses of plants to various environmental stimuli. Spatial transcriptomics technologies complement single-cell approaches by preserving the spatial context of gene expression profiles, allowing for the in situ localization of transcripts. Together, single-cell and spatial transcriptomics facilitate the discovery of novel genes and gene regulatory networks that can be targeted for genetic manipulation and breeding strategies aimed at enhancing crop yield, quality, and resilience. This review highlights significant findings from recent studies, discusses the expanding roles of these technologies, and explores future opportunities for their application in crop improvement.
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